Accessibility navigation


Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo

Pagel, M. and Meade, A. (2006) Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. American Naturalist, 167 (6). pp. 808-825. ISSN 0003-0147

Full text not archived in this repository.

To link to this article DOI: 10.1086/503444

Abstract/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.

Item Type:Article
Refereed:Yes
Divisions:Faculty of Life Sciences > School of Biological Sciences
ID Code:10209
Uncontrolled Keywords:correlated evolution, Bayesian, MCMC, discrete, reversible-jump, comparative methods, PHYLOGENETIC INFERENCE, SEXUAL SWELLINGS, MODEL, TREES, SELECTION, SEQUENCE, PRIMATES, QUALITY

University Staff: Request a correction | Centaur Editors: Update this record

Page navigation