Axelsson Erik, Ellegren Hans
Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
Mol Biol Evol. 2009 May;26(5):1073-9. doi: 10.1093/molbev/msp019. Epub 2009 Feb 2.
Whether protein evolution is mainly due to fixation of beneficial alleles by positive selection or to random genetic drift has remained a contentious issue over the years. Here, we use two genomewide polymorphism data sets collected from chicken populations, together with divergence data from >5,000 chicken-zebra finch gene orthologs expressed in brain, to assess the amount of adaptive evolution in protein-coding genes of birds. First, we show that estimates of the fixation index (FI, the ratio of fixed nonsynonymous-to-synonymous changes over the ratio of the corresponding polymorphisms) are highly dependent on the character of the underlying data sets. Second, by using polymorphism data from high-frequency alleles, to avoid the confounding effect of slightly deleterious mutations segregating at low frequency, we estimate that about 20% of amino acid changes have been brought to fixation through positive selection during avian evolution. This estimate is intermediate to that obtained in humans (lower) and flies as well as bacteria (higher), and is consistent with population genetics theory that stipulates a positive relationship between the efficiency of selection and the effective population size. Further, by comparing the FIs for common and all alleles, we estimate that approximately 20% of nonsynonymous variation segregating in chicken populations represent slightly deleterious mutations, which is less than in Drosophila. Overall, these results highlight the link between the effective population size and positive as well as negative selection.
多年来，蛋白质进化主要是由于正选择使有益等位基因固定，还是由于随机遗传漂变，一直是一个有争议的问题。在这里，我们使用从鸡群体中收集的两个全基因组多态性数据集，以及在大脑中表达的5000多个鸡 - 斑胸草雀基因直系同源物的分歧数据，来评估鸟类蛋白质编码基因中的适应性进化量。首先，我们表明固定指数（FI，固定非同义替换与同义替换的比率相对于相应多态性的比率）的估计高度依赖于基础数据集的特征。其次，通过使用高频等位基因的多态性数据，以避免低频分离的轻微有害突变的混杂效应，我们估计在鸟类进化过程中约20%的氨基酸变化是通过正选择固定下来的。这个估计值介于人类（较低）以及果蝇和细菌（较高）中获得的值之间，并且与群体遗传学理论一致，该理论规定选择效率与有效种群大小之间存在正相关关系。此外，通过比较常见等位基因和所有等位基因的固定指数，我们估计鸡群体中分离的非同义变异约20%代表轻微有害突变，这比果蝇中的要少。总体而言，这些结果突出了有效种群大小与正选择和负选择之间的联系。
