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A Practical Guide to Phylogenetics for Nonexperts
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Revisiting an equivalence between maximum parsimony and maximum likelihood methods in phylogenetics.

Mareike Fischer1, Bhalchandra Thatte

  • 1Allan Wilson Centre for Molecular Ecology and Evolution, Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand. email@mareikefischer.de

Bulletin of Mathematical Biology
|September 30, 2009
PubMed
Summary

Phylogenetic methods maximum likelihood and maximum parsimony are not always equivalent. Small changes to evolutionary models, like bounded substitution probabilities, can cause these methods to conflict in phylogenetic tree reconstruction.

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Area of Science:

  • Evolutionary biology
  • Computational biology
  • Bioinformatics

Background:

  • Maximum likelihood (ML) and maximum parsimony (MP) are key phylogenetic inference methods.
  • Tuffley and Steel (1997) established their equivalence under specific evolutionary models.
  • This equivalence has been a foundational concept in phylogenetics.

Purpose of the Study:

  • To investigate the conditions under which ML and MP methods diverge.
  • To explore the impact of relaxed evolutionary model assumptions on phylogenetic inference.
  • To identify scenarios where ML and MP yield conflicting tree topologies.

Main Methods:

  • Analysis of phylogenetic inference under modified substitution models.
  • Examination of bounded substitution probabilities and the molecular clock assumption.
  • Comparative evaluation of ML and MP tree selection criteria.

Main Results:

  • Equivalence between ML and MP is broken by relaxing model assumptions.
  • Bounded substitution probabilities and molecular clock constraints can lead to conflicting phylogenetic trees.
  • Under sufficiently small upper bounds on substitution probabilities, all ML trees are also MP trees, but not conversely.

Conclusions:

  • The equivalence of ML and MP methods is sensitive to model assumptions.
  • Relaxed evolutionary models necessitate careful consideration of method choice in phylogenetics.
  • Understanding these divergences is crucial for accurate phylogenetic reconstruction.