http://hydrodictyon.eeb.uconn.edu/eebedia/api.php?action=feedcontributions&user=Russell+Meister&feedformat=atomEEBedia - User contributions [en]2024-03-19T12:44:00ZUser contributionsMediaWiki 1.25.2http://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29695Molecular Systematics Spring 20142014-05-07T02:59:06Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%2030%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon" {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2010.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%201..pdf}}<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one, Wednesday, April 30th) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Lockhart%20and%20Steel%202005.%20A%20tale%20of%20two%20proces.pdf}}, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Gruenheit%20et%20al.%20%28Lockhart%29%202008.%20Covarion%20under%20changing%20proportions%20var%20sites.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11Bib.pdf}} || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2011.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%202..pdf}}<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M10-NextGen_Wade.pdf}}<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
'''Final Exam Files''' <br/><br />
Final Exam Instuctions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Final%20Exam%20EEB350%20Instructns.pdf}}, Shull et al Manuscript {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Shull_et_al._28Oct%20MS.pdf}}, Shull et al figures {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Shull%20et%20al.%20figures1-7%2C%20Tabs%201-5.pdf}}, Published Shul et al 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Shull%20et%20al.%202001%20SYB.pdf}}.<br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29694Molecular Systematics Spring 20142014-05-07T02:58:46Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%2030%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon" {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2010.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%201..pdf}}<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one, Wednesday, April 30th) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Lockhart%20and%20Steel%202005.%20A%20tale%20of%20two%20proces.pdf}}, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Gruenheit%20et%20al.%20%28Lockhart%29%202008.%20Covarion%20under%20changing%20proportions%20var%20sites.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11Bib.pdf}} || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2011.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%202..pdf}}<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M10-NextGen_Wade.pdf}}<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
Final Exam Files <br/><br />
Final Exam Instuctions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Final%20Exam%20EEB350%20Instructns.pdf}}, Shull et al Manuscript {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Shull_et_al._28Oct%20MS.pdf}}, Shull et al figures {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Shull%20et%20al.%20figures1-7%2C%20Tabs%201-5.pdf}}, Published Shul et al 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Shull%20et%20al.%202001%20SYB.pdf}}.<br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29693Molecular Systematics Spring 20142014-05-07T02:58:11Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%2030%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon" {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2010.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%201..pdf}}<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one, Wednesday, April 30th) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Lockhart%20and%20Steel%202005.%20A%20tale%20of%20two%20proces.pdf}}, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Gruenheit%20et%20al.%20%28Lockhart%29%202008.%20Covarion%20under%20changing%20proportions%20var%20sites.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11Bib.pdf}} || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2011.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%202..pdf}}<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M10-NextGen_Wade.pdf}}<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
Final Exam Files <br/><br />
Final Exam Instuctions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Final%20Exam%20EEB350%20Instructns.pdf}}, Shull et al Manuscript {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Shull_et_al._28Oct%20MS.pdf}}, Shull et al figures {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Shull%20et%20al.%20figures1-7%2C%20Tabs%201-5.pdf}}, Published Shul et al 2001.<br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29692Molecular Systematics Spring 20142014-05-07T02:57:33Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%2030%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon" {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2010.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%201..pdf}}<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one, Wednesday, April 30th) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Lockhart%20and%20Steel%202005.%20A%20tale%20of%20two%20proces.pdf}}, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Gruenheit%20et%20al.%20%28Lockhart%29%202008.%20Covarion%20under%20changing%20proportions%20var%20sites.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11Bib.pdf}} || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2011.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%202..pdf}}<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M10-NextGen_Wade.pdf}}<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
Final Exam Files <br/><br />
Final Exam Instuctions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Final%20Exam%20EEB350%20Instructns.pdf}}, Shull et al Manuscript {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Shull_et_al._28Oct%20MS.pdf}}, Shull et al figures, Published Shul et al 2001.<br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29691Molecular Systematics Spring 20142014-05-07T02:57:00Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%2030%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon" {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2010.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%201..pdf}}<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one, Wednesday, April 30th) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Lockhart%20and%20Steel%202005.%20A%20tale%20of%20two%20proces.pdf}}, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Gruenheit%20et%20al.%20%28Lockhart%29%202008.%20Covarion%20under%20changing%20proportions%20var%20sites.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11Bib.pdf}} || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2011.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%202..pdf}}<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M10-NextGen_Wade.pdf}}<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
Final Exam Files <br/><br />
Final Exam Instuctions, Shull et al Manuscript {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Shull_et_al._28Oct%20MS.pdf}}, Shull et al figures, Published Shul et al 2001.<br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29690Molecular Systematics Spring 20142014-05-07T02:56:24Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%2030%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon" {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2010.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%201..pdf}}<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one, Wednesday, April 30th) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Lockhart%20and%20Steel%202005.%20A%20tale%20of%20two%20proces.pdf}}, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Gruenheit%20et%20al.%20%28Lockhart%29%202008.%20Covarion%20under%20changing%20proportions%20var%20sites.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11Bib.pdf}} || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2011.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%202..pdf}}<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M10-NextGen_Wade.pdf}}<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
Final Exam Files <br/><br />
Final Exam Instuctions, Shull et al Manuscript {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Shull_et_al._28Oct%20MS.pdf}}, Shull et al figures, Published Shul et al 2001.<br />
<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29670Molecular Systematics Spring 20142014-05-01T01:47:37Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%2030%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon" {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2010.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%201..pdf}}<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one, Wednesday, April 30th) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Lockhart%20and%20Steel%202005.%20A%20tale%20of%20two%20proces.pdf}}, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Gruenheit%20et%20al.%20%28Lockhart%29%202008.%20Covarion%20under%20changing%20proportions%20var%20sites.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11Bib.pdf}} || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2011.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%202..pdf}}<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M10-NextGen_Wade.pdf}}<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29668Molecular Systematics Spring 20142014-04-30T23:05:58Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%2030%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon" {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2010.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%201..pdf}}<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one, Wednesday, April 30th) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Lockhart%20and%20Steel%202005.%20A%20tale%20of%20two%20proces.pdf}}, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Gruenheit%20et%20al.%20%28Lockhart%29%202008.%20Covarion%20under%20changing%20proportions%20var%20sites.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11Bib.pdf}} || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2011.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%202..pdf}}<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29667Molecular Systematics Spring 20142014-04-30T23:04:59Z<p>Russell Meister: </p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%2030%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon" {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2010.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%201..pdf}}<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one, Wednesday, April 30th) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Lockhart%20and%20Steel%202005.%20A%20tale%20of%20two%20proces.pdf}}, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Gruenheit%20et%20al.%20%28Lockhart%29%202008.%20Covarion%20under%20changing%20proportions%20var%20sites.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11Bib-Covarion%2C%20Heterotachy%2C%20bias%20readings%202014.pdf}} || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2011.