Quantifying and comparing the amount of adaptive evolution among different species is key to understanding how evolution works. 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 jointly estimate the proportion and selection coefficient (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 with that of D. melanogaster and mice. We show that this result cannot be caused by biased gene conversion or hypermutable CpG sites. We discuss possible biological explanations that could generate the observed differences in the amount of adaptive evolution across species.

中文翻译：

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与小鼠和黑腹果蝇相比，人类具有更强的选择强度和更高比例的有益氨基酸改变突变

量化和比较不同物种之间的适应性进化量是理解进化如何运作的关键。先前的研究表明不同物种的适应性进化存在差异；然而，它们的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群物种和祖先种群的人口统计历史，并估计人类和外群物种之间至少有 20% 的非同义替换是通过正选择固定的。这个估计比之前的估计要高得多，之前的估计没有校正外群物种和祖先种群的大小。接下来，我们联合估计比例和选择系数（p ⁺和s ⁺，分别）通过检查多态性和分歧的模式，在人类、小鼠和黑腹果蝇中新出现的有益非同义突变。我们开发了一个新的复合似然框架来测试这些参数是否因物种而异。总体而言，我们拒绝了具有相同p ⁺和s ⁺的跨物种有益突变模型，并估计与黑腹果蝇相比，人类具有更高的p ⁺ s ⁺和老鼠。我们表明该结果不是由偏向基因转换或超变 CpG 位点引起的。我们讨论了可能的生物学解释，这些解释可以产生观察到的跨物种适应性进化量的差异。