Evidence for pervasive adaptive protein evolution in wild mice.
Evidence for pervasive adaptive protein evolution in wild mice.
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DOI：
10.1371/journal.pgen.1000825
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发表时间：
2010-01-22
期刊：
影响因子：
4.5
通讯作者：
Keightley PD
中科院分区：
文献类型：
--
作者：
Halligan DL;Oliver F;Eyre-Walker A;Harr B;Keightley PD
中性取代和适应性取代对分子进化的相对贡献是40多年来进化生物学中最具争议的问题之一。种内核苷酸多态性和种间分歧数据的分析支持在某些类群的适应性蛋白质进化的广泛作用。例如，在肠道细菌和果蝇中，适应性氨基酸取代（α）的比例估计为50%或更高。相比之下，最近估计的原始人类的α最多为13%。在这里，我们估计α的蛋白质序列的鼠科啮齿动物的基础上，从多个基因的核苷酸多态性数据在一个人口的家鼠亚种小家鼠castaneus，居住的祖先范围的小鼠物种复合体和M之间的核苷酸分歧。M. castaneus和M. famulus或老鼠。我们估计，57%的氨基酸取代鼠科动物已被驱动的积极选择。因此，人科动物在适应性蛋白质进化的低水平上是例外的。野生小鼠中适应性氨基酸替换的高频率与其大的有效种群规模相一致，从而导致分子水平上的有效自然选择。有效的自然选择还表现为M中缺乏有效的中性非同义突变。M.与人类相比。自然选择在DNA水平上的普遍性在进化生物学中仍然是一个有争议的问题。特别是，对适应性氨基酸变化（α）比例的估计在不同分类群之间差异很大，在细菌和果蝇中为50%或更多，但在人科动物中最多为13%。在这里，我们推断的频率多态性的蛋白质编码基因的15家鼠种复合体的祖先范围内采样的小家鼠个体。将多态性数据与核苷酸差异相结合，对近缘种鼠M. famulus和大鼠，我们得到α的估计值为57%。这是对人类以外的哺乳动物的α的首次估计。野生小鼠和其他类群的适应性蛋白质进化率很高，这意味着原始人类的适应性蛋白质进化率很低，这在某种程度上是不寻常的。其中一个可能的原因是人类的有效种群规模较低，预计这将导致自然选择效率较低和适应性突变较少。这与我们在分析中推断的人科动物中近中性有害氨基酸突变的频率高于鼠科动物是一致的。
The relative contributions of neutral and adaptive substitutions to molecular evolution has been one of the most controversial issues in evolutionary biology for more than 40 years. The analysis of within-species nucleotide polymorphism and between-species divergence data supports a widespread role for adaptive protein evolution in certain taxa. For example, estimates of the proportion of adaptive amino acid substitutions (α) are 50% or more in enteric bacteria and Drosophila. In contrast, recent estimates of α for hominids have been at most 13%. Here, we estimate α for protein sequences of murid rodents based on nucleotide polymorphism data from multiple genes in a population of the house mouse subspecies Mus musculus castaneus, which inhabits the ancestral range of the Mus species complex and nucleotide divergence between M. m. castaneus and M. famulus or the rat. We estimate that 57% of amino acid substitutions in murids have been driven by positive selection. Hominids, therefore, are exceptional in having low apparent levels of adaptive protein evolution. The high frequency of adaptive amino acid substitutions in wild mice is consistent with their large effective population size, leading to effective natural selection at the molecular level. Effective natural selection also manifests itself as a paucity of effectively neutral nonsynonymous mutations in M. m. castaneus compared to humans. The prevalence of natural selection at the DNA level remains a controversial issue in evolutionary biology. In particular, estimates of the proportion of adaptive amino acid changes (α) vary greatly between taxa, being 50% or more in bacteria and fruit flies, but at most 13% in hominids. Here, we infer the frequencies of polymorphisms in protein-coding genes of 15 Mus musculus castaneus individuals sampled from the ancestral range of the house mouse species complex. By combining the polymorphism data with nucleotide divergence to the related murid species M. famulus and the rat, we obtain an estimate for α of 57%. This represents the first estimate of α for a mammal other than humans. The high rate of adaptive protein evolution in wild mice and other taxa implies that hominids may be somewhat unusual in having low rates of adaptive protein evolution. One possible cause of this is the low effective population size in humans, which is predicted to lead to less effective natural selection and fewer adaptive mutations. This is consistent with the higher frequency of nearly neutral deleterious amino acid mutations in hominids than murids that we infer in our analysis.
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