Skip to Main content Skip to Navigation
Journal articles

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

Abstract : 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, non adaptive 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 non model 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
Complete list of metadata

https://hal.archives-ouvertes.fr/hal-01806906
Contributor : Anne-Gestion Labo Duputié Connect in order to contact the contributor
Submitted on : Wednesday, June 16, 2021 - 12:08:25 PM
Last modification on : Friday, October 22, 2021 - 2:58:35 PM
Long-term archiving on: : Friday, September 17, 2021 - 6:35:51 PM

File

msy015.pdf
Publisher files allowed on an open archive

Licence


Distributed under a Creative Commons Attribution 4.0 International License

Identifiers

Citation

Nicolas Galtier, Camille Roux, Marjolaine Rousselle, Jonathan Romiguier, Emeric Figuet, et al.. Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion. Molecular Biology and Evolution, Oxford University Press (OUP), 2018, 35 (5), pp.1092 - 1103. ⟨10.1093/molbev/msy015⟩. ⟨hal-01806906⟩

Share

Metrics

Record views

387

Files downloads

49