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%202..pdf}}<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29666Molecular Systematics Spring 20142014-04-30T23:03:31Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/MolSys_Syllabus_19APR14.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon" {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2010.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%201..pdf}}<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one, Wednesday, April 30th) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Lockhart%20and%20Steel%202005.%20A%20tale%20of%20two%20proces.pdf}}, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Gruenheit%20et%20al.%20%28Lockhart%29%202008.%20Covarion%20under%20changing%20proportions%20var%20sites.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11Bib-Covarion%2C%20Heterotachy%2C%20bias%20readings%202014.pdf}} || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2011.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%202..pdf}}<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29636Molecular Systematics Spring 20142014-04-29T11:59:46Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/MolSys_Syllabus_19APR14.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon" {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%2010.%20Error%2C%20Covarion%2C%20heterotachy%2C%20ALRV%20part%201..pdf}}<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one, Wednesday, April 30th) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Lockhart%20and%20Steel%202005.%20A%20tale%20of%20two%20proces.pdf}}, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Gruenheit%20et%20al.%20%28Lockhart%29%202008.%20Covarion%20under%20changing%20proportions%20var%20sites.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11Bib-Covarion%2C%20Heterotachy%2C%20bias%20readings%202014.pdf}} || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29616Molecular Systematics Spring 20142014-04-27T14:58:17Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/MolSys_Syllabus_19APR14.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one, Wednesday, April 30th) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Lockhart%20and%20Steel%202005.%20A%20tale%20of%20two%20proces.pdf}}, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Gruenheit%20et%20al.%20%28Lockhart%29%202008.%20Covarion%20under%20changing%20proportions%20var%20sites.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11Bib-Covarion%2C%20Heterotachy%2C%20bias%20readings%202014.pdf}} || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29615Molecular Systematics Spring 20142014-04-27T14:46:19Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/MolSys_Syllabus_19APR14.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one, Due date coming soon) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Lockhart%20and%20Steel%202005.%20A%20tale%20of%20two%20proces.pdf}}, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Gruenheit%20et%20al.%20%28Lockhart%29%202008.%20Covarion%20under%20changing%20proportions%20var%20sites.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11Bib-Covarion%2C%20Heterotachy%2C%20bias%20readings%202014.pdf}} || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29614Molecular Systematics Spring 20142014-04-27T14:46:02Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/MolSys_Syllabus_19APR14.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Lockhart%20and%20Steel%202005.%20A%20tale%20of%20two%20proces.pdf}}, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Gruenheit%20et%20al.%20%28Lockhart%29%202008.%20Covarion%20under%20changing%20proportions%20var%20sites.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11Bib-Covarion%2C%20Heterotachy%2C%20bias%20readings%202014.pdf}} || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29613Molecular Systematics Spring 20142014-04-27T14:45:23Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/MolSys_Syllabus_19APR14.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Lockhart%20and%20Steel%202005.%20A%20tale%20of%20two%20proces.pdf}}, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Gruenheit%20et%20al.%20%28Lockhart%29%202008.%20Covarion%20under%20changing%20proportions%20var%20sites.pdf}}, Bibliography || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29612Molecular Systematics Spring 20142014-04-27T14:43:21Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/MolSys_Syllabus_19APR14.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-Lockhart%20and%20Steel%202005.%20A%20tale%20of%20two%20proces.pdf}}, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites, Bibliography || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29611Molecular Systematics Spring 20142014-04-27T14:42:09Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/MolSys_Syllabus_19APR14.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| Lockhart et al. 2006. Heterotachy and trees (Summarize this one) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec11-SUMMARIZE-Lockhart%20et%20al.%202006.%20Heterotachy%20and%20trees.pdf}}, Lockhart and Steel 2005. A tale of two processes , Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites, Bibliography || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29592Molecular Systematics Spring 20142014-04-24T01:44:43Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/MolSys_Syllabus_19APR14.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Tests of topology and problems associated with nodal support {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%209.%20Branch%20support%20%28cont.%29%2C%20Comparing%20trees%202014.pdf}}<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29534Molecular Systematics Spring 20142014-04-22T00:25:00Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/MolSys_Syllabus_19APR14.