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Related Experiment Videos

Likelihood-based tests of topologies in phylogenetics.

N Goldman1, J P Anderson, A G Rodrigo

  • 1University Museum of Zoology, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK. N.Goldman@zoo.cam.ac.uk

Systematic Biology
|July 16, 2002
PubMed
Summary

The common Kishino-Hasegawa test for evolutionary trees is often invalid. Researchers should use alternative statistical tests for more reliable evolutionary hypothesis testing.

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Area of Science:

  • Evolutionary biology
  • Statistical genetics
  • Phylogenetic analysis

Background:

  • Likelihood-based statistical tests for comparing evolutionary hypotheses (tree topologies) have existed for about ten years.
  • The Kishino-Hasegawa test is the most frequently employed method for such comparisons.
  • However, its validity is contingent upon specific assumptions that limit its practical application.

Purpose of the Study:

  • To review the theoretical underpinnings of the Kishino-Hasegawa test.
  • To highlight the limitations and potential biases of the Kishino-Hasegawa test in common applications.
  • To advocate for the use of alternative statistical tests in phylogenetic analysis.

Main Methods:

  • Theoretical review of the Kishino-Hasegawa test's assumptions and validity conditions.

Related Experiment Videos

  • Analysis of scenarios where the Kishino-Hasegawa test may yield biased results, particularly when the maximum likelihood topology is tested.
  • Review and discussion of appropriate nonparametric and parametric alternative statistical tests.

    • Main Results:

    • The Kishino-Hasegawa test is only valid when tree topologies are specified a priori.
    • The test is often severely biased when applied to cases where the topology was selected based on the data (e.g., maximum likelihood topology).
    • Previously published results using invalid applications of the Kishino-Hasegawa test require cautious re-evaluation.

    Conclusions:

    • The Kishino-Hasegawa test should not be used in its majority of popular applications due to potential bias.
    • Researchers should exercise extreme caution with prior results obtained from invalid applications of this test.
    • Future phylogenetic analyses should employ validated alternative statistical tests for comparing evolutionary hypotheses.