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MBE Advance Access originally published online on December 12, 2007
Molecular Biology and Evolution 2008 25(2):447-453; doi:10.1093/molbev/msm274
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© The Author 2007. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Articles

Topology-Bayes versus Clade-Bayes in Phylogenetic Analysis

Ward C. Wheeler* and Kurt M. Pickett{dagger}

* Division of Invertebrate Zoology, American Museum of Natural History, NY
{dagger} Department of Biology, University of Vermont

E-mail: wheeler{at}amnh.org.

Accepted for publication November 29, 2007.

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.

Key Words: Bayes • phylogeny • systematics • support

Barbara Holland, Associate Editor


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