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MBE Advance Access published online on December 12, 2007
Molecular Biology and Evolution, 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 Article

Topology-Bayes versus Clade-Bayes in Phylogenetic Analysis

Ward C. Wheeler1 and Kurt M. Pickett2

1 Division of Invertebrate Zoology, American Museum of Natural History, Central Park West @ 79th Street, New York, NY 10024-5192, USA, wheeler{at}amnh.org, 212-769-5754
2 Department of Biology, University of Vermont, 120A Marsh Life Science Building, 109 Carrigan Drive, Burlington, VT 05405, USA, Kurt.Pickett{at}uvm.edu, 802-656-0460

Received for publication November 24, 2007. 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


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