Course on Comparative Methods
This repository contains tutorials structured in 7 different lectures that gives examples of application of phylogenetic comparative methods in the statistical software R.
Acknowledgements
I would like to thank people that share their own tutorials on the web. I have consulted many of them over the years and they have been important my understanding of comparative methods and for the developpement of these tutorials. I thank Liam Revell, Samantha Price, Brian O'Meara, and many others...
How to?
There are several ways you could use the material. You could for example download the whole folder by choosing the download zip option. But it is perhaps more interesting to fork the repository (you will need to create an account on github) and then clone your new forked repository on your desktop (you will have to browse the help pages of githup to get started). This will take longer to set-up, but it will give you the opportunity to automatically recieve updates when the tutorials get modified (which might well happen) and even propose modifications to the tutorials if you find mistakes or to propose new analyses.
Lecture 1 - Introduction
Tutorials
Introduction to phylogenies in R
Lecture 2 - Phylogenetic Comparative Methods
The Brownian Motion (BM) model, Phylogenetic Independent Contrasts (PIC), Phylogenetic General Least Squares (PGLS), Phylogenetic Principal Component Analysis (pPCA).
Tutorials
Phylogenetic Comparative Methods
Reading and making phylogenetic trees in R
Lecture 3 - Ancestral states reconstruction
Reconstruction of ancestral states on phylogenies for quantitative and qualitative (discrete) characters, marginal vs joint estimation, model selection, stochastic character mapping.
Tutorial
Ancestral states reconstruction
Lecture 4 - BayesTraits
Bayesian reconstruction of ancestral states using BayesTraits, Testing the correlated evolution of discrete traits, Markov chain Monte Carlo (MCMC) analyses, MCMC chain convergence.
Tutorial
Lecture 5 - Other methods of trait evolution
Ornstein-Uhlenbeck (OU) model, Early-Burst model, Speciational model, Simulating data under different evolutionary models, OU models with multiple selection regimes, Accounting for phylogenetic uncertainty.
Tutorial
Lecture 6 - Phylogenetic signal and phylogenetic diversity
Phylogenetic signal (Moran's I, Abouheif's c, Pagel's lambda, Blomberg's K, Moran's I correlograms); Phylogenetic diversity; Evolutionary distinctiveness; phylogenetic beta-diversity; Parametric bootstrapping; Phylogenies in community ecology.
Tutorial
Lecture 7 - Diversification analyses
Lineage through-time (ltt) plots; diversification rate estimation; Yule and Birth-and-death models; Diversification through time (dtt) plots; Trait dependent speciaton and extinction (BISSE model).
Tutorial
Useful ressources
Paradis, E. 2012. Analysis of Phylogenetics and Evolution with R. Springer: New York. (available in pdf)
Bodega's applied phylogenetic workshop website: Tree thinkers