Course information

Course title
Using Geiger, Phytools, and other Computational Tools to Study Macroevolution on Phylogenies
University / Organization
Transmitting Science
Els Hostalets de Pierola, Barcelona
Academic level
Both Msc and PhD
Transmitting Science
Course director
Course lecturer(s)
Dr Liam Revell (University of Massachusetts Boston, United States of America) Dr Luke J. Harmon (University of Idaho, United States of America)
Course aim
2nd Edition *USING GEIGER, PHYTOOLS, AND OTHER COMPUTATIONAL TOOLS TO STUDY MACROEVOLUTION ON PHYLOGENIES* October 8th-11th, 2018, Barcelona (Spain) This is a course on phylogenetic comparative methods. Requirements Graduate or postgraduate degree in Life or Earth Sciences. Basic knowledge of R and statistics. All participants must bring their own personal laptop. We would like to encourage participants to bring along their own data.
Course contents / programme
Program Monday, October 8th, 2018. Morning: 1. Introduction to phylogenies and the comparative method. [Lecture] 2. Introduction the basics of the R statistical computing environment. [Exercise] 3. Introduction to reading, writing, manipulating, and visualizing phylogenies and comparative data in R. [Exercise] Afternoon: 4. Models of phenotypic trait evolution on trees: Brownian motion. [Lecture] 5. Simulating Brownian motion on trees using R. [Exercise] 6. Introduction to the phylogenetic comparative method: Phylogenetic independent contrasts. [Lecture] 7. Phylogenetic independent contrasts and exploring the properties of contrasts regression using simulation in R. [Exercise] 8. Phylogenetic generalized least squares regression and phylogenetic generalized ANOVA. [Exercise] Tuesday, October 9th, 2018. Morning: 9. Multivariate statistical methods with phylogenies: Phylogenetic principal components analysis, canonical correlation analysis, and other approaches. [Lecture] 10. Phylogenetic PCA and phylogenetic CCA in R. [Exercise] 11. Continuous character models of trait evolution on phylogenies. [Lecture] Afternoon: 12. Fitting continuous character models to univariate trait data in R. [Exercise] 13. Ancestral state reconstruction I: Continuous characters. [Lecture] 14. Reconstructing ancestral states for continuous traits on phylogenies using R. [Exercise] Wednesday, October 10th, 2018. Morning: 15. Ancestral state reconstruction II: Discrete characters. [Lecture] 16. Reconstructing ancestral states for discrete traits on phylogenies using R. [Exercise] 17. Exploring the limitations of ancestral state reconstruction for continuous and discrete characters on phylogenies using R. [Exercise] Afternoon: 18. Testing for the influence of one discrete character on a second using Pagel’s (1994) method. [Lecture] 19. Exploring the promise and limitations of the Pagel (1994) method using R. [Exercise] 20. Analysing discrete character coevolution, and the evolution of discrete and continuous characters using the threshold model. [Lecture] Thursday, October 11th, 2018. Morning: 21. Fitting models of discrete and continuous character evolution on trees using the threshold model. [Exercise] 22. Multi-rate, multi-regime, and multivariate models of character evolution on phylogenies. [Lecture] 23. Fitting multi-regime and multivariate models for continuous character evolution in R. [Exercise] Afternoon: 24. Visualizing trees and phylogenetic comparative data. [Lecture] 25. Plotting phylogenies and comparative data using R. [Exercise] 26. Wrap-up and optional additional exercise or lecture.
Required Knowledge and preparation
Teaching methods
Course type
Consecutive days
Online course
Duration (net days)
October 8th-11th, 2018
Course fee
Direct e-mail to register
Paper submission required?
Logo of institution
front approval