T. Collins: Applied Phylogenetics

Applied Phylogenetics, PCB 5616

Course Description:

An introduction to modern computer-based methods of reconstructing evolutionary relationships and tracing evolutionary histories of lineages and characters of interest, with an emphasis on pragmatic issues for evolutionary biologists, ecologists, and epidemiologists. I will focus on PAUP* 4.0b4, the Maddison Brother's program MacClade 4.0, and to a lesser extent, Joe Felsenstein's collection of programs, PHYLIP. These 3 programs form a solid foundation for phylogenetic analyses. Other programs will be investigated as well (see below). Typically (but not always) we will have a lecture on Monday, and laboratory demonstrations, laboratory exercises, and/or discussion of papers on Wednesday.
Prerequisites: permission of instructor, and basic computer skills.

Contact Information:

Tim Collins: HLS 318B, PH: 305-348-1730, e-mail:CollinsT@fiu.edu.
Office hours: Tuesday 9:00-12:00. You can also see me after class (not before class), or by appointment.

Schedule:

For lectures and discussions we will meet in HLS 216 (M 1:00-2:15 PM). For laboratories we will meet in PC 449 (W 1-4 PM, the Macintosh computer lab). For class presentations or demonstrations that require the Proxima computer projector, we will meet in HLS 416 (campus map). If in doubt, give me a call or e-mail.

Date	Topic	Due

M 08/30	Organizational meeting: Readings: A Phylogenetic Perspective
W 09/01	Intro to Phylogenetic Inference I: Basic Concepts & Terminology
M 09/06	Labor Day Holiday
W 09/08	Intro to Phylogenetic Inference, Lab I. Manual Parsimony & MacClade Tutorial
M 09/13	Intro to Phylogenetic Inference II: Rooting & Character state reconstruction
W 09/15	Intro to Phylogenetic Inference, Lab II. MacClade II: File Structure
M 09/20	Character fit to trees, Consensus trees
W 09/22	Intro to PAUP, Lab III. PAUP basics, basic tree search methodology	Software Presentation Ideas
M 09/27	Finding Optimal Trees, Heuristic methods
W 09/29	Intermediate PAUP*, Lab IV. Heuristic Searches & Islands of Trees
M 10/04	Homology & Alignment	Software Presentation Proposal
W 10/06	CLUSTAL X & PAUP* Advanced, Lab V. Alignment, Command line interface, MPRs & Consensus trees
M 10/11	Missing Data, Character Weighting
W 10/13	Character weighting, Lab VI	Main Project Ideas
M 10/18	Models in Phylogenetic Inference
W 10/20	PHYLIP, Lab VII
M 10/25	Distance Methods	Main Project Proposal & Data
W 10/27	Distance Methods, Lab VII
M 11/01	Software Presentations (15 minutes each)
W 11/03	Software Presentations (15 minutes each)
M 11/08	Maximum Likelihood and Bayesian Methods
W 11/10	Bayesian analysis with MrBayes
M 11/15	Evaluating Support for Hypotheses
W 11/17	Evaluating Support, Lab VIII
M 11/22	Separate versus combined analysis of discrete data sets: Process partitions
W 11/24	Process partitions. Lab IX
M 11/29 W 12/01	Simulating Evolution Simulating Evolution Lab X
M 12/06	Student Main Project Presentations (15 minutes each + 5 for questions)	Main Project Paper
W 12/08	Student Main Project Presentations (15 minutes each + 5 for questions)

Letter Grades will be assigned. There will be no exams. Grades will be based on class projects, presentations, participation, and laboratory exercises. I expect you to attend all classes, and to be on time. Grades will be based on the following:

1/3 Software Demonstration: You will choose a program from the list below (one that mirrors your specific interests) and (1) acquire the program or source code, (2) get the software up and running on a local computer system, (3) submit a short report.
1/3 Main Project: This will be a project that involves extensive use of one of the main programs (PAUP*, MacClade, PHYLIP). This isn't just an exercise where you generate lots of trees. You need to define a problem, do analyses, and reach a conclusion. No Wimpy Data Sets. No data sets with less than 10 taxa or 30 characters. See me if you are having trouble locating an interesting data set.
1/3 Class participation and laboratory exercises: Laboratory exercises will include questions that must be answered and turned in. Answers are due by the beginning of the next class (Monday). Write answers in the spaces provided on lab, and turn them in. Labs will be returned the following week. You may discuss lab exercises with your classmates. These are not, however, group efforts. Labs that are essentially duplicates of one another are unacceptable and will result in a failing grade for both parties.

Textbooks: MacClade 4 Manual, by David and Wayne Maddison, supplied to you as a PDF file on a zip disk and Molecular Evolution:A Phylogenetic Approach, 1998 by Rod Page and Eddie Holmes, Blackwell Science Limited, available in the book store. I will also give each of you a 100MB zip disk for data files to be used in labs and demonstrations. These are not cheap. If you lose the disk, you will need to buy a replacement.