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.


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