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Codon Usage Bias in...
Codon Usage Bias in Animals : Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion
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- Galtier, Nicolas (author)
- Univ Montpellier, Inst Sci Evolut, EPHE, CNRS,UMR5554,IRD, Montpellier, France
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- Roux, Camille (author)
- Univ 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
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- Rousselle, Marjolaine (author)
- Univ Montpellier, Inst Sci Evolut, EPHE, CNRS,UMR5554,IRD, Montpellier, France
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- Romiguier, Jonathan (author)
- Univ Montpellier, Inst Sci Evolut, EPHE, CNRS,UMR5554,IRD, Montpellier, France; Univ Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland
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- Figuet, Emeric (author)
- Univ Montpellier, Inst Sci Evolut, EPHE, CNRS,UMR5554,IRD, Montpellier, France
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- Glémin, Sylvain (author)
- Uppsala universitet,Växtekologi och evolution,Univ Montpellier, Inst Sci Evolut, EPHE, CNRS,UMR5554,IRD, Montpellier, France
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- Bierne, Nicolas (author)
- Univ Montpellier, Inst Sci Evolut, EPHE, CNRS,UMR5554,IRD, Montpellier, France
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- Duret, Laurent (author)
- Univ Lyon 1, Univ Lyon, CNRS, Lab Biometrie & Biol Evolut,UMR 5558, Villeurbanne, France
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(creator_code:org_t)
- 2018-01-30
- 2018
- English.
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In: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 35:5, s. 1092-1103
- Related links:
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https://academic.oup...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Subject headings
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- 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.
Subject headings
- NATURVETENSKAP -- Biologi -- Evolutionsbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Evolutionary Biology (hsv//eng)
Keyword
- synonymous codon usage
- GC-content
- recombination
- evolution
- gene expression
- nonmodel organisms
Publication and Content Type
- ref (subject category)
- art (subject category)
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