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Journal Articles Genome Biology Year : 2019

GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes

Abstract

Background:The nearly neutral theory of molecular evolutionpredicts that the efficacy of natural selectionincreases with the effective population size. This prediction has been verified by independent observations indiverse taxa, which show that life-history traits are strongly correlated with measures of the efficacy of selection,such as thedN/dSratio. Surprisingly, avian taxa are an exception to this theory because correlations betweenlife-history traits anddN/dSare apparently absent. Here we explore the role of GC-biased gene conversion onestimates of substitution rates as a potential driver of these unexpected observations. Results:We analyze the relationship betweendN/dSestimated from alignments of 47 avian genomes and severalproxies for effective population size. To distinguish the impact of GC-biased gene conversion from selection, weuse an approach that accounts for non-stationary base composition and estimatedN/dSseparately for changesaffected or unaffected by GC-biased gene conversion. This analysis shows that the impact of GC-biased geneconversion on substitution rates can explain the lack of correlations between life-history traits anddN/dS. Strongcorrelations between life-history traits anddN/dSare recovered after accounting for GC-biased gene conversion.The correlations are robust to variation in base composition and genomic location. Conclusions:Our study shows that gene sequence evolution across a wide range of avian lineages meets theprediction of the nearly neutral theory, the efficacy ofselection increases with effective population size.Moreover, our study illustrates that accounting for GC-biased gene conversion is important to correctly estimatethe strength of selection.
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Dates and versions

hal-02329971 , version 1 (20-11-2020)

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Paulina Bolívar, Laurent Guéguen, Laurent Duret, Hans Ellegren, Carina Mugal. GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes. Genome Biology, 2019, 20 (1), ⟨10.1186/s13059-018-1613-z⟩. ⟨hal-02329971⟩
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