Weber Claudia C, Boussau Bastien, Romiguier Jonathan, Jarvis Erich D, Ellegren Hans
Genome Biol. 2014;15(12):549. doi: 10.1186/s13059-014-0549-1.
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. 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.
Employing 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.
Our 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.
虽然有效种群大小（Ne）和诸如世代时间等生活史特征已知会影响替换率，但其对碱基组成进化的潜在影响却了解较少。在哺乳动物中，GC含量随着体重的降低而增加，这与重组相关的GC偏向性基因转换（gBGC）对这些谱系的影响更强是一致的。然而，物种间染色体结构和重组格局的变化可能会使这些结果的解释变得复杂。在鸟类中，染色体间重排很少见且重组格局是保守的，这表明该类群非常适合评估生活史对碱基组成的影响。
利用来自45个新测序和3个先前测序的鸟类基因组的数据，这些基因组涵盖了广泛的分类群，我们发现种群大且世代短的谱系具有更高的GC含量。这种效应延伸到编码和非编码位点，表明这不是由于密码子使用的选择。与重组驱动碱基组成一致，GC含量和异质性与重组率呈正相关。此外，我们观察到大多数谱系中的GC含量持续增加。
我们的结果提供了证据，表明gBGC可能驱动鸟类基因组中的核苷酸组成模式，并且与在大种群中更有效的gBGC以及单位时间内更多的减数分裂一致；也就是说，世代时间更短。因此，与理论预测一致，碱基组成进化受到物种生活史的显著调节。
