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

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 r...

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Bibliographic Details
Published in:The American naturalist 2006-06, Vol.167 (6), p.808-825
Main Authors: Pagel, Mark, Meade, Andrew
Format: Article
Language:English
Subjects:
Advertising rates
Animals
Bayes Theorem
Bayesian analysis
Biological Evolution
Estimates
Estrus
Evolution
Female
Hypotheses
Male
Markov Chains
Mating behavior
Mating systems
Models, Genetic
Monkeys
Monte Carlo Method
Parametric models
Phylogenetics
Phylogeny
Primates - genetics
Rates
Ratings & rankings
Sexual Behavior, Animal
States
Statistical methods
Testing
Tests
Uncertainty
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Description
Summary: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 estimates the posterior distributions of the rate parameters of the model of trait evolution. These posterior distributions can be used to test among alternative evolutionary scenarios to explain the observed data. All results are integrated over a sample of phylogenetic trees to account for phylogenetic uncertainty. We implement the method in a program called RJ Discrete and illustrate it by analyzing the question of whether mating system and advertisement of estrus by females have coevolved in the Old World monkeys and great apes.
ISSN:0003-0147
1537-5323
DOI:10.1086/503444