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Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods

Z Yang1

  • 1Department of Zoology, Natural History Museum, London, United Kingdom.

Journal of Molecular Evolution
|September 1, 1994
PubMed
Summary
This summary is machine-generated.

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Two new methods for phylogenetic estimation accurately model variable substitution rates across nucleotide sites. The discrete gamma model performed well, with four categories approximating continuous distributions effectively.

Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Phylogenetic estimation aims to reconstruct evolutionary history.
  • Accurate phylogenetic inference requires accounting for rate variation across sites.
  • Existing methods often assume a single substitution rate for all sites.

Purpose of the Study:

  • To propose and evaluate two approximate methods for maximum likelihood phylogenetic estimation that accommodate rate variation.
  • To compare the performance of these methods against established models using empirical data.

Main Methods:

  • Discrete Gamma Model: Approximates the gamma distribution using discrete rate categories, with category means representing site rates.
  • Fixed-Rates Model: Classifies sites into rate categories based on star tree predictions and uses these fixed rates for other topologies.

Related Experiment Videos

  • Empirical Analysis: Tested both methods on three diverse datasets.

    • Main Results:

    • The discrete gamma model demonstrated good performance, with four categories providing near-optimal fit and approximating continuous distributions well.
    • The fixed-rates model yielded reasonable results but showed tendencies similar to least-squares methods, such as zero interior branch lengths in non-best trees.
    • Both proposed methods had computational requirements comparable to Felsenstein's single-rate model.

    Conclusions:

    • The discrete gamma model is a robust and efficient approach for phylogenetic estimation with rate variation.
    • The fixed-rates model offers an alternative but may have limitations in certain scenarios.
    • These methods provide valuable tools for more accurate phylogenetic inference in molecular evolution studies.