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20Branch-Nodal%20Support%202014.pdf}}<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29533Molecular Systematics Spring 20142014-04-22T00:23:43Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/MolSys_Syllabus_19APR14.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M8-AncientDNA_tmw.pdf}}<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29517Molecular Systematics Spring 20142014-04-21T12:33:02Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/MolSys_Syllabus_19APR14.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Summary due April 25th, 2014 || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29516Molecular Systematics Spring 20142014-04-21T12:32:33Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/MolSys_Syllabus_19APR14.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}} || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29515Molecular Systematics Spring 20142014-04-21T12:31:49Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/MolSys_Syllabus_19APR14.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, Salichos and Rokas 2013 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec9-Betancur%20et%20al.%202014.%20Comment%20on%20Salichos%20%26%20Rokas%20Syst%20Biol.pdf}}, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) {{pdf|}} || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29514Molecular Systematics Spring 20142014-04-21T12:29:13Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/MolSys_Syllabus_19APR14.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| Nodal Support Readings {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Nodal_support_bib.pdf}}, || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29513Molecular Systematics Spring 20142014-04-21T12:28:28Z<p>Russell Meister: </p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/MolSys_Syllabus_19APR14.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29467Molecular Systematics Spring 20142014-04-18T14:41:34Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%209%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, ASRV Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Combining Data & Partitioning Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''PDF of Paul Fransden lecture''' <br />
|| rRNA structure & Alignment Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Molecular Clocks Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> SECONDARY STRUCTURE HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Long branches, Taxon Sampling, Big Trees Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Long%20Branch%2C%20Taxon%20Sampling%2C%20Big%20Trees%20Bibliography.pdf}} Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29435Molecular Systematics Spring 20142014-04-16T22:51:58Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%209%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''*See syllabus for note*''' Chris did not lecture on this day, so no lecture posted.<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%208.%20%20Long%20Branches%20and%20Big%20Trees%20%202014.pdf}} || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29431Molecular Systematics Spring 20142014-04-16T14:05:49Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%209%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''*See syllabus for note*''' Chris did not lecture on this day, so no lecture posted.<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M7-Mini%20Presentation%20-%20GenBAnk.pdf}}<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29430Molecular Systematics Spring 20142014-04-16T14:05:11Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%209%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''*See syllabus for note*''' Chris did not lecture on this day, so no lecture posted.<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M6-Gallagher_Cloning%20DNA.pdf}}<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29426Molecular Systematics Spring 20142014-04-14T23:34:06Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%209%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''*See syllabus for note*''' Chris did not lecture on this day, so no lecture posted.<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%207.%20Molecular%20Clocks%202014.pdf}}<br />
|| Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29397Molecular Systematics Spring 20142014-04-14T13:20:44Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%209%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''*See syllabus for note*''' Chris did not lecture on this day, so no lecture posted.<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April 16th || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29396Molecular Systematics Spring 20142014-04-14T12:56:58Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%209%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''*See syllabus for note*''' Chris did not lecture on this day, so no lecture posted.<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} Due April (not sure yet) || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29395Molecular Systematics Spring 20142014-04-14T12:56:19Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%209%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''*See syllabus for note*''' Chris did not lecture on this day, so no lecture posted.<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| Swofford et al. 2001 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec7-Swofford%20et%20al.