Molecular Systematics Spring 2014

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2 Credits- half-semester module, 20 March-26 April 2012

Lectures: Tu & Th 12:30-1:45 Bio-Pharm 3rd floor conference room Labs: Tu & Th 2:00-4:00 (first half-hour in conference room, remainder in BioPharm 325).

Instructor: Chris Simon, Biopharm 305D, 6-4640, <> Graduate Assistant: Chris Owen, 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 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.

Short Assignments: 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). There will be a short "secondary structure alignment assignment" during the semester.

The laboratory 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. Each student will keep a laboratory notebook and hand-in data collected during the course in the form of an alignment, 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.

Minipresentation assignments: Each student will present one 10 minute mini-presentation on a lab technique as described in the lab syllabus; Chris 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, these mini-presentations can be used as a starting point to revise and develop lectures you may teach.

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 questions. 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.

Monday April 30th: Lab project and notebook due. Take Home FINAL EXAM handed out.

Sunday May 6th: Take home final due.