Molecular Systematics Spring 2014

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2 Credits- half-semester module, 20 March-26 April 2012
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2 Credits- half-semester module, 24 March-30 April 2014
  
Lectures: Tu & Th 12:30-1:45 Bio-Pharm 3rd floor conference room
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'''Lectures:''' <br/>
Labs:        Tu & Th 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).
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Mon & Wed 12:30-1:45 Bio-Pharm 3rd floor conference room
  
Instructor: Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu>
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'''Labs:'''<br/>
Graduate Assistant: Chris Owen, Biopharm 325A, <christopher.l.owen@uconn.edu>; 6-3947
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Mon & Wed 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).
  
Readings: will be posted as PDF’s.  
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'''Instructor:'''<br/>
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Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu>
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Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 6-3947
  
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).  
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'''Readings:''' will be posted as PDF’s. <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.  
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Handy reference books1) 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).
  
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.   
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'''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 treesLectures 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.
  
Short Assignments:
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'''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. 
  
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 an outline and a summary of the importance of each focal paper (1-2 pages; 1-2 papers per week). 
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'''Short Assignments:'''
  
2) On the first day, you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics.  In certain sections you are asked to describe ways in which this list can be modified for your research topic and you will be asked to check off or plan a date to accomplish some of the items.
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'''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).
  
3) There will be a short "secondary structure alignment assignment" during the semester.  
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'''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.
  
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.
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'''3)''' There will be a short "secondary structure alignment assignment" during the semester.  
  
5) Each student will present one 10 minute mini-presentation Powerpoint on a lab technique as described in the lab syllabus; Chris Owen will be available to advise you and point you toward relevant references but use the web search engines 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, they can be used as a starting point to revise and develop lectures you may teach.
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'''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.
  
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 and answer pre-specified questionsThe 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.
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'''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 ownThese 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 Due DatesMonday April 30th: Lab project and notebook dueTake Home FINAL EXAM handed outSunday May 6th: Take home final due.
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'''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 versionThe 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.
  
Syllabus
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'''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.'''
  
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%20rev%2027%20March%2012%20CLO-CS.pdf}}Syllabus Molecular Systematics rev 28 Mar 12.pdf
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'''Syllabus:''' {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Syllabus%20Molecular%20Systematics%2030%20April%2014.pdf}}
  
Assignment 1.
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=='''Schedule'''==
 
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{| border="1" cellpadding="2"
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/%20Checks%26Data_Molec%20Syst%20Sp%202012%20rev.doc}} Checks&Data_Molec Syst Sp 2012 rev.doc
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!style="background:#99cccc;" width="90" align="center"|Day
 
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!style="background:#2A52BE;" width="365"|Topics
First Reading Assignment:
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!style="background:#008080;" width="315"|Reading/Assignment
 
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!style="background:#00B7EB;" width="275"|Lab
Simon, C., F. Frati, A. Beckenbach, B. Crespi, H. Liu, and P. Flook.  1994.  Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved PCR primers.  Annals Entomol. Soc. Am. 87: 651-701. PDF will be mailed to you because it is too large to post here.
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|-
 
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|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/>
Sample outline (note- a summary is also required but is not illustrated).
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|| 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
 
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/%20%20Molecular%20Systematics%20Sample%20Outline%20%26%20Guide.pdf}} Molecular Systematics Sample Outline & Guide.pdf
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|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}}.
 
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'''LAB:''' Chelex extraction. Finish Nucleospin extractions
Readings for Lecure 1.  "How Molecules Evolve and Models of Evolution"
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|-
 
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|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/>
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/How%20molecules%20evolve%20Readings%2012.pdf}}How molecules evolve Readings 12.pdf
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|| 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}}
 
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'''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
Lecture 1. Notes.
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|-
 
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|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'''
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20Day%201%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2020Mar12.pdf}}EEB 5350 Day 1 How Molecules Evolve. Parts I & II 20Mar12.pdf
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'''LAB:''' Set-up PCR reaction (mtDNA of Tettigades species, COI barcode, two directions), run gel
 
