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Related Experiment Videos

Multiple local maxima for likelihoods of phylogenetic trees: a simulation study.

J S Rogers1, D L Swofford

  • 1Department of Biological Sciences, University of New Orleans, Louisiana 70148, USA. jsrogers@uno.edu

Molecular Biology and Evolution
|October 3, 1999
PubMed
Summary

Maximum likelihood phylogenetic tree analysis is generally reliable. Simulation studies show that the true tree rarely has multiple local maxima, reassuring its use as a criterion for tree selection.

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Area of Science:

  • Computational biology
  • Phylogenetics
  • Bioinformatics

Background:

  • The maximum likelihood method is widely used for phylogenetic tree reconstruction.
  • Concerns exist regarding the potential for multiple local maxima in the likelihood function, which could complicate tree selection.

Purpose of the Study:

  • To investigate the frequency and impact of multiple local maxima in phylogenetic tree likelihood functions.
  • To assess the reliability of maximum likelihood as a criterion for selecting the best phylogenetic tree.

Main Methods:

  • Conducted simulation studies using various datasets.
  • Analyzed the behavior of the maximum likelihood function for phylogenetic trees.
  • Evaluated trees with high likelihood values and the true evolutionary tree.

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Main Results:

  • Multiple local maxima were rarely observed for the true phylogenetic tree and other high-likelihood trees.
  • This phenomenon did not appear to compromise the applicability of maximum likelihood for tree selection in simulations.
  • The findings held even when using an incorrect nucleotide substitution model.

Conclusions:

  • Maximum likelihood remains a robust criterion for phylogenetic tree selection.
  • The presence of multiple local maxima is unlikely to hinder the identification of the best tree estimates.
  • These results support the continued use of maximum likelihood in phylogenetics.