Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis.
Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis.
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DOI：
10.1371/journal.pgen.1005774
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发表时间：
2016-01
期刊：
影响因子：
4.5
通讯作者：
Galtier N
中科院分区：
文献类型：
--
作者：
Galtier N
基因组适应环境变化的速率和分子进化中适应过程的普遍性是当前进化遗传学中两个有争议的问题。先前试图通过氨基酸取代来量化全基因组适应率的尝试揭示了模式的惊人多样性，一些物种（例如果蝇）经历了非常高的适应率，而其他物种（例如人类）则由近乎中性的过程主导。有人认为，这种差异反映了物种间有效种群规模的差异。然而，已发表的研究主要集中在模式生物上，并依赖于不同的数据集和方法，因此目前缺乏对自然界中适应性蛋白质进化的普遍性的概述。在这里，我们扩展现有的估计的氨基酸适应率明确建模有利的突变对非同义多态性模式的影响，我们将这些方法应用到一个新建立的，同质的数据集的44个非模型动物物种对。数据分析揭示了适应性进化对所有主要后生动物门的氨基酸替代过程的主要贡献，但人类和灵长类动物除外。适应性氨基酸取代比例与物种有效种群大小正相关。然而，这种关系似乎主要是由近中性氨基酸取代率下降，因为更有效的纯化选择在大人口。我们的研究结果表明，自适应过程在大多数动物物种的蛋白质的进化占主导地位，但并没有证实的假设，即自适应取代积累在一个更快的速度在大的人口。关于影响人类与其他生物体的适应性进化和阳性选择检测率的因素的影响进行了讨论。物种适应环境变化的速度是一个有争议的话题。该理论预测，大种群的适应比小种群更容易，对模式生物的基因组研究表明，大种群规模的苍蝇比小种群规模的人类和猿的适应率要高得多。在这里，我们建立和分析了一个大型的蛋白质编码序列数据集，该数据集由44对物种中的数千个基因组成，这些物种来自不同的动物群体，包括昆虫，软体动物，环节动物，棘皮动物，爬行动物，鸟类和哺乳动物。扩展和改进现有的数据分析方法，我们表明，适应是所有动物门的蛋白质进化的一个主要过程：在大多数物种中，适应性发生的氨基酸取代的比例超过50%，并达到90%。我们的分析并没有证实，人口规模，这里接近物种遗传多样性和生态特征，确实影响适应性分子进化的速度，但指出人类和猿作为一个特殊的情况下，与其他动物相比，在适应性基因组过程。
The rate at which genomes adapt to environmental changes and the prevalence of adaptive processes in molecular evolution are two controversial issues in current evolutionary genetics. Previous attempts to quantify the genome-wide rate of adaptation through amino-acid substitution have revealed a surprising diversity of patterns, with some species (e.g. Drosophila) experiencing a very high adaptive rate, while other (e.g. humans) are dominated by nearly-neutral processes. It has been suggested that this discrepancy reflects between-species differences in effective population size. Published studies, however, were mainly focused on model organisms, and relied on disparate data sets and methodologies, so that an overview of the prevalence of adaptive protein evolution in nature is currently lacking. Here we extend existing estimators of the amino-acid adaptive rate by explicitly modelling the effect of favourable mutations on non-synonymous polymorphism patterns, and we apply these methods to a newly-built, homogeneous data set of 44 non-model animal species pairs. Data analysis uncovers a major contribution of adaptive evolution to the amino-acid substitution process across all major metazoan phyla—with the notable exception of humans and primates. The proportion of adaptive amino-acid substitution is found to be positively correlated to species effective population size. This relationship, however, appears to be primarily driven by a decreased rate of nearly-neutral amino-acid substitution because of more efficient purifying selection in large populations. Our results reveal that adaptive processes dominate the evolution of proteins in most animal species, but do not corroborate the hypothesis that adaptive substitutions accumulate at a faster rate in large populations. Implications regarding the factors influencing the rate of adaptive evolution and positive selection detection in humans vs. other organisms are discussed. The rate at which species adapt to environmental changes is a controversial topic. The theory predicts that adaptation is easier in large than in small populations, and the genomic studies of model organisms have revealed a much higher adaptive rate in large population-sized flies than in small population-sized humans and apes. Here we build and analyse a large data set of protein-coding sequences made of thousands of genes in 44 pairs of species from various groups of animals including insects, molluscs, annelids, echinoderms, reptiles, birds, and mammals. Extending and improving existing data analysis methods, we show that adaptation is a major process in protein evolution across all phyla of animals: the proportion of amino-acid substitutions that occurred adaptively is above 50% in a majority of species, and reaches up to 90%. Our analysis does not confirm that population size, here approached through species genetic diversity and ecological traits, does influence the rate of adaptive molecular evolution, but points to human and apes as a special case, compared to other animals, in terms of adaptive genomic processes.