%202001%20SYB%2050-525.pdf}} || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29385Molecular Systematics Spring 20142014-04-13T12:25:25Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%209%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''*See syllabus for note*''' Chris did not lecture on this day, so no lecture posted.<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29384Molecular Systematics Spring 20142014-04-13T12:24:58Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%209%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. }}pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M3-Mini%20Presentation%20-%20Polymerase%20Chain%20Reaction%20%28PCR%29.pdf}} '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''*See syllabus for note*''' Chris did not lecture on this day, so no lecture posted.<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29360Molecular Systematics Spring 20142014-04-11T18:27:29Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%209%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''*See syllabus for note*''' Chris did not lecture on this day, so no lecture posted.<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} <br/> HOMEWORK ASSIGNMENT {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB5350_secondary_structure_assignment.pdf}}, associated reading sent by Chris, too large to post|| '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29353Molecular Systematics Spring 20142014-04-11T11:23:23Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%209%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''*See syllabus for note*''' Chris did not lecture on this day, so no lecture posted.<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} || '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29352Molecular Systematics Spring 20142014-04-11T00:50:53Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%209%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/frandsen_uconn_summary.pdf}} '''*See syllabus for note*''' Chris did not lecture on this day, so no lecture posted.<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} || '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29351Molecular Systematics Spring 20142014-04-10T16:47:13Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%209%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. '''*See syllabus for note*''' Chris did not lecture on this day, so no lecture posted.<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} || '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M5-BigDyeMiniPresentation.pdf}}<br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29339Molecular Systematics Spring 20142014-04-10T00:27:31Z<p>Russell Meister: </p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%209%20April%2014.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. '''*See syllabus for note*''' Chris did not lecture on this day, so no lecture posted.<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} || '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting <br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29338Molecular Systematics Spring 20142014-04-10T00:24:15Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/00/MolSys14Syl.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 || Lecture 5 Guest Speaker. Paul Frandsen. '''*See syllabus for note*''' Chris did not lecture on this day, so no lecture posted.<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%205.%20%20Alignment%20%26%20Secondary%20Structure%202014.pdf}} || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} || '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting <br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29320Molecular Systematics Spring 20142014-04-08T23:14:27Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/00/MolSys14Syl.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 ||Lecture 5. Guest Speaker. Paul Frandsen. '''*See syllabus for note*''' Chris did not lecture on this day, so no lecture posted.<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} || '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting <br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29319Molecular Systematics Spring 20142014-04-08T23:13:54Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/00/MolSys14Syl.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 ||Lecture 5. Guest Speaker. Paul Frandsen. '''*See syllabus for note*'''<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} <br/> Chris did not lecture on this day, so no lecture posted.|| | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} || '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting <br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29316Molecular Systematics Spring 20142014-04-08T12:09:34Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/00/MolSys14Syl.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 ||Lecture 5. Guest Speaker. Paul Frandsen. '''*See syllabus for note*'''<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} || '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting <br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
'''Russ'''<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29258Molecular Systematics Spring 20142014-04-06T20:48:29Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/00/MolSys14Syl.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 ||Lecture 5. Guest Speaker. Paul Frandsen. '''*See syllabus for note*'''<br />
|| Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks || Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 6 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec6_Bib.pdf}} || '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting <br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
