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.
Wheeler
Ward C
WC
Division of Invertebrate Zoology, American Museum of Natural History, NY, USA. wheeler@amnh.org
Pickett
Kurt M
KM
D001499:Bayes Theorem; D019143:Evolution, Molecular; D008957:Models, Genetic; D010802:Phylogeny