Difference between revisions of "Molecular Systematics Spring 2014"

Latest revision as of 16:59, 1 May 2016

2 Credits- half-semester module, 24 March-30 April 2014

Lectures:
Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room

Labs:
Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).

Instructor:
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu> Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947

Readings: will be posted as PDF’s.

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).

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.

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.

Short Assignments:

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).

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.

3) There will be a short "secondary structure alignment assignment" during the semester.

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.

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.

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.

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.

Syllabus:

Schedule

Day	Topics	Reading/Assignment	Lab
Mar 24	An introduction to looking at your data: How molecules evolve.	Reading too big to post, sent out by Chris. How Molecules Evolve Bibliography	Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project . Start Nucleospin kit extractions
Mar 26	The many roles of biological systematics	Kjer & Honeycutt , Soubrier et al. , Sullivan & Swofford , ASRV Bibliography	Mini-presentation: DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) Russ. Also, Johana gave a small presentation about her work with different extraction methods. LAB: Chelex extraction. Finish Nucleospin extractions
Mar 31	Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees)	Bull et al 1993 , Pagel and Mead 2004 , Combining Data & Partitioning Bibliography	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 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
Apr 2	Lecture 4. Choosing partitions, comparing trees		Mini-presentation: The Polymerase Chain Reaction- how it works & optimizing reactions. Johana Goyes LAB: Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel
Apr 7	Lecture 5 Guest Speaker. Paul Frandsen. PDF of Paul Fransden lecture	rRNA structure & Alignment Bibliography	Mini-presentation: Different methods for cleaning PCR products for sequencing reactions Jimmy Bernot LAB: Purify PCR products and set-up sequencing reactions
Apr 9	Lecture 6. Secondary structure & alignment (cont.); Molecular clocks	Brandley et al. 2011 , Molecular Clocks Bibliography SECONDARY STRUCTURE HOMEWORK ASSIGNMENT , associated reading sent by Chris, too large to post	Mini-presentation: How Big Dye works, chromatograms, and troubleshooting Andrew Frank LAB: Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank
Apr 14	Lecture 7. Long branches, taxon sampling, Felsenstein-zone & anti-felsenstein zone; long branch pruning strategy	Long branches, Taxon Sampling, Big Trees Bibliography Swofford et al. 2001 Due April 16th	Mini-presentation: - Cloning DNA Kaitlin LAB: Cloning- Long Lab.
Apr 16	Lecture 8. Big Trees, Long Branches, & Simulations		Mini-presentation: Depositing sequences in GenBank Benedict LAB: PCR clones/Set up sequencing reactions- Long Lab
Apr 21	Lecture 9: Among Lineage rate variation: nucleotide bias among taxa	Nodal Support Readings , Salichos and Rokas 2013 , Betancur et al. 2014 (Comments on Salichos and Rokas 2013) , Summary due April 25th, 2014	Mini-presentation: Ancient DNA & Museum DNA protocols Tanisha LAB: Sephadex and put clone samples on ABI
Apr 23	Lecture 10: Tests of topology and problems associated with nodal support		Mini-presentation: Numts Sarah LAB: Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences
Apr 28	Lecture 11: ALRV: heterotachy, covarion models; long branch problems, taxon sampling, meaning of "basal taxon"	Lockhart et al. 2006. Heterotachy and trees (Summarize this one, Wednesday, April 30th) , 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 Russ LAB: RNA isolation- Nucleospin RNA Kit
Apr 30	Lecture 12: Among Lineage rate variation: Covarion evolution: codon models		Guest Lecture: Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis
May 4	Lab notebook due. Take home final handed out.	Nothing new	No Lab
May 11	Final Exam due, emailed to Russ	Nothing new	You are so done with this class

Final Exam Files
Final Exam Instuctions , Shull et al Manuscript , Shull et al figures , Published Shul et al 2001 .