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Lab 1. Minipresentation
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20First%20Lab%20mini%20lecture%202012.pdf}}EEB 5350 First Lab mini lecture 2012.pdf
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Lecture 2. Notes
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20Day%202%20Models%2C%20ASRV%20History%202012.pdf}}EEB 5350 Day 2 Models, ASRV History 2012.pdf
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Lab 2. Minipresentation
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20Minipresentation.%20Chris%20Owen.%20DNA%20Extraction%2022Mar12.pdf}}EEB 5350 Minipresentation. Chris Owen. DNA Extraction 22Mar12.pdf
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Readings for Lecture 2. Among Site Rate Variation
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/%20EEB%205350%20ASRV%20readings_Sp%2012.pdf}} EEB 5350 ASRV readings_Sp 12.pdf
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Lecture 3. Notes
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20Day%203%20ASRV%2C%20Partitions%2C%20Clocks.pdf}}EEB 5350 Day 3 ASRV, Partitions, Clocks.pdf
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Lab 3. Minipresentation
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lab.%203.%20Minipresentation%20DNA%20extractions%20museums%202012%20Chris%20Owen%20sm.pdf}}EEB 5350 Lab. 3. Minipresentation DNA extractions museums 2012 Chris Owen.pdf
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Molecular Clock Readings
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Molecular%20Clock%20Readings%202012.pdf}}EEB 5350 Molecular Clock Readings 2012.pdf
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Lecture 4. Notes
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20Day%204%20Molecular%20Clocks%20Systematic%20Error%20Biases%202012.pdf}}EEB 5350 Day 4 Molecular Clocks Systematic Error Biases 2012.pdf
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Lab 4. Minipresentation
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205305.%20Minipresentation.%20PCR.%20Ursula%20King.pdf}}EEB 5305. Lab 4 Minipresentation. PCR. Ursula King.pdf
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Lecture 5. Notes
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Day%205%20EEB%205350%20nucleotide%20bias%2C%20covarion%20evolution%20part%20I%202012.pdf}}EEB 5350 Day 5 EEB 5350 nucleotide bias, covarion evolution part I 2012.pdf
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Lab 5. Minipresentation
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/PatGero%20MolecSyst%20Minipresentation%204-3.pdf}}EEB 5305 Lab 5. PatGero MolecSyst Minipresentation 4-3.pdf
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Nucleotide Bias, Covarion Readings:
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Covarion%2C%20Heterotachy%2C%20bias%20readings%202012%20rev.doc}}Covarion, Heterotachy, bias readings 2012 rev.doc
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Pages%20from%20Daniel%20Fan%20dissertation%20Chp%203%20Heterotachy.pdf}}Pages from Daniel Fan dissertation Chp 3 Heterotachy.pdf
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Whelan%20et%20al.%202011.%20%20Heterotachy%20Mol%20Biol%20Evol.pdf}}Whelan et al. 2011.  Heterotachy Mol Biol Evol.pdf
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Lecture 6. Notes
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Day%206.%202010%20Heterotachy%2C%20Covarion%20evolution%20Taxon%20Sampling%2C%20Long%20Branches%202012.pdf}}EEB 5350 Day 6. 2010 Heterotachy, Covarion evolution Taxon Sampling, Long Branches 2012.pdf
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Lab 6. Minipresentation
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lab%206-Minipresentation%20Big%20Dye%20Russ%20Meister.pdf}}EEB 5350 Lab 6-Minipresentation Big Dye Russ Meister.pdf
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Long Branches Big Trees Readings
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/LBA%2C%20taxon%20sampling%2C%20big%20trees%20readings%202012.pdf}}LBA, taxon sampling, big trees readings 2012.pdf
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Philippe%20et%20al.%202011.%20%20More%20sequences%20not%20enough.pdf}}Philippe et al. 2011More sequences not enough.pdf
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Lecture 7. Notes
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Day%207.%20%20Long%20Branches%20and%20Big%20Trees%20%202012.pdf}}EEB 5350 Day 7Long Branches and Big Trees  2012.pdf
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Lab 7. Minipresentation
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lab%207.%20RNA%20isolation%20minipresentation%20Hamid%20Razifard%209Apr12.pdf}}EEB 5350 Lab 7. RNA isolation minipresentation Hamid Razifard 9Apr12.pdf
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Lecture 8. Notes
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Day%208%20Long%20Branches%20cont.%20Combining%20data%202012.pdf}}EEB 5350 Day 8 Long Branches cont. Combining data 2012.pdf
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Lab 8. Minipresentation
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lab%208.%20Kasey%20Pregler%20MiniPresentation%2012April12.pdf}}EEB 5350 Lab 8. Kasey Pregler MiniPresentation 12April12.pdf
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Lecture 9. Notes
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Day%209%20Combining%20Data%2C%20Species%20Trees%202012.pdf}}EEB 5350 Day 9 Combining Data, Species Trees 2012.pdf
