An introduction to PCM
Luke Harmon has written and released an introductory textbook on phylogenetic comparative methods. It’s a tremendous resource, and I hope the open-source publishing model proves successful.
In this book, I describe methods to connect evolutionary processes to broad-scale patterns in the tree of life. I focus mainly — but not exclusively — on phylogenetic comparative methods. Comparative methods combine biology, mathematics, and computer science to learn about a wide variety of topics in evolution using phylogenetic trees and other associated data (see Harvey and Pagel 1991 for an early review). For example, we can find out which processes must have been common, and which rare, across clades in the tree of life; whether evolution has proceeded differently in some lineages compared to others; and whether the evolutionary potential that we see playing out in real time is sufficient to explain the diversity of life on earth, or whether we might need additional processes that may come into play only very rarely or over very long timescales, like adaptive radiation or species selection.