Topology-Bayes versus Clade-Bayes in phylogenetic analysis

Several features of currently used Bayesian methods in phylogenetic analysis are discussed. The distinction between Clade-Bayes and Topology-Bayes is presented and illustrated with an empirical example. Three problems with Bayesian phylogenetic methods-exaggerated clade support, inconsistently biased priors, and the impossibility of hypothesis testing of cladograms-are shown to be the result of using a Clade-based Bayesian approach. Topology-based Bayesian methods do not share these shortcomings.