中性演化的统计性质
Statistical properties of neutral evolution
摘要：
中性进化是最简单的分子进化模型，因此它最适合于全面的理论研究。在本文中，我们描述了中性进化的蛋白质的统计性质的要求下，天然状态保持化学稳定，并比较它们的木村的中性进化模型。我们的研究是基于我们最近提出的结构约束中性（SCN）模型。我们发现，在SCN模型中，替代率随着时间间隔的延长而降低，并且从进化树的一个分支到另一个分支强烈波动，导致替代过程的非泊松统计。这种强烈的波动也是由于单个残基的中性取代率与大多数残基对强烈相关的事实。有趣的是，结构保守的残基，其特征是远低于平均取代率，也与其他残基的相关性低得多，并以更有规律的方式进化。我们的研究结果可以改进旨在区分中性和适应性取代的方法，以及用于计算两个蛋白质序列分歧以来发生的预期取代数的方法。
英文摘要：
Neutral evolution is the simplest model of molecular evolution and thus it is most amenable to a comprehensive theoretical investigation. In this paper, we characterize the statistical properties of neutral evolution of proteins under the requirement that the native state remains thermodynamically stable, and compare them to the ones of Kimura's model of neutral evolution. Our study is based on the Structurally Constrained Neutral (SCN) model which we recently proposed. We show that, in the SCN model, the substitution rate decreases as longer time intervals are considered, and fluctuates strongly from one branch of the evolutionary tree to another, leading to a non-Poissonian statistics for the substitution process. Such strong fluctuations are also due to the fact that neutral substitution rates for individual residues are strongly correlated for most residue pairs. Interestingly, structurally conserved residues, characterized by a much below average substitution rate, are also much less correlated to other residues and evolve in a much more regular way. Our results could improve methods aimed at distinguishing between neutral and adaptive substitutions as well as methods for computing the expected number of substitutions occurred since the divergence of two protein sequences.
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