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Lab 9. Minipresentation.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20Lab%209.%20Minipresentation%20RT-PCR%20Brigette.pdf}}EEB 5350 Lab 9. Minipresentation RT-PCR Brigette.pdf
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Lecture 10. Notes.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Day%2010.%20Choosing%20Partitions%2C%20Comparing%20Trees.pdf}}EEB 5350 Day 10. Choosing Partitions, Comparing Trees.pdf
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Lab 10.  Minipresentation
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20Lab%2010.%20Minipresentation%20Cloning%2C%20Emily%20Ellis.pdf}}EEB 5350 Lab 10. Minipresentation Cloning, Emily Ellis.pdf
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Combining Data, Species trees, Comparing Trees Readings
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Comparing%20Trees%20Combining%20Data%20Readings%202012.pdf}}Comparing Trees Combining Data Readings 2012.pdf
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Reading for Tuesday: Summarizes most material covered in the class. Write a summary of each major section using one to two pages. Outline not necessary.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Simon%2C%20Buckley%2C%20Frati%2C%20Stewart%2C%20Beckenbach%202006%20AREES%20%26%20supplement.pdf}}Simon, Buckley, Frati, Stewart, Beckenbach 2006 AREES & supplement.pdf
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Lecture 11. notes.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20Day%2011%20Nodal%20Support%202012.pdf}}EEB 5350 Day 11 Nodal Support 2012.pdf
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Nodal/Branch Support Readings
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/%20%20Nodal%20support%20readings%20Sp%202012.doc}} Nodal support readings Sp 2012.doc
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Lab 11. Minipresentation
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350.%20Lab%2011%20Minipresentation%20Blast%20Veronica%20Bueno.pdf}}EEB 5350. Lab 11 Minipresentation Blast Veronica Bueno.pdf
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Lecture 12.  Notes.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20Day%2012.%20%20Alignment%20%26%20Secondary%20Structure%202012.pdf}}EEB 5350 Day 12Alignment & Secondary Structure 2012.pdf
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Hickson et al. Structure paper:
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Hickson%20et%20al.%201996.%20Secondary%20structure%20evolution%20MBE.pdf}}Hickson et al. 1996. Secondary structure evolution MBE.pdf
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Robin Gutell structure paper:
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Gutell%20et%20al.%202002.%20rRNA%20structures.%20curr.%20opin.struct.%20Biol.}}Gutell et al. 2002. rRNA structures. curr. opin.struct. Biol.
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Secondary Structure Assignment:
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20secondary%20structure%20%20assignment%20Sp12.pdf%20.pdf}}EEB 5350 secondary structure  assignment Sp12.pdf .pdf
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20Hickson%20et%20al.%201996.%20rRNA%20template.pdf}}EEB 5350 Hickson et al. 1996. rRNA template.pdf
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Lab 12Minipresentation. Genomics.
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/CLOwen_Genomics%20Minpresentation_FINAL.pdf}}Lab 12. CLOwen_Genomics Minpresentation.pdf
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Secondary structure readings:   
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/%20Structure_Alignmnt_readings_Sp%2012.pdf}} Structure_Alignmnt_readings_Sp 12.pdf
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Final Exam Instructions, Shull et al. paper to review, figures for Shull et al.:
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/%20Final%20Exam%20EEB350%20Reviewer%27s_instructns_S12.pdf}} Final Exam EEB350 Reviewer's_instructns_S12.pdf
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/%20Shull_et_al._28Oct%20MS.pdf}} Shull_et_al._28Oct Manuscript.pdf
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Shull%20et%20al.%20figures1-7%2C%20Tabs%201-5.pdf}}Shull et al. figures1-7, Tabs 1-5.pdf
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|-
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|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}}
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|-
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|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
 +
|-
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|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.
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|-
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|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
 +
|-
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|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}}
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|| 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
 +
|-
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|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
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'''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}}.
  
