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

Justin B. Miller, Ariel A. Hippen, Jonathon R. Belyeu, Michael F. Whiting, Perry G. Ridge

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


Although many studies have documented codon usage bias in different species, the importance of codon usage in a phylogenetic framework remains largely unknown. We demonstrate that a phylogenetic signal is present in the codon usage and non-usage biases of 17 717 orthologues evaluated across 72 tetrapod species using a simple parsimony analysis of a binary matrix of codon characters. Phylogenies estimated using stop codons were more congruent with previous hypotheses than phylogenies based on any other single codon or a combination of codons. Although each codon is present in every species, specific genes have different codon preferences and may or may not use every possible codon. This observation allowed us to map the pattern of codon usage and non-usage across the topology. These results suggest that codon usage is phylogenetically conserved across shallow and deep levels within tetrapods.

Original languageEnglish
Pages (from-to)545-556
Number of pages12
Issue number5
StatePublished - Oct 2017

Bibliographical note

Funding Information:
We appreciate the contributions of Brigham Young University for sponsoring our research and providing a facility in which to work and for the Fulton Supercomputing Laboratory at Brigham Young University, without which these analyses would not have been possible. Duke Rogers, Brandon Pickett and Anton Suvorov provided expert suggestions. The free use of the software, TNT, was made available to us through the sponsorship of the Willi Hennig Society, and we appreciate its efforts in keeping science accessible to everyone.

Publisher Copyright:
© The Willi Hennig Society 2017

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics


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