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MBE Advance Access originally published online on November 4, 2008
Molecular Biology and Evolution 2009 26(1):1-3; doi:10.1093/molbev/msn250
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© The Author 2008. 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

Letter

Choice of Topology Estimators in Bayesian Phylogenetic Analysis

Jeet Sukumaran and Charles W. Linkem

Department of Ecology and Evolutionary Biology, Biodiversity Institute and Natural History Museum, University of Kansas

E-mail: jeet{at}ku.edu.

Accepted for publication October 29, 2008.

Wheeler WC and Pickett KM (2008. Topology-Bayes versus clade-Bayes in phylogenetic analysis. Mol Biol Evol. 25:447–453.) discuss two ways of summarizing the posterior probability distribution of a Bayesian phylogenetic analysis, which they refer to as "topology-Bayes" and "clade-Bayes." They claim that the clade-Bayes approach leads to problems such as "exaggerated clade support, inconsistently biased priors, and the impossibility of topology hypothesis testing," which are not problems for the topology-Bayes approach. However, their argument for topology-Bayes over clade-Bayes is based on errors in the interpretation of summary statistics associated with Bayesian phylogenetic analysis. Although there is a well-documented difference between the maximum posterior probability topology and the majority-rule consensus topology (the established terms for topology-Bayes and clade-Bayes summaries, respectively), both have a place in phylogenetic analysis. Choice of summarization strategy should be driven by choice of parameters that need to be estimated versus those to be marginalized given the evolutionary questions being asked or hypotheses being tested.

Key Words: Bayesian phylogenetics • summaries • topology estimators • support

Scott Edwards, Associate Editor


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