The importance of adaptive mutations in molecular evolution is extensively debated. Recent developments in population genomics allow inferring rates of adaptive mutations by fitting a distribution of fitness effects to the observed patterns of polymorphism and divergence at sites under selection and sites assumed to evolve neutrally. Here, we summarize the current state-of-the-art of these methods and review the factors that affect the molecular rate of adaptation. Several studies have reported extensive cross-species variation in the proportion of adaptive amino-acid substitutions (α) and predicted that species with larger effective population sizes undergo less genetic drift and higher rates of adaptation. Disentangling the rates of positive and negative selection, however, revealed that mutations with deleterious effects are the main driver of this population size effect and that adaptive substitution rates vary comparatively little across species. Conversely, rates of adaptive substitution have been documented to vary substantially within genomes. On a genome-wide scale, gene density, recombination and mutation rate were observed to play a role in shaping molecular rates of adaptation, as predicted under models of linked selection. At the gene level, it has been reported that the gene functional category and the macromolecular structure substantially impact the rate of adaptive mutations. Here, we deliver a comprehensive review of methods used to infer the molecular adaptive rate, the potential drivers of adaptive evolution and how positive selection shapes molecular evolution within genes, across genes within species and between species.

中文翻译：

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物种之间和基因组内适应性替代率的变化

适应性突变在分子进化中的重要性引起了广泛的争论。群体基因组学的最新发展允许通过将适应度效应的分布拟合到在选择的位点和假定为中性进化的位点上观察到的多态性和分歧模式来推断适应性突变率。在这里，我们总结了这些方法的最新进展，并回顾了影响分子适应率的因素。几项研究报告了适应性氨基酸替代 (α) 比例的广泛跨物种变异，并预测具有较大有效种群规模的物种经历较少的遗传漂移和较高的适应率。然而，理清正选择和负选择的比率，揭示具有有害影响的突变是这种种群规模效应的主要驱动因素，并且适应性替代率在不同物种之间变化相对较小。相反，已记录的适应性替代率在基因组内有很大差异。在全基因组范围内，观察到基因密度、重组和突变率在塑造分子适应率方面发挥作用，正如在关联选择模型下预测的那样。在基因水平上，据报道基因功能类别和大分子结构对适应性突变率有重大影响。在这里，我们全面回顾了用于推断分子适应率、适应性进化的潜在驱动因素以及正选择如何塑造基因内分子进化的方法，