Quantifying and comparing the amount of adaptive evolution among different species is key to understanding evolutionary processes. Previous studies have shown differences in adaptive evolution across species; however, their specific causes remain elusive. Here, we use improved modeling of weakly deleterious mutations and the demographic history of the outgroup species and ancestral population and estimate that at least 20% of nonsynonymous substitutions between humans and an outgroup species were fixed by positive selection. This estimate is much higher than previous estimates, which did not correct for the sizes of the outgroup species and ancestral population. Next, we directly estimate the proportion and selection coefficients (p+ and s+, respectively) of newly arising beneficial nonsynonymous mutations in humans, mice, and Drosophila melanogaster by examining patterns of polymorphism and divergence. We develop a novel composite likelihood framework to test whether these parameters differ across species. Overall, we reject a model with the same p+ and s+ of beneficial mutations across species, and estimate that humans have a higher p+s+ compared to D. melanogaster and mice. We demonstrate that this result cannot be caused by biased gene conversion or hypermutable CpG sites. In summary, we find the proportion of beneficial mutations to be higher in humans than in D. melanogaster or mice, suggesting that organismal complexity, which increases the number of steps required in adaptive walks, may be a key predictor of the amount of adaptive evolution within a species.

中文翻译：

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与小鼠和果蝇相比，人类的选择强度更高，有益氨基酸改变突变的比例更高

量化和比较不同物种间适应性进化的数量是理解进化过程的关键。先前的研究表明，物种间适应性进化的差异。但是，其具体原因仍然难以捉摸。在这里，我们使用弱有害突变的改进模型以及外来物种和祖先种群的人口历史记录，并估计至少有20％的人与外来物种之间的非同义替代是通过正选择固定的。这个估计值比以前的估计值要高得多，之前的估计值并未校正外来物种和祖先种群的大小。接下来，我们直接估算人类，小鼠，人和动物中新出现的有益的非同义突变的比例和选择系数（分别为p +和s +），果蝇和果蝇通过检查多态性和发散的模式。我们开发了一种新颖的复合似然框架，以测试这些参数是否在物种之间有所不同。总体而言，我们拒绝了具有跨物种有益突变的p +和s +的模型，并估计与黑腹果蝇和小鼠相比，人类具有更高的p + s +。我们证明该结果不能由偏向基因转换或超变CpG站点引起。总而言之，我们发现人类中有益突变的比例高于黑腹果蝇或小鼠，这表明机体复杂性增加了适应性行走所需的步数，可能是适应性进化量的关键预测指标在一个物种内。我们开发了一种新颖的复合似然框架，以测试这些参数是否在物种之间有所不同。总体而言，我们拒绝了具有跨物种有益突变的p +和s +的模型，并估计与黑腹果蝇和小鼠相比，人类具有更高的p + s +。我们证明该结果不能由偏向基因转换或超变CpG站点引起。总而言之，我们发现人类中有益突变的比例高于黑腹果蝇或小鼠，这表明机体复杂性增加了适应性行走所需的步数，可能是适应性进化量的关键预测因子在一个物种内。我们开发了一种新颖的复合似然框架，以测试这些参数是否在物种之间有所不同。总体而言，我们拒绝了具有跨物种有益突变的p +和s +的模型，并估计与黑腹果蝇和小鼠相比，人类具有更高的p + s +。我们证明该结果不能由偏向基因转换或超变CpG站点引起。总而言之，我们发现人类中有益突变的比例高于黑腹果蝇或小鼠，这表明机体复杂性增加了适应性行走所需的步数，可能是适应性进化量的关键预测因子在一个物种内。并估计人类比黑腹果蝇和小鼠具有更高的p + s +。我们证明该结果不能由偏向基因转换或超变CpG站点引起。总而言之，我们发现人类中有益突变的比例高于黑腹果蝇或小鼠，这表明机体复杂性增加了适应性行走所需的步数，可能是适应性进化量的关键预测指标在一个物种内。并估计人类比黑腹果蝇和小鼠具有更高的p + s +。我们证明该结果不能由偏向基因转换或超变CpG站点引起。总而言之，我们发现人类中有益突变的比例高于黑腹果蝇或小鼠，这表明机体复杂性增加了适应性行走所需的步数，可能是适应性进化量的关键预测因子在一个物种内。