Using GEIGER, PHYTOOLS, & other computational tools to study macroevolution on phylogenies

Registration is open for Transmitting Science course: “Using Geiger, Phytools, and other Computational Tools to Study Macroevolution on Phylogenies”


Dates and place: July 16th-19th, 2019, Crete (Greece).

Instructors: Dr Liam Revell (University of Massachusetts Boston, USA) and Dr Luke Harmon (University of Idaho, USA).



– Introduction to phylogenies and the comparative method. [Lecture] – Introduction the basics of the R statistical computing environment. [Exercise] – Introduction to reading, writing, manipulating, and visualizing phylogenies and comparative data in R. [Exercise] – Models of phenotypic trait evolution on trees: Brownian motion. [Lecture] – Simulating Brownian motion on trees using R. [Exercise] – Introduction to the phylogenetic comparative method: Phylogenetic independent contrasts. [Lecture] – Phylogenetic independent contrasts and exploring the properties of contrasts regression using simulation in R. [Exercise] – Phylogenetic generalized least squares regression and phylogenetic generalized ANOVA. [Exercise]


– Multivariate statistical methods with phylogenies: Phylogenetic principal components analysis, canonical correlation analysis, and other approaches. [Lecture] – Phylogenetic PCA and phylogenetic CCA in R. [Exercise] – Continuous character models of trait evolution on phylogenies. [Lecture] – Fitting continuous character models to univariate trait data in R. [Exercise] – Ancestral state reconstruction I: Continuous characters. [Lecture] – Reconstructing ancestral states for continuous traits on phylogenies using R. [Exercise]


– Ancestral state reconstruction II: Discrete characters. [Lecture] – Reconstructing ancestral states for discrete traits on phylogenies using R. [Exercise] – Exploring the limitations of ancestral state reconstruction for continuous and discrete characters on phylogenies using R. [Exercise] – Testing for the influence of one discrete character on a second using Pagel’s (1994) method. [Lecture] – Exploring the promise and limitations of the Pagel (1994) method using R. [Exercise] – Analysing discrete character coevolution, and the evolution of discrete and continuous characters using the threshold model. [Lecture]


– Fitting models of discrete and continuous character evolution on trees using the threshold model. [Exercise] – Multi-rate, multi-regime, and multivariate models of character evolution on phylogenies. [Lecture] – Fitting multi-regime and multivariate models for continuous character evolution in – [Exercise] – Visualizing trees and phylogenetic comparative data. [Lecture] – Plotting phylogenies and comparative data using R. [Exercise] – Wrap-up and optional additional exercise or lecture.