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Phylogenetic estimation under codon models can be biased by codon usage heterogeneity.

Yuji Inagaki1, Andrew J Roger

  • 1Center for Computational Sciences, Institute of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan. yuji@ccs.tsukuba.ac.jp

Molecular Phylogenetics and Evolution
|May 2, 2006
PubMed
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Codon models can inaccurately group species due to uneven codon usage, leading to biased phylogenetic estimations. Always confirm codon usage homogeneity before applying these models for accurate evolutionary analysis.

Area of Science:

  • Molecular Evolution
  • Bioinformatics
  • Phylogenetics

Background:

  • Codon models theoretically offer accurate descriptions of protein-coding gene evolution by considering nucleotide substitution dependencies and synonymous/non-synonymous changes.
  • Practical application of codon models is limited by a lack of understanding regarding the frequency and impact of assumption violations.

Purpose of the Study:

  • To investigate the impact of violated codon model assumptions, specifically codon usage heterogeneity, on phylogenetic estimations.
  • To demonstrate how codon usage bias can lead to artifactual groupings in phylogenetic analyses.

Main Methods:

  • Analysis of a concatenated plastid gene data set using nucleotide-based phylogenies focusing on first and second codon positions.
  • Evaluation of phylogenetic estimations under violated assumptions of codon model homogeneity.

Related Experiment Videos

  • Identification of parallel heterogeneity in leucine (Leu) and serine (Ser) codon usages as a source of artifactual grouping.

    • Main Results:

    • Codon-based phylogenetic estimations were seriously biased, robustly uniting dinoflagellate and haptophyte plastids into a monophyletic clade when codon composition homogeneity was violated.
    • This artifactual grouping was attributed to parallel heterogeneity in leucine and serine codon usages.
    • The study highlights that codon usage heterogeneity can introduce significant biases in phylogenetic analyses.

    Conclusions:

    • Codon usage heterogeneity across taxa can lead to significant biases and artifactual clades in codon model-based phylogenetic estimations.
    • The findings suggest that similar phylogenetic artifacts may arise from codon usage heterogeneity involving other amino acids.
    • It is crucial to confirm codon usage homogeneity across taxa before employing codon model-based phylogenetic estimations to ensure reliable evolutionary inferences.