Molecular Systematics Spring 2014

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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, <> Graduate Assistant: Russ Meister, Biopharm 325A, <>; 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.

Syllabus Coming soon!

  1. Pdficon small.gifSyllabus Molecular Systematics rev 28 Mar 12.pdf

Assignment 1.

Pdficon small.gif Checks&Data_Molec Syst Sp 2012 rev.doc

First Reading Assignment:

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.

Sample outline (note- a summary is also required but is not illustrated).

Pdficon small.gif Molecular Systematics Sample Outline & Guide.pdf

Readings for Lecure 1. "How Molecules Evolve and Models of Evolution"

Pdficon small.gifHow molecules evolve Readings 12.pdf

Lecture 1. Notes.

Pdficon small.gifEEB 5350 Day 1 How Molecules Evolve. Parts I & II 20Mar12.pdf

Lab 1. Minipresentation

Pdficon small.gifEEB 5350 First Lab mini lecture 2012.pdf

Lecture 2. Notes

Pdficon small.gifEEB 5350 Day 2 Models, ASRV History 2012.pdf

Lab 2. Minipresentation

Pdficon small.gifEEB 5350 Minipresentation. Chris Owen. DNA Extraction 22Mar12.pdf

Readings for Lecture 2. Among Site Rate Variation

Pdficon small.gif EEB 5350 ASRV readings_Sp 12.pdf

Lecture 3. Notes

Pdficon small.gifEEB 5350 Day 3 ASRV, Partitions, Clocks.pdf

Lab 3. Minipresentation

Pdficon small.gifEEB 5350 Lab. 3. Minipresentation DNA extractions museums 2012 Chris Owen.pdf

Molecular Clock Readings

Pdficon small.gifEEB 5350 Molecular Clock Readings 2012.pdf

Lecture 4. Notes

Pdficon small.gifEEB 5350 Day 4 Molecular Clocks Systematic Error Biases 2012.pdf

Lab 4. Minipresentation

Pdficon small.gifEEB 5305. Lab 4 Minipresentation. PCR. Ursula King.pdf

Lecture 5. Notes

Pdficon small.gifEEB 5350 Day 5 EEB 5350 nucleotide bias, covarion evolution part I 2012.pdf

Lab 5. Minipresentation

Pdficon small.gifEEB 5305 Lab 5. PatGero MolecSyst Minipresentation 4-3.pdf

Nucleotide Bias, Covarion Readings:

Pdficon small.gifCovarion, Heterotachy, bias readings 2012 rev.doc
Pdficon small.gifPages from Daniel Fan dissertation Chp 3 Heterotachy.pdf
Pdficon small.gifWhelan et al. 2011. Heterotachy Mol Biol Evol.pdf

Lecture 6. Notes

Pdficon small.gifEEB 5350 Day 6. 2010 Heterotachy, Covarion evolution Taxon Sampling, Long Branches 2012.pdf

Lab 6. Minipresentation

Pdficon small.gifEEB 5350 Lab 6-Minipresentation Big Dye Russ Meister.pdf

Long Branches Big Trees Readings

Pdficon small.gifLBA, taxon sampling, big trees readings 2012.pdf
Pdficon small.gifPhilippe et al. 2011. More sequences not enough.pdf

Lecture 7. Notes

Pdficon small.gifEEB 5350 Day 7. Long Branches and Big Trees 2012.pdf

Lab 7. Minipresentation

Pdficon small.gifEEB 5350 Lab 7. RNA isolation minipresentation Hamid Razifard 9Apr12.pdf

Lecture 8. Notes

Pdficon small.gifEEB 5350 Day 8 Long Branches cont. Combining data 2012.pdf

Lab 8. Minipresentation

Pdficon small.gifEEB 5350 Lab 8. Kasey Pregler MiniPresentation 12April12.pdf

Lecture 9. Notes

Pdficon small.gifEEB 5350 Day 9 Combining Data, Species Trees 2012.pdf

Lab 9. Minipresentation.

Pdficon small.gifEEB 5350 Lab 9. Minipresentation RT-PCR Brigette.pdf

Lecture 10. Notes.

Pdficon small.gifEEB 5350 Day 10. Choosing Partitions, Comparing Trees.pdf

Lab 10. Minipresentation

Pdficon small.gifEEB 5350 Lab 10. Minipresentation Cloning, Emily Ellis.pdf

Combining Data, Species trees, Comparing Trees Readings

Pdficon small.gifComparing Trees Combining Data Readings 2012.pdf

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.

Pdficon small.gifSimon, Buckley, Frati, Stewart, Beckenbach 2006 AREES & supplement.pdf

Lecture 11. notes.

Pdficon small.gifEEB 5350 Day 11 Nodal Support 2012.pdf

Nodal/Branch Support Readings

Pdficon small.gif Nodal support readings Sp 2012.doc

Lab 11. Minipresentation

Pdficon small.gifEEB 5350. Lab 11 Minipresentation Blast Veronica Bueno.pdf

Lecture 12. Notes.

Pdficon small.gifEEB 5350 Day 12. Alignment & Secondary Structure 2012.pdf

Hickson et al. Structure paper:

Pdficon small.gifHickson et al. 1996. Secondary structure evolution MBE.pdf

Robin Gutell structure paper:

Pdficon small.gifGutell et al. 2002. rRNA structures. curr. opin.struct. Biol.

Secondary Structure Assignment:

Pdficon small.gifEEB 5350 secondary structure assignment Sp12.pdf .pdf
Pdficon small.gifEEB 5350 Hickson et al. 1996. rRNA template.pdf

Lab 12. Minipresentation. Genomics.

Pdficon small.gifLab 12. CLOwen_Genomics Minpresentation.pdf

Secondary structure readings:

Pdficon small.gif Structure_Alignmnt_readings_Sp 12.pdf

Final Exam Instructions, Shull et al. paper to review, figures for Shull et al.:

Pdficon small.gif Final Exam EEB350 Reviewer's_instructns_S12.pdf
Pdficon small.gif Shull_et_al._28Oct Manuscript.pdf
Pdficon small.gifShull et al. figures1-7, Tabs 1-5.pdf