Phylogenetic Comparative Methods in R

Phylogenetic Comparative Methods in R

Theodosius Dobzhansky said in 1973 that “nothing in biology makes sense except in the light of evolution”. Statistical comparative phylogenetic methods are one of the ways that allow us to understand historical patterns of life within an evolutionary context. In this course, I propose to cover some of the families of comparative phylogenetic analyses of trait evolution and correlation, for both discrete and continuous data. My objective is to provide a short background in statistical and comparative phylogenetic methods, to allow participants to explore their research questions on their own.

This is a short course/tutorial I developed to help researchers cover some of the families of phylogenetic comparative analyses of trait evolution and correlation, diversification rates, as well as community structure. My objective is to provide a short background in statistical and comparative phylogenetic methods, to further allow researchers to explore their research questions on their own. A big part of the inspiration for this workshop came from the book Phylogenies in Ecology, by Marc W. Cadotte and Jonathan Davies, as well as from courses and workshops on ecophylogenetics taught by Dr. Will Pearse, Dr. Jonathan Davies and Dr. Steven Kembel.

By the end of the course, students should be able to:

1. Read and interpret phylogenetic trees;
2. Explore some of the most commonly used phylogenetic comparative methods to:
3. Perform ancestral state reconstruction;
4. Fit evolutionary models to traits;
5. Estimate diversification rates;
6. Estimate phylogenetic fields of clades;
7. Assess the phylogenetic structure of communities.
8. Integrate different approaches of phylogenetic methods using R;
9. Be comfortable navigating primary literature in statistical comparative methods.

Workshop material