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MBE Advance Access published online on November 4, 2008
Molecular Biology and Evolution, 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 Sukumaran1,2 and Charles W. Linkem1,3

1 Department of Ecology and Evolutionary Biology, Biodiversity Institute and Natural History Museum, University of Kansas, 1345 Jayhawk Blvd, Lawrence, KS 66045, USA, 785-864-3439

2 jeet{at}ku.edu

3 cwlinkem{at}ku.edu

Received for publication July 21, 2008. Revision received October 23, 2008. Accepted for publication October 29, 2008.

Wheeler and Pickett (2008) 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. While 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


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