In this book, I outline statistical procedures for analyzing comparative data. Some methods – such as those for estimating patterns of speciation and extinction through time – require an ultrametric phylogenetic tree. Other approaches model trait evolution, and thus require data on the traits of species that are included in the phylogenetic tree. The methods also differ as to whether or not they require the phylogenetic tree to be complete – that is, to include every living species descended from a certain ancestor – or can accommodate a smaller sample of the living species.
The book begins with a general discussion of model-fitting approaches to statistics (Chapter 2), with a particular focus on maximum likelihood and Bayesian approaches. In Chapters 3-9, I describe models of character evolution. I discuss approaches to simulating and analyzing the evolution of these characters on a tree. Chapters 10-12 focus on models of diversification, which describe patterns of speciation and extinction through time. I describe methods that allow us to simulate and fit these models to comparative data. Chapter 13 covers combined analyses of both character evolution and lineage diversification. Finally, in Chapter 14 I discuss what we have learned so far about evolution from these approaches, and what we are likely to learn in the future.
There are a number of computer software tools that can be used to carry out the methods described here. In this book, I focus on the statistical software environment R. For each chapter, my course website, in progress, provides sample R code that can be used to carry out all described analyses. I hope that this R code will allow further development of this language for comparative analyses. However, it is possible to carry out the algorithms we describe using other computer software or programming languages (e.g. Arbor, http://www.arborworkflows.com).
Statistical comparative methods represent a promising future for evolutionary studies, especially as our knowledge of the tree of life expands. I hope that the methods described in this book can serve as a Rosetta stone that will help us read the tree of life as it is being built.