The Posterior and the Prior in Bayesian Phylogenetics

Bayesian analysis has enjoyed explosive growth in phylogenetics over the past five years. Accompanying this popularity has been increased focus on the meaning of the posterior probability (PP) and the role of the prior in phylogenetic inference. Here we discuss the behavior of the PP in Bayesian and frequentist terms and its relationship to parametric and nonparametric bootstrapping. We also review the use of priors in phylogenetics and the issues surrounding the specification of informative and minimally informative prior distributions.