Bayesian estimation of ancestral character states on phylogenies

M Pagel, A Meade, Daniel Barker

Research output: Contribution to journalArticlepeer-review

832 Citations (Scopus)


Biologists frequently attempt to infer the character states at ancestral nodes of a phylogeny from the distribution of traits observed in contemporary organisms. Because phylogenies are normally inferences from data, it is desirable to account for the uncertainty in estimates of the tree and its branch lengths when making inferences about ancestral states or other comparative parameters. Here we present a general Bayesian approach for testing comparative hypotheses across statistically justified samples of phylogenies, focusing on the specific issue of reconstructing ancestral states. The method uses Markov chain Monte Carlo techniques for sampling phylogenetic trees and for investigating the parameters of a statistical model of trait evolution. We describe how to combine information about the uncertainty of the phylogeny with uncertainty in the estimate of the ancestral state. Our approach does not constrain the sample of trees only to those that contain the ancestral node or nodes of interest, and we show how to reconstruct ancestral states of uncertain nodes using a most-recent-common-ancestor approach. We illustrate the methods with data on ribonuclease evolution in the Artiodactyla. Software implementing the methods ( BayesMultiState) is available from the authors.

Original languageEnglish
Pages (from-to)673-684
Number of pages12
JournalSystematic Biology
Issue number5
Publication statusPublished - Oct 2004


  • ancestral states
  • comparative methods
  • maximum likelihood
  • MCMC
  • phylogeny


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