articleThe American NaturalistJun 1, 2006Closed access

Bayesian Analysis of Correlated Evolution of Discrete Characters by Reversible‐Jump Markov Chain Monte Carlo

MPMark PagelAMAndrew Meade

University of Reading · Henley College

PubMed
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Abstract

We describe a Bayesian method for investigating correlated evolution of discrete binary traits on phylogenetic trees. The method fits a continuous-time Markov model to a pair of traits, seeking the best fitting models that describe their joint evolution on a phylogeny. We employ the methodology of reversible-jump (RJ) Markov chain Monte Carlo to search among the large number of possible models, some of which conform to independent evolution of the two traits, others to correlated evolution. The RJ Markov chain visits these models in proportion to their posterior probabilities, thereby directly estimating the support for the hypothesis of correlated evolution. In addition, the RJ Markov chain simultaneously…

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Topics & keywords

Topics
Keywords
  • Markov chain Monte Carlo
  • Reversible-jump Markov chain Monte Carlo
  • Markov chain
  • Phylogenetic tree
  • Bayesian probability
  • Posterior probability
  • Phylogenetic comparative methods
  • Evolutionary biology
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