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Detecting correlation between characters in a comparative analysis with uncertain phylogeny.

John P Huelsenbeck1, Bruce Rannala

  • 1Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093-0116, USA. johnh@biomail.ucsd.edu

Evolution; International Journal of Organic Evolution
|August 5, 2003
PubMed
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This study introduces a new Bayesian method to account for phylogenetic uncertainty in comparative analyses. It improves evolutionary inferences by averaging over all possible evolutionary trees, enhancing accuracy for trait evolution studies.

Area of Science:

  • Evolutionary Biology
  • Phylogenetics
  • Comparative Genomics

Background:

  • Comparative analyses commonly assume known phylogenetic trees, neglecting uncertainty.
  • Existing methods inadequately address phylogenetic uncertainty, especially with available phylogenetic data.
  • Phylogenetic uncertainty can bias inferences about trait evolution.

Purpose of the Study:

  • To develop a novel method for comparative analysis that explicitly incorporates phylogenetic uncertainty.
  • To extend Felsenstein's independent contrasts method within a Bayesian framework.
  • To improve the accuracy of evolutionary inferences by accounting for uncertainty in phylogenetic trees.

Main Methods:

  • Developed a Bayesian framework to average over all possible phylogenetic trees.

Related Experiment Videos

  • Weighted each tree by its posterior probability to account for uncertainty.
  • Utilized Markov chain Monte Carlo (MCMC) for high-dimensional summations and integrations.
  • Extended Felsenstein's independent contrasts method.

    • Main Results:

    • The new method effectively accommodates uncertainties in phylogeny and branch lengths.
    • Demonstrated the method's application using comparative characters from Anolis lizards.
    • Provided a robust approach for phylogenetic comparative analysis.

    Conclusions:

    • The developed Bayesian method offers a more accurate way to perform comparative analyses by addressing phylogenetic uncertainty.
    • This approach enhances the reliability of evolutionary inferences, particularly when phylogenetic data are informative.
    • The method is broadly applicable to various comparative studies in evolutionary biology.