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Related Experiment Videos

Polytomies and Bayesian phylogenetic inference.

Paul O Lewis1, Mark T Holder, Kent E Holsinger

  • 1Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043 (P.O.L.), Storrs, CN 06269-3043, USA. paul.lewis@uconn.edu

Systematic Biology
|July 14, 2005
PubMed
Summary
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Bayesian phylogenetic analyses can yield misleadingly high support for incorrect tree topologies. A reversible-jump Markov chain Monte Carlo (MCMC) method resolves this by exploring all tree space, including polytomies.

Area of Science:

  • Systematics
  • Molecular Evolution
  • Computational Biology

Background:

  • Bayesian phylogenetic analyses are widely used due to their flexible models.
  • However, high Bayesian posterior probabilities can conflict with low bootstrap support, especially with polytomies.
  • Star phylogenies demonstrate unpredictable Bayesian behavior with increasing data size.

Purpose of the Study:

  • To address the issue of high posterior probabilities supporting incorrect resolutions of polytomies in Bayesian phylogenetics.
  • To develop a method that accounts for unresolved tree topologies (polytomies).

Main Methods:

  • Implemented a reversible-jump Markov chain Monte Carlo (MCMC) algorithm.
  • This algorithm explores the entire tree space, including topologies with polytomies.

Related Experiment Videos

  • Incorporated prior distributions that allow weighting of less-resolved tree topologies.

    • Main Results:

    • The reversible-jump MCMC approach effectively eliminates misleadingly high posteriors for arbitrary polytomy resolutions.
    • Prioritizing less-resolved topologies does not significantly compromise support assessment for existing branches.
    • The method successfully analyzed an empirical example with evidence of polytomies.

    Conclusions:

    • Reversible-jump MCMC provides a robust solution for Bayesian phylogenetic analyses involving polytomies.
    • This method enhances the reliability of phylogenetic inference by properly handling unresolved relationships.
    • The approach offers a more accurate representation of evolutionary history when polytomies are present.