Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 25, Issue 2, Pages 447-453Publisher
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msm274
Keywords
Bayes; phylogeny; systematics; support
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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.
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