________________________________<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29257Molecular Systematics Spring 20142014-04-06T20:47:30Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/00/MolSys14Syl.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 ||Lecture 5. Guest Speaker. Paul Frandsen. '''*See syllabus for note*'''<br />
|| Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}}, Lecture 5 Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5Bib.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks || || '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting <br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
________________________________<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29256Molecular Systematics Spring 20142014-04-06T20:46:32Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/00/MolSys14Syl.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 ||Lecture 5. Guest Speaker. Paul Frandsen. '''*See syllabus for note*'''<br />
|| Brandley et al. 2011 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec5-Brandley-2011-Accommodating%20hetero.pdf}} || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks || || '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting <br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
________________________________<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29235Molecular Systematics Spring 20142014-04-03T01:51:55Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/00/MolSys14Syl.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} Lecture 4. Choosing partitions, comparing trees || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 ||Lecture 5. Guest Speaker. Paul Frandsen. '''*See syllabus for note*'''<br />
|| || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks || || '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting <br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
________________________________<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2014&diff=29234Molecular Systematics Spring 20142014-04-03T01:51:26Z<p>Russell Meister: /* Schedule */</p>
<hr />
<div>2 Credits- half-semester module, 24 March-30 April 2014 <br />
<br />
'''Lectures:''' <br/><br />
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room<br />
<br />
'''Labs:'''<br/><br />
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).<br />
<br />
'''Instructor:'''<br/><br />
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu><br />
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947<br />
<br />
'''Readings:''' will be posted as PDF’s. <br/><br />
<br />
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010).<br />
<br />
'''Lecture Goals:''' The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. <br />
<br />
'''Laboratory Goals:''' Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones. <br />
<br />
'''Short Assignments:'''<br />
<br />
'''1)''' For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a one-page summary of the importance of each focal paper (1 or occasionally 2 papers per week). <br />
<br />
'''2)''' The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.<br />
<br />
'''3)''' There will be a short "secondary structure alignment assignment" during the semester. <br />
<br />
'''4)''' Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus. <br />
<br />
'''5)''' For each Lab, one student will present a 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.<br />
<br />
'''Final Exam:''' The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.<br />
<br />
'''Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.'''<br />
<br />
'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/00/MolSys14Syl.pdf}}<br />
<br />
=='''Schedule'''==<br />
{| border="1" cellpadding="2" <br />
!style="background:#99cccc;" width="90" align="center"|Day<br />
!style="background:#2A52BE;" width="365"|Topics<br />
!style="background:#008080;" width="315"|Reading/Assignment<br />
!style="background:#00B7EB;" width="275"|Lab<br />
|-<br />
|Mar 24 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lect.%201.%20Molecular%20Systematics-%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2024%20Mar%2014.pdf}}An introduction to looking at your data: How molecules evolve. <br/><br />
|| Reading too big to post, sent out by Chris. Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec1_Bib.pdf}} || | Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/TettigadesIntroSmall.pdf}}. Start Nucleospin kit extractions<br />
|-<br />
|Mar 26 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%202.%20Models%2C%20ASRV%20History%202014.pdf}}The many roles of biological systematics <br/> || Kjer & Honeycutt {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Kjer%20%26%20Honeycutt_2007.pdf}}, Soubrier et al. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Soubrier%2C%20Steel%20et%20al.%202012.%20%20%20ASRV%20and%20time%20dependent%20rates%20mbe_paper.pdf}}, Sullivan & Swofford {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2-Sullivan%20%26%20Swofford2001.pdf}}, Bibliography{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec2_Bib.pdf}} || '''Mini-presentation:''' DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M1-DNAExtractioRCM.pdf}}. Also, Johana gave a small presentation about her work with different extraction methods{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Johanne_Extraction_small.pdf}}.<br />
'''LAB:''' Chelex extraction. Finish Nucleospin extractions<br />
|-<br />
|Mar 31 ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%203.%20Combining%20Data%2C%20Partitions%2C%2031%20March%202014.pdf}} Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees) <br/><br />