Old Site

Molecular Systematics Website from 2012 (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)

@@ Line 1: / Line 1: @@
-Current Issues in Environmental Science (EEB 3205)
+Credits- half-semester module, 24 March-30 April 2014
-From eebedia
-Jump to: navigation, search
-Syllabus: Current Issues in Environmental Science (honors) EEB 3205
+'''Lectures:''' <br/>
+Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room
-        Fall 2011, Tuesday-Thursday 12:30-1:45 PM, Room:  BRON 124
+'''Labs:'''<br/>
+Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).
-Target Audience: This interdisciplinary course targets students who wish to increase their understanding of alternative futures . Discussions of environmental issues and the science behind them will lay the groundwork. Although designed as an honors course, other students in good standing can enroll pending instructors’ permission.
+'''Instructor:'''<br/>
+Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu>
+Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947
-Instructor: Chris Simon, Professor, Ecology and Evolutionary Biology
+'''Readings:''' will be posted as PDF’s. <br/>
-Texts: G. Tyler Miller & Scott Spoolman. Living in the Environment. 17th Edition (Used copies are available; also available as an “e-book”.)
+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).
-The Control of Nature, by John McPhee. Section 1 of this book will be discussed in Class in Mid Semester; the book was written in 1989 but is still relevant today. You can get used and new copies on-line starting at $4.
+'''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.
-Quiz & Current Events: Each Tuesday except the first, there will be a quiz consisting of up to ten questions related to the readings for the previous Thursday and the current Tuesday. Reading the text is required. Each Thursday at the beginning of class current events assignment are due and five volunteers will present their findings in 4 minutes or less. Each student is required to present three of their current events assignments orally.
+'''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.
-Attendance: As with all your classes, you will take away knowledge in proportion to the energy you put in. Students are expected to attend every class and read the text book weekly. However, UCONN policy states that students involved in activities supervised by a University faculty member or official (e.g, scholarly or artistic presentations or etc.) should inform me in writing prior to the anticipated absence and take the initiative to make up missed work in a timely fashion.) The same applies to medical and family emergencies that are documented in writing.
+'''Short Assignments:'''
-Grades: 25% - Current Events & Class participation (including class discussions, Conrol of Nature group project and the final class futures discussion.) 25% - Quizzes; 25% - Final Presentation; 25% - Final Exam.
+'''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).
-Office Hrs: Any time (including evenings or weekends if necessary). Contact me after class or by e-mail for an appointment: chris.simon@uconn.edu. E-mail is better than phone. Office: Bio-pharmacy 305D; Lab Bio-pharmacy 323 & 325, Office phone: 486-4640; lab phone- 486-3947
+'''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.
-Seminars: Several scientific lectures (seminars) are listed on the syllabus. Some of these are part of UCONN’s multidisciplinary long- running TEALE Lecture Series, “Nature and the Environment.” Because these generally take place at 4:00 PM on Thursdays and could conflict with your class schedule, they are not mandatory. They are, however, highly recommended. Most represent talks by well-known international experts and relate to course material. These talks can be written up in place of a current events assignment that week.
+'''3)''' There will be a short "secondary structure alignment assignment" during the semester.
-    Pdficon small.gifSyllabus_EEB3205_F11 25Oct11.pdf
+'''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.
-    Pdficon small.gifEEB3205 Lecture 1 introduction.pdf
+'''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.
-    Pdficon small.gifEEB 3205 Lecture 2 Energy Laws 17e.pdf
+'''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.
-    Pdficon small.gifEEB 3205 Lecture 3 Ch3 webs, nutrient cycles 17e.pdf
+'''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.'''