 +
=='''Old Site'''==
 +
Molecular Systematics Website from 2012  (http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/MolSys2012)
 +
<br/>
 
[[Category:EEB Courses]]
 
[[Category:EEB Courses]]

Latest revision as of 21:59, 6 May 2014

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: Pdficon small.gif

Schedule

Day Topics Reading/Assignment Lab
Mar 24 Pdficon small.gifAn introduction to looking at your data: How molecules evolve.
Reading too big to post, sent out by Chris. How Molecules Evolve BibliographyPdficon small.gif Data checks at every step. Mechanics of Lab; Explanation of class Tettigades project Pdficon small.gif. Start Nucleospin kit extractions
Mar 26 Pdficon small.gifThe many roles of biological systematics
Kjer & Honeycutt Pdficon small.gif, Soubrier et al. Pdficon small.gif, Sullivan & Swofford Pdficon small.gif, ASRV BibliographyPdficon small.gif Mini-presentation: DNA extraction- ultrapure to ultradirty, (phenol-chloroform/CsCl gradients to filters to salting out to chelex, etc.) RussPdficon small.gif. Also, Johana gave a small presentation about her work with different extraction methodsPdficon small.gif.

LAB: Chelex extraction. Finish Nucleospin extractions

Mar 31 Pdficon small.gif Problems associated combining data, multiple gene histories for single taxa (Species trees and gene trees)
Bull et al 1993 Pdficon small.gif, Pagel and Mead 2004 Pdficon small.gif, Combining Data & Partitioning Bibliography Pdficon small.gif 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 Pdficon small.gif

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 Pdficon small.gif Lecture 4. Choosing partitions, comparing trees Mini-presentation: The Polymerase Chain Reaction- how it works & optimizing reactions. Pdficon small.gif 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. Pdficon small.gif PDF of Paul Fransden lecture rRNA structure & Alignment Bibliography Pdficon small.gif Mini-presentation: Different methods for cleaning PCR products for sequencing reactions Jimmy Bernot

LAB: Purify PCR products and set-up sequencing reactions Pdficon small.gif

Apr 9 Lecture 6. Secondary structure & alignment (cont.); Molecular clocks Pdficon small.gif Brandley et al. 2011 Pdficon small.gif, Molecular Clocks Bibliography Pdficon small.gif
SECONDARY STRUCTURE HOMEWORK ASSIGNMENT Pdficon small.gif, associated reading sent by Chris, too large to post
Mini-presentation: How Big Dye works, chromatograms, and troubleshooting Pdficon small.gif

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 Pdficon small.gif Long branches, Taxon Sampling, Big Trees Bibliography Pdficon small.gif Swofford et al. 2001 Pdficon small.gif Due April 16th Mini-presentation: - Cloning DNA Pdficon small.gif

Kaitlin LAB: Cloning- Long Lab.

Apr 16 Lecture 8. Big Trees, Long Branches, & Simulations Pdficon small.gif Mini-presentation: Depositing sequences in GenBank Pdficon small.gif

Benedict
LAB: PCR clones/Set up sequencing reactions- Long Lab

Apr 21 Lecture 9: Among Lineage rate variation: nucleotide bias among taxa Pdficon small.gif Nodal Support Readings Pdficon small.gif, Salichos and Rokas 2013 Pdficon small.gif, Betancur et al. 2014 (Comments on Salichos and Rokas 2013) Pdficon small.gif, Summary due April 25th, 2014 Mini-presentation: Ancient DNA & Museum DNA protocols Pdficon small.gif

Tanisha
LAB: Sephadex and put clone samples on ABI

Apr 23 Lecture 10: Tests of topology and problems associated with nodal support Pdficon small.gif 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" Pdficon small.gif Lockhart et al. 2006. Heterotachy and trees (Summarize this one, Wednesday, April 30th) Pdficon small.gif, Lockhart and Steel 2005. A tale of two processes Pdficon small.gif, Gruenheit et al. (Lockhart) 2008. Covarion under changing proportions var sites Pdficon small.gif, Bibliography Pdficon small.gif 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 Pdficon small.gif Guest Lecture: Beth Wade, Next Gen sequencing applications, Transcriptomics, Rad Tags, Class Discussion on the implications for modeling data for phylogenetic analysis Pdficon small.gif
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 Pdficon small.gif, Shull et al Manuscript Pdficon small.gif, Shull et al figures Pdficon small.gif, Published Shul et al 2001 Pdficon small.gif.

Old Site

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

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