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MBE Advance Access originally published online on March 19, 2004
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Mol. Biol. Evol. 21(6):1123-1133. 2004
DOI: 10.1093/molbev/msh123
© 2004 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

Bayesian Phylogenetic Model Selection Using Reversible Jump Markov Chain Monte Carlo

John P. Huelsenbeck*, Bret Larget{dagger},{ddagger} and Michael E. Alfaro*

* Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego
{dagger} Department of Statistics, University of Wisconsin
{ddagger} Department of Botany, University of Wisconsin

E-mail: johnh{at}biomail.ucsd.edu.

A common problem in molecular phylogenetics is choosing a model of DNA substitution that does a good job of explaining the DNA sequence alignment without introducing superfluous parameters. A number of methods have been used to choose among a small set of candidate substitution models, such as the likelihood ratio test, the Akaike Information Criterion (AIC), the Bayesian Information Criterion (BIC), and Bayes factors. Current implementations of any of these criteria suffer from the limitation that only a small set of models are examined, or that the test does not allow easy comparison of non-nested models. In this article, we expand the pool of candidate substitution models to include all possible time-reversible models. This set includes seven models that have already been described. We show how Bayes factors can be calculated for these models using reversible jump Markov chain Monte Carlo, and apply the method to 16 DNA sequence alignments. For each data set, we compare the model with the best Bayes factor to the best models chosen using AIC and BIC. We find that the best model under any of these criteria is not necessarily the most complicated one; models with an intermediate number of substitution types typically do best. Moreover, almost all of the models that are chosen as best do not constrain a transition rate to be the same as a transversion rate, suggesting that it is the transition/transversion rate bias that plays the largest role in determining which models are selected. Importantly, the reversible jump Markov chain Monte Carlo algorithm described here allows estimation of phylogeny (and other phylogenetic model parameters) to be performed while accounting for uncertainty in the model of DNA substitution.

Key Words: Bayesian phylogenetic inference • Markov chain Monte Carlo • maximum likelihood • reversible jump Markov chain Monte Carlo • substitution models


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