Phylogenetic comparative methods
CEB 35300, Spring 2010 (2012 syllabus will be posted in the spring)

Andrew Hipp, Herbarium Curator, Morton Arboretum. email, Ph: 630-725-2094
Rick Ree, Associate Curator, Botany Dept., Field Museum. email

Course overview

Time: Spring quarter 2010, Wednesdays, 9:30 to 11:30 a.m.
Location: Zoology classroom, the Field Museum
Prerequisites: Systematics, or general familiarity with methods for estimating phylogenies
Software / computer requirements: Computer tutorials will be held in class, primarily utilizing the open-source R and Python languages. Students will need to have a laptop computer with them or share a laptop with a classmate.
Goals and summary: This is a graduate seminar course about the uses of phylogenetic trees in evolution and ecology, emphasizing historical inference of phenotypic traits, geographic ranges, and community ecology. (This is not a course on how to infer phylogenies, or their uses in studies of molecular evolution and population genetics.) Within this scope we will focus on topics of popular interest and relevance to student research, working our way from model assumptions and statistical underpinnings to practical implementation of methods. The 2-hour weekly meeting will include lectures on main topics, discussion of primary literature, and tutorials on and opportunities to work hands-on with software (bring your own laptop). Additionally, each week one student will present a case study from the literature or from their own research. Focus in these presentations will be on the comparative questions and approaches taken by the authors.

Grades will be based on the clarity of the presentations as well as on class participation. Each week, all students will be expected to email to the instructor two questions they have based on the readings. Questions should be mailed by Monday evening, and they will be considered a part of class participation. Students who are presenting in a given week will not be required to submit questions, but they will be required to send a copy of the paper(s) they will be presenting to all class participants by Monday evening.

Course schedule

Week 1 (March 31): Independent contrasts and phylogenetic regression I
Tutorial: Regression in R [Hipp]
Prior to class, install R and the packages ape, geiger, nlme

Week 2 (April 7): Regression II: Model fit and phylogenetic rates
Tutorial: Regression in R part II, model-fitting in R [Hipp]

Week 3 (April 14): Adaptation and ancestral states of continuous characters
Tutorial: Selection and its effects on character evolution [Hipp]

Week 4 (April 21): Ancestral states of discrete traits

Week 5 (April 28): Correlated trait evolution
Tutorial: Tree structures and tree traversal in Python [Ree]

Week 6 (May 5): Diversification rates and patterns
Tutorial: Simulating phylogenies in Python [Ree]

Week 7 (May12): Key innovations

Week 8 (May 19): Integrative approaches to diversification and trait evolution

Week 9 (May 26): Historical biogeography [Ree]
Tutorial: Using Lagrange [Ree]

Week 10 (June 2): Phylogenetics and community ecology