by Emmanuel Paradis
Simulating phylogenetic data is a powerful tool for evolutionists, but this can be a complicated task. This chapter gives an overview on the methods to simulate species traits, particularly on a phylogeny. We show that building from three fundamental models (Brownian motion, Ornstein–Uhlenbeck, and Markov chains), many biologically relevant scenarios can be simulated. We also review briefly the simulation of phylogenies and the available software for phylogenetic data simulation. The on-line materials give several examples, including some complex cases, using R.