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Systematic Biology 2007 56(4):578-590; doi:10.1080/10635150701485091
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© 2007 Society of Systematic Biologists

Summarizing a Posterior Distribution of Trees Using Agreement Subtrees

Karen A. Cranston1 and Bruce Rannala2

1 Department of Ecology and Evolutionary Biology, University of Arizona Tucson, Arizona, 85721, USA E-mail: cranston{at}email.arizona.edu
2 Genome Center, University of California Davis, One Shields Avenue Davis, California, 95616, USA E-mail: brannala{at}ucdavis.edu

Edited by Paul Lewis: Associate Editor


  Abstract

Bayesian inference of phylogeny is unique among phylogenetic reconstruction methods in that it produces a posterior distribution of trees rather than a point estimate of the best tree. The most common way to summarize this distribution is to report the majority-rule consensus tree annotated with the marginal posterior probabilities of each partition. Reporting a single tree discards information contained in the full underlying distribution and reduces the Bayesian analysis to simply another method for finding a point estimate of the tree. Even when a point estimate of the phylogeny is desired, the majority-rule consensus tree is only one possible method, and there may be others that are more appropriate for the given data set and application. We present a method for summarizing the distribution of trees that is based on identifying agreement subtrees that are frequently present in the posterior distribution. This method provides fully resolved binary trees for subsets of taxa with high marginal posterior probability on the entire tree and includes additional information about the spread of the distribution.

Keywords: Agreement subtrees; Bayesian phylogenetic inference; credible sets; posterior distribution of trees; threshold accepting

Received September 29, 2006; Revised February 26, 2007; Accepted April 8, 2007
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