Botany 940 / Zoology 956

Phylogenetic Comparative Methods Seminar

Instructors | Course Information | Readings and Notes

Instructors

Cécile Ané, Tony Ives, and Bret Larget are offering a joint Botany/Zoology seminar on Phylogenetic Comparative Methods.

Course Information

Botany 940 / Zoology 956 will meet in Birge 447 (instead of Birge 350) on Tuesdays from 4:00 to 4:50 pm.

The course will present both biological and statistical perspectives for examining trait evolution in a phylogenetic context. This seminar course will follow the directions indicated by case studies proposed by and selected by the participants. The course will combine practical instruction on how to use software to carry out data analysis, discussion of the selection of appropriate statistical methods, and inference to address biological questions of interest.

The course syllabus provides more details.

Software Links

Comparative methods in R: wiki pages developed for the 2011 Bodega applied phylogenetics workshop. Here is a page linking to various tutorials, in R and in Mesquite.
BayesTraits with discrete traits: still from the 2011 Bodega workshop.

Readings and Notes

Date	Topic	Leader	Readings	Other Materials
January 18	Introduction, Survey, and Brainstorming	Instructors		Overview of the types of questions one might ask of comparative data and of the types of analyses one might use.
January 25	Comparative Methods from a biologist's point of view	Ives	Garland et al. (2005)	lecture notes
February 1	Comparative Methods from a statistician's point of view	Ané	Blomberg et al. (2003)	lecture notes
February 8	Tree and divergence time estimation for comparative methods (paper more about Bayesian methods, discrete trait models)	Larget	Huelsenbeck et al. (2003)	lecture notes
February 15	Case Studies Competition and selection of three complementary case studies	Instructors
February 22	Case Study #1: Symbiont inhibition of specialized pathogen	Eric Caldera	Introduction to the system: Caldera et al. (2009) Gerardo and Caldera (2007) Attine news piece (short, an easy read)	Send questions to Eric and Tony.
March 1	Case Study #1	Charlie Mason	Zheng et al. (2009)	Send questions to Eric, Charlie and Tony.
March 8	Case Study #1	Charlie & Eric
March 15	Spring Break
March 22	Case Study #2: Epiphytism and character evolution in orchids	Rafael Arévalo	Barker et al. (2007) Silvera et al. (2009)	Notes on models for discrete trait evolution, and models used in Silvera et al. (2009). Send questions to Rafael and Cecile.
March 29	Case Study #2	Alejandro Zuluaga	Friedman & Barrett (2008) (The papers on diversification rates will probably be for next week)	Send questions to Alejandro and Cecile. Overview of the types of questions one might ask of comparative data and of the types of analyses one might use.
April 5	Case Study #2	Brent Berger	Alfaro et al. (2009) Maddison et al. (2007) Gravendeel et al. (2004)
April 12	Case Study #3: Bulb morphology evolution in Oxalis	Andy Gardner
April 19	Case Study #3	Alison Scott		Larget's oxalis slides File with 37-taxon consensus tree File with 24-taxon consensus tree File with data for 24 oxalis taxa with scaled bulbs
April 26	Case Study #3	Abigail Mazie	Revell (2009) Chapin et al. (1990) Proches et al. (2005)	Abby and Cecile's oxalis slides on PCA and regression in a phylogenetic context.
May 3	Wrap up	Instructors	Suggested: Overview chart, and Butler & King (2004) on OU models to detect shifts in selection regimes.

Last modified: March 3, 2011

Bret Larget, brlarget@wisc.edu