Singh Nadia D, Larracuente Amanda M, Clark Andrew G
Department of Molecular Biology and Genetics, Cornell University, USA.
Mol Biol Evol. 2008 Feb;25(2):454-67. doi: 10.1093/molbev/msm275. Epub 2007 Dec 13.
To investigate the relative efficacy of both positive and purifying natural selection on the X chromosome and the autosomes in Drosophila, we compared rates and patterns of molecular evolution between these chromosome sets using the newly available alignments of orthologous genes from 12 species. Parameters that may influence the relative X versus autosomal substitution rates include the relative effective population sizes, the male and female germline mutation rates, the distribution of allelic effects on fitness, and the degree of dominance of novel mutations. Our analysis reveals that codon usage bias is consistently greater for X-linked genes, suggesting that purifying selection consistently has greater efficacy on the X chromosome than on the autosomes across the Drosophila phylogeny. However, our results are less consistent with respect to the efficacy of positive selection, with only some lineages showing a higher substitution rate on the X chromosome. This suggests that either the distribution of selective effects of mutations or other relevant parameters are sufficiently variable across species to tip the balance in different ways in individual lineages. These data suggest that rates of substitution are not solely governed by adaptive evolution. This genome-wide analysis provides a clear picture that the efficacy of selection varies intragenomically and that this effect is markedly more consistent across the phylogeny in the case of purifying selection. Our results also suggest that simple models that predict systematic differences in rates of evolution between the X and the autosomes can only be made to be compatible with these Drosophila data if the relevant population genetic parameters that drive substitution rates differ among species and chromosomal contexts.
为了研究正向自然选择和净化自然选择对果蝇X染色体和常染色体的相对影响，我们利用新获得的12个物种直系同源基因比对，比较了这些染色体组之间的分子进化速率和模式。可能影响X染色体与常染色体相对替换率的参数包括相对有效种群大小、雄性和雌性生殖系突变率、等位基因对适合度的影响分布以及新突变的显性程度。我们的分析表明，X连锁基因的密码子使用偏好始终更大，这表明在整个果蝇系统发育过程中，净化选择对X染色体的影响始终大于对常染色体的影响。然而，关于正向选择的效果，我们的结果不太一致，只有一些谱系在X染色体上显示出更高的替换率。这表明，要么突变的选择效应分布，要么其他相关参数在不同物种间变化足够大，从而在不同谱系中以不同方式打破平衡。这些数据表明，替换率并非仅由适应性进化决定。这项全基因组分析清楚地表明，选择效果在基因组内存在差异，而且在净化选择的情况下，这种效应在整个系统发育过程中更为一致。我们的结果还表明，只有当驱动替换率的相关群体遗传参数在不同物种和染色体环境中存在差异时，预测X染色体和常染色体进化速率系统差异的简单模型才能与这些果蝇数据相匹配。
