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Missing something? Codon aversion as a new character system in phylogenetics.

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Codon usage bias shows a phylogenetic signal across tetrapod species. Phylogenies derived from stop codon usage align with evolutionary hypotheses, indicating conserved codon patterns.

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Codon usage bias is documented across species, but its phylogenetic significance is understudied.
  • Understanding codon usage patterns can reveal evolutionary relationships and constraints.

Purpose of the Study:

  • To investigate the presence and significance of a phylogenetic signal in codon usage bias across tetrapod species.
  • To determine if codon usage patterns are conserved across evolutionary timescales.

Main Methods:

  • Analyzed codon usage and non-usage biases of 17,717 orthologues in 72 tetrapod species.
  • Employed parsimony analysis on a binary matrix of codon characters.
  • Constructed phylogenies using different codon sets, including stop codons.

Main Results:

  • A significant phylogenetic signal was detected in codon usage and non-usage biases.
  • Phylogenies derived from stop codons demonstrated higher congruence with established hypotheses compared to other codons.
  • Codon usage patterns were found to be phylogenetically conserved across both shallow and deep evolutionary divergences in tetrapods.

Conclusions:

  • Codon usage bias contains a discernible phylogenetic signal within tetrapods.
  • Stop codons are particularly informative for reconstructing evolutionary relationships.
  • Codon usage represents a conserved evolutionary feature across a wide range of tetrapod species.