Botany 940 / Zoology 956

Phylogenetic Comparative Methods Seminar

Instructors | Course Information | Readings and Notes

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

DateTopicLeaderReadingsOther 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,