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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements
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Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements

机译：生命历史特征驱动着哺乳动物编码和非编码基因组元件的进化速率

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摘要

A comprehensive phylogenetic framework is indispensable for investigating the evolution of genomic features in mammals as a whole, and particularly in humans. Using the ENCODE sequence data, we estimated mammalian neutral evolutionary rates and selective pressures acting on conserved coding and noncoding elements. We show that neutral evolutionary rates can be explained by the generation time (GT) hypothesis. Accordingly, primates (especially humans), having longer GTs than other mammals, display slower rates of neutral evolution. The evolution of constrained elements, particularly of nonsynonymous sites, is in agreement with the expectations of the nearly neutral theory of molecular evolution. We show that rates of nonsynonymous substitutions (dN) depend on the population size of a species. The results are robust to the exclusion of hypermutable CpG prone sites. The average rate of evolution in conserved noncoding sequences (CNCs) is 1.7 times higher than in nonsynonymous sites. Despite this, CNCs evolve at similar or even lower rates than nonsynonymous sites in the majority of basal branches of the eutherian tree. This observation could be the result of an overall gradual or, alternatively, lineage-specific relaxation of CNCs. The latter hypothesis was supported by the finding that 3 of the 20 longest CNCs displayed significant relaxation of individual branches. This observation may explain why the evolution of CNCs fits the expectations of the nearly neutral theory less well than the evolution of nonsynonymous sites.
机译：一个全面的系统发育框架对于调查整个哺乳动物，尤其是人类的基因组特征的进化是必不可少的。使用ENCODE序列数据，我们估计了作用于保守编码和非编码元件的哺乳动物中性进化速率和选择性压力。我们表明，中性进化率可以由生成时间（GT）假设解释。因此，具有比其他哺乳动物更长的GT的灵长类（特别是人类）显示出较慢的中性进化速率。受约束的元素，特别是非同义位点的进化，与近乎中立的分子进化理论的期望是一致的。我们表明，非同义替换（dN）的速率取决于物种的种群规模。结果对于排除高变CpG倾向位点是可靠的。保守的非编码序列（CNC）的平均进化速率是非同义位点的1.7倍。尽管如此，在大多数以太坊树的基部分支中，CNC的发展速度与非同义站点的发展速度相近甚至更低。此观察结果可能是CNC逐渐整体或特定于谱系放宽的结果。后一个假设得到以下发现的支持：在20个最长的CNC中，有3个显示出明显的单个分支松弛。这一观察结果可以解释为什么CNCs的进化不如非同义位点的进化更符合近乎中立理论的期望。

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