Ohta T
National Institute of Genetics, Mishima, Japan.
J Mol Evol. 1995 Jan;40(1):56-63. doi: 10.1007/BF00166595.
The nearly neutral theory of molecular evolution predicts larger generation-time effects for synonymous than for nonsynonymous substitutions. This prediction is tested using the sequences of 49 single-copy genes by calculating the average and variance of synonymous and nonsynonymous substitutions in mammalian star phylogenies (rodentia, artiodactyla, and primates). The average pattern of the 49 genes supports the prediction of the nearly neutral theory, with some notable exceptions. The nearly neutral theory also predicts that the variance of the evolutionary rate is larger than the value predicted by the completely neutral theory. This prediction is tested by examining the dispersion index (ratio of the variance to the mean), which is positively correlated with the average substitution number. After weighting by the lineage effects, this correlation almost disappears for nonsynonymous substitutions, but not quite so for synonymous substitutions. After weighting, the dispersion indices of both synonymous and nonsynonymous substitutions still exceed values expected under the simple Poisson process. The results indicate that both the systematic bias in evolutionary rate among the lