Topology-Bayes versus Clade-Bayes in Phylogenetic Analysis

摘要

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.