-    Pdficon small.gifFive most important problems F 2011.pdf
+'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%2030%20April%2014.pdf}}
-    Pdficon small.gif EEB 3205 Lectures 4& 5 Chp 4 Evolution & Biodiversity 17e.pdf
+=='''Schedule'''==
+{| border="1" cellpadding="2"
+!style="background:#99cccc;" width="90" align="center"|Day
+!style="background:#2A52BE;" width="365"|Topics
+!style="background:#008080;" width="315"|Reading/Assignment
+!style="background:#00B7EB;" width="275"|Lab
+|-
+|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/>
+|| 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
+|-
+|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}}.
+'''LAB:''' Chelex extraction.  Finish Nucleospin extractions
+|-
+|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/>
+|| 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}}
+'''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
+|-
+|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'''
+'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel
-    Pdficon small.gifEEB 3205 Lecture 6 Ch 7 & 19 Climate.pdf
+|-
+|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'''
+|| 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'''
+'''LAB:'''  Purify PCR products and set-up sequencing reactions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/M4-Bernot_PCR_cleanup.pdf}}
+|-
+|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}}
+'''Andrew Frank'''<br/>
+'''LAB:''' Sephadex and put samples on the ABI; Looking at sequences using Sequencher/Geneious, making contigs, blasting sequences in Genbank
+|-
+|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}}
+|| 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}}
+'''Kaitlin'''
+'''LAB:''' Cloning- Long Lab.
+|-
+|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}}
+'''Benedict''' <br/>
+'''LAB:''' PCR clones/Set up sequencing reactions- Long Lab
+|-
+|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}}
+|| 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}}
+'''Tanisha''' <br/>
+'''LAB:'''  Sephadex and put clone samples on ABI
+|-
+|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}}
+||  || | '''Mini-presentation:''' Numts
+'''Sarah''' <br/>
+'''LAB:''' Compare products with those from PCR with DNA vs cloning template and complete mtDNA sequences
+|-
+|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}}
+|| 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
+'''Russ'''
+'''LAB:''' RNA isolation- Nucleospin RNA Kit
+|-
+|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}}
+||  || | '''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}}
+|-
+|May 4 || Lab notebook due.  Take home final handed out.|| Nothing new || No Lab
+|-
+|May 11||Final Exam due, emailed to Russ|| Nothing new || You are ''so'' done with this class
+|}
+<br/>
+'''Final Exam Files''' <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}}.
-    Pdficon small.gifEEB 3205 Lecture 7 Chp 5,7,4 Ecology & Popln growth.pdf
+=='''Old Site'''==
+Molecular Systematics Website from 2012  (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)
-    Pdficon small.gifEEB 3205 Lecture 8 Ch 6 Human Population.pdf
+<br/>
-    Pdficon small.gifEEB 3250 Lecture 9 Ch 12 Soil&Food.pdf
-    Pdficon small.gifEEB 3205 Lecture 10 GMO-Silbart 29Sep11.pdf
-    Pdficon small.gifEEB 3205 Lecture 11 Ch 12 Pesticides.pdf
-    Pdficon small.gifEEB 3205 Lecture 12 Ch 9 Biodiversity (species).pdf
-    Pdficon small.gifControl of Nature Assignment F2011.doc
-    Pdficon small.gifEEB 3205 Lecture 13. Part 1. Invertebrate Conservation 2011_Wagner.pdf
-    Pdficon small.gifEEB 3205 Lecture 13, Part 2 Invertebrate Conservation 2011_Wagner.pdf
-    Pdficon small.gifEEB 3205 Lectures 14. & 15. Hawaiian Biodiversity 20 Oct 11.pdf
-    Pdficon small.gifEEB 3205 Lecture 16. minerals, water & pollution.pdf
-    Pdficon small.gifEEB 3205 Lecture 17.Ch 18 Water & Air Pollution F11.pdf
-    Pdficon small.gifEEB 3205 Lecture 18 Gene Likens Lecture Uconn Environ Sci - 2011.pdf
-    Pdficon small.gifEEB 3205 Lecture 19 Solid & Toxic Wastes F 09.pdf
-    Pdficon small.gifEEB 3205 Handout for Lect 19. Alternative cleaning products & Clasic newspaper stories.pdf
-    Pdficon small.gifEEB 3205. Toxic waste. LOE.ORG 4 Nov 11.pdf
-    Pdficon small.gifEEB 3205 Lecture 20 chp. 15 non-renewable fuels.pdf
-    Pdficon small.gifEEB 3205 Lecture 21 ch 16 alternative energy.pdf

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