The genomic rate of adaptive amino acid substitution in Drosophila
The genomic rate of adaptive amino acid substitution in Drosophila
复制标题
DOI：
10.1093/molbev/msh134
复制
发表时间：
2004-07-01
影响因子：
10.7
通讯作者：
Eyre-Walker, A
中科院分区：
文献类型：
--
作者：
Bierne, N;Eyre-Walker, A
通过扩展McDonald-Kreitman检验，可以从多态和分歧数据中潜在地估计由适应性进化驱动的氨基酸替换的比例。我们已经开发了一种最大似然方法来做这件事，并将我们的方法应用于来自三个果蝇物种的几个数据集：黑腹果蝇、拟果蝇和雅库巴果蝇。每个密码子的自适应替换的估计数量并不均匀地分布在基因之间，而是遵循尖峰分布。然而，通过适应性进化固定的氨基酸替代的比例在整个基因组中似乎非常稳定(即，在快速进化和缓慢进化的基因中，适应性氨基酸替代的比例似乎是相同的；快速进化的基因具有更多的适应性替代和中性替代)。我们的估计似乎不会因为对同义密码子使用的选择或不同位点之间独立的假设而产生明显的偏见。然而，由于存在略微有害的突变和有效种群数量的变化，准确的估计受到了阻碍。对几个果蝇数据集的分析表明，大约25%的+/-20%的氨基酸替换是由正选择驱动的，在模拟果蝇和雅库巴果蝇之间的分歧。
The proportion of amino acid substitutions driven by adaptive evolution can potentially be estimated from polymorphism and divergence data by an extension of the McDonald-Kreitman test. We have developed a maximum-likelihood method to do this and have applied our method to several data sets from three Drosophila species: D. melanogaster, D. simulans, and D. yakuba. The estimated number of adaptive substitutions per codon is not uniformly distributed among genes, but follows a leptokurtic distribution. However, the proportion of amino acid substitutions fixed by adaptive evolution seems to be remarkably constant across the genome (i.e., the proportion of amino acid substitutions that are adaptive appears to be the same in fast-evolving and slow-evolving genes; fast-evolving genes have higher numbers of both adaptive and neutral substitutions). Our estimates do not seem to be significantly biased by selection on synonymous codon use or by the assumption of independence among sites. Nevertheless, an accurate estimate is hampered by the existence of slightly deleterious mutations and variations in effective population size. The analysis of several Drosophila data sets suggests that approximately 25% +/- 20% of amino acid substitutions were driven by positive selection in the divergence between D. simulans and D. yakuba.