|| Bull et al 1993 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Bull%20et%20al.%201993%20Syst.%20Biol.pdf}}, Pagel and Mead 2004 {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3-Pagel%20and%20Meade.%202004.%20Mixture%20Model.pdf}}, Bibliography {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lec3BIB.pdf}} || | Before lab, read the introduction to the primer compilation, study the primer comparisons among animals for the COI and COII genes in Simon et al. 1994. And Simon et al. 2006. '''Mini-presentation:''' Primer Design- Primer exercise introduction; the beginning of Genious. '''Russ''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M2-Primer_Design.pptx}}<br />
'''LAB:''' Run extractions on gels. Demonstrate DNA & RNA extraction quantification and the use of the nanodrop. '''Homework:''' Troubleshoot and improve “universal” primers for COI and COII in comparison to four complete Tettigades sequences<br />
|-<br />
|Apr 2 ||Lecture 4. Choosing partitions, comparing trees {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lecture%204.%20%20Partitions%20%26%20Mixtures%202014.pdf}} || || '''Mini-presentation:''' The Polymerase Chain Reaction- how it works & optimizing reactions. '''Johana Goyes'''<br />
'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel<br />
<br />
|-<br />
|Apr 7 ||Lecture 5. Guest Speaker. Paul Frandsen. '''*See syllabus for note*'''<br />
|| || | '''Mini-presentation:''' Different methods for cleaning PCR products for sequencing reactions '''Jimmy Bernot'''<br />
'''LAB:''' Purify PCR products and set-up sequencing reactions<br />
|-<br />
|Apr 9 ||Lecture 6. Secondary structure & alignment (cont.); Molecular clocks || || '''Mini-presentation:''' How Big Dye works, chromatograms, and troubleshooting <br />
'''Andrew Frank'''<br/><br />
'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank<br />
|-<br />
|Apr 14 ||Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy<br />
|| || | '''Mini-presentation:''' - Cloning DNA<br />
'''Kaitlin''' <br />
'''LAB:''' Cloning- Long Lab.<br />
|-<br />
|Apr 16 ||Lecture 8. Big Trees, Long Branches, & Simulations || || '''Mini-presentation:''' Depositing sequences in GenBank<br />
'''Benedict''' <br/><br />
'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab<br />
|-<br />
|Apr 21 ||Lecture 9: Among Lineage rate variation: nucleotide bias among taxa<br />
|| || | '''Mini-presentation:''' Ancient DNA & Museum DNA protocols<br />
'''Tanisha''' <br/><br />
'''LAB:''' Sephadex and put clone samples on ABI<br />
|-<br />
|Apr 23 ||Lecture 10: Among Lineage rate variation: Covarion evolution: codon models<br />
|| || | '''Mini-presentation:''' Numts<br />
'''Sarah''' <br/><br />
'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences<br />
|-<br />
|Apr 28 ||Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"<br />
|| || | '''Mini-presentation:''' RNA: extraction and what it can be used for<br />
________________________________<br />
'''LAB:''' RNA isolation- Nucleospin RNA Kit<br />
|-<br />
|Apr 30 ||Lecture 12: Tests of topology and problems associated with nodal support<br />
|| || | '''Guest Lecture:''' Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis.<br />
|-<br />
|May 4 || Lab notebook due. Take home final handed out.|| Nothing new || No Lab<br />
|-<br />
|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class<br />
|}<br />
<br/><br />
<br />
=='''Old Site'''==<br />
Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)<br />
<br/><br />
[[Category:EEB Courses]]</div>Russell Meisterhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Seminar_speaker_sign-up&diff=29218Seminar speaker sign-up2014-04-02T15:08:17Z<p>Russell Meister: /* Thursday, 3 April 2014 */</p>
<hr />
<div><span style="font-size: larger">'''Seminar Speaker:''' Mark Moffett <br><br />
'''Institution:''' National Museum of Natural History <br><br />
'''Web site: ''http://www.doctorbugs.com'' ''''<br><br />
'''Seminar Title:''' ''Human Identity and the Evolution of Societies''<br><br />
'''Time and Place:''' 4:00PM Thursday, 3 April in BPB 130<br><br />
'''Contact:''' Peter Turchin (peter.turchin@uconn.edu) <br><br><br />
<br />
==Thursday, 3 April 2014 ==<br />
{|border=1 cellpadding=8<br />
<br />
| '''Time''' || '''Name''' || '''Room'''<br />
|-<br />
|8:00 a.m. || || Breakfast at the Tolland Inn<br />
|-<br />
|9:30 a.m. || Beth Wade || PharmBio 323<br />
|-<br />
|10:00 a.m. || David Wagner || <br />
|-<br />
|10:30 a.m. || Eldridge Adams || <br />
|-<br />
|11:00 a.m. || Kent Wells || TLS 380<br />
|-<br />
|11:30 a.m. || Eric Schultz || PharmBio 205B<br />
|-<br />
|12:00 p.m. || Grad Student Lunch || Bamford Room (TLS 171B)<br />
|-<br />
|1:00 p.m. || Brigette Zacharczenko || TLS 473<br />
|-<br />
|1:30 p.m. || Kristiina Hurme & Alejandro Rico-Guevara || TLS 379<br />
|-<br />
|2:00 p.m. || Jessie Rack || PharmBio 211<br />
|-<br />
|2:30 p.m. || Mark Urban || BioPharm 200A<br />
|-<br />
|3:00 p.m. || Undergraduates/Bill's Seminar Class || TLS 181 <br />
|-<br />
|4:00 p.m. || Presentation || BPB 130<br />
|-<br />
|6:00 p.m. || Dinner || Turchin, Adams, Wagner<br />
|-<br />
|}<br />
<br><br><br />
<br />
==Friday, 4 April 2014 ==<br />
{|border=1 cellpadding=8<br />
<br />
| '''Time''' || '''Name''' || '''Room'''<br />
|-<br />
| a.m. || Eldridge picks up at the Tolland Inn ||<br />
|-<br />
|9:00 p.m. || Social Insects with Eldridge Adams || <br />
|-<br />
|10:00 a.m. || || <br />
|-<br />
|11:00 a.m. || Peter Turchin || TLS 462 <br />
|-<br />
|12:00 p.m. || lunch ||<br />
|-</div>Russell Meister