Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion

Galtier, NicolasUniv Montpellier, Inst Sci Evolut, EPHE, CNRS,UMR5554,IRD, Montpellier, France (author)

Codon Usage Bias in Animals : Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion

Selection on codon usage bias is well documented in a number of microorganisms. Whether codon usage is also generally shaped by natural selection in large organisms, despite their relatively small effective population size (Ne), is unclear. In animals, the population genetics of codon usage bias has only been studied in a handful of model organisms so far, and can be affected by confounding, nonadaptive processes such as GC-biased gene conversion and experimental artefacts. Using population transcriptomics data, we analyzed the relationship between codon usage, gene expression, allele frequency distribution, and recombination rate in 30 nonmodel species of animals, each from a different family, covering a wide range of effective population sizes. We disentangled the effects of translational selection and GC-biased gene conversion on codon usage by separately analyzing GC-conservative and GC-changing mutations. We report evidence for effective translational selection on codon usage in large-Ne species of animals, but not in small-Ne ones, in agreement with the nearly neutral theory of molecular evolution. C- and T-ending codons tend to be preferred over synonymous G- and A-ending ones, for reasons that remain to be determined. In contrast, we uncovered a conspicuous effect of GC-biased gene conversion, which is widespread in animals and the main force determining the fate of AT↔GC mutations. Intriguingly, the strength of its effect was uncorrelated with Ne.

Roux, CamilleUniv Montpellier, Inst Sci Evolut, EPHE, CNRS,UMR5554,IRD, Montpellier, France; Univ Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland; Univ Lille Sci & Technol, CNRS, UMR Evo Eco Paleo 8198, Villeneuve Dascq, France (author)
Rousselle, MarjolaineUniv Montpellier, Inst Sci Evolut, EPHE, CNRS,UMR5554,IRD, Montpellier, France (author)
Romiguier, JonathanUniv Montpellier, Inst Sci Evolut, EPHE, CNRS,UMR5554,IRD, Montpellier, France; Univ Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland (author)
Figuet, EmericUniv Montpellier, Inst Sci Evolut, EPHE, CNRS,UMR5554,IRD, Montpellier, France (author)
Glémin, SylvainUppsala universitet,Växtekologi och evolution,Univ Montpellier, Inst Sci Evolut, EPHE, CNRS,UMR5554,IRD, Montpellier, France(Swepub:uu)sylgl118 (author)
Bierne, NicolasUniv Montpellier, Inst Sci Evolut, EPHE, CNRS,UMR5554,IRD, Montpellier, France (author)
Duret, LaurentUniv Lyon 1, Univ Lyon, CNRS, Lab Biometrie & Biol Evolut,UMR 5558, Villeurbanne, France (author)
Univ Montpellier, Inst Sci Evolut, EPHE, CNRS,UMR5554,IRD, Montpellier, FranceUniv Montpellier, Inst Sci Evolut, EPHE, CNRS,UMR5554,IRD, Montpellier, France; Univ Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland; Univ Lille Sci & Technol, CNRS, UMR Evo Eco Paleo 8198, Villeneuve Dascq, France (creator_code:org_t)

In:Molecular biology and evolution: Oxford University Press (OUP)35:5, s. 1092-11030737-40381537-1719

By the author/editor: Galtier, Nicolas; Roux, Camille; Rousselle, Marjo ...; Romiguier, Jonat ...; Figuet, Emeric; Glémin, Sylvain; show more...; Bierne, Nicolas; Duret, Laurent; show less...

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Evolutionary Bio ...

Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.