Abstract
BackgroundWhile effective population size (Ne) and life history traits such as generation time are known to impact substitution rates, their potential effects on base composition evolution are less well understood. GC content increases with decreasing body mass in mammals, consistent with recombination-associated GC biased gene conversion (gBGC) more strongly impacting these lineages. However, shifts in chromosomal architecture and recombination landscapes between species may complicate the interpretation of these results. In birds, interchromosomal rearrangements are rare and the recombination landscape is conserved, suggesting that this group is well suited to assess the impact of life history on base composition.ResultsEmploying data from 45 newly and 3 previously sequenced avian genomes covering a broad range of taxa, we found that lineages with large populations and short generations exhibit higher GC content. The effect extends to both coding and non-coding sites, indicating that it is not due to selection on codon usage. Consistent with recombination driving base composition, GC content and heterogeneity were positively correlated with the rate of recombination. Moreover, we observed ongoing increases in GC in the majority of lineages.ConclusionsOur results provide evidence that gBGC may drive patterns of nucleotide composition in avian genomes and are consistent with more effective gBGC in large populations and a greater number of meioses per unit time; that is, a shorter generation time. Thus, in accord with theoretical predictions, base composition evolution is substantially modulated by species life history.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-014-0549-1) contains supplementary material, which is available to authorized users.
Highlights
While effective population size (Ne) and life history traits such as generation time are known to impact substitution rates, their potential effects on base composition evolution are less well understood
Correlation between GC content at third codon positions (GC3) and life history traits is consistent with stronger GC biased gene conversion (gBGC) in large populations with short generation times Given the substantial heterogeneity in GC3 content between avian species [33,47] (Figure 1), we asked whether there is evidence that third codon sites, which should be the least constrained coding positions, might be subject to the influence of recombination-associated gBGC
Despite the limited number of species for which data are available, maximum longevity and age of first female sexual maturity showed similar trends, consistent with the possibility that short generation times lead to an increase in GC3 assuming equilibrium has not yet been reached
Summary
While effective population size (Ne) and life history traits such as generation time are known to impact substitution rates, their potential effects on base composition evolution are less well understood. GC content increases with decreasing body mass in mammals, consistent with recombination-associated GC biased gene conversion (gBGC) more strongly impacting these lineages. Life history traits (LHTs) and, by extension, effective population size (Ne) have long been connected to patterns of sequence evolution. Species with short generation times experience a greater number of meioses per unit time, and more frequent gBGC In agreement with this idea, Romiguier et al [21] observed that mammalian lineages show negative correlations between both body mass, expected to be negatively associated with Ne, and generation time and GC. Subsequent studies on mammals have reinforced these findings [24,25]
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