Molecular Systematics Spring 2014
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, <firstname.lastname@example.org> Graduate Assistant: Chris Owen, Biopharm 325A, <email@example.com>; 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).
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.
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).
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.
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) 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.
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 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.
Final Due Dates: Monday April 30th: Lab project and notebook due. Take Home FINAL EXAM handed out. Sunday May 6th: Take home final due.
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).
Readings for Lecure 1. "How Molecules Evolve and Models of Evolution"
Lecture 1. Notes.
Lab 1. Minipresentation
Lecture 2. Notes
Lab 2. Minipresentation
Readings for Lecture 2. Among Site Rate Variation
Lecture 3. Notes
Lab 3. Minipresentation
Molecular Clock Readings
Lecture 4. Notes
Lab 4. Minipresentation
Lecture 5. Notes
Lab 5. Minipresentation
Nucleotide Bias, Covarion Readings:
Lecture 6. Notes
Lab 6. Minipresentation
Long Branches Big Trees Readings
Lecture 7. Notes
Lab 7. Minipresentation
Lecture 8. Notes
Lab 8. Minipresentation
Lecture 9. Notes
Lab 9. Minipresentation.
Lecture 10. Notes.
Lab 10. Minipresentation
Combining Data, Species trees, Comparing Trees Readings
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.
Lecture 11. notes.
Nodal/Branch Support Readings
Lab 11. Minipresentation
Lecture 12. Notes.
Hickson et al. Structure paper:
Robin Gutell structure paper:
Secondary Structure Assignment:
Lab 12. Minipresentation. Genomics.
Secondary structure readings: Coming Soon
Final Exam Instructions, Shull et al. paper to review, figures for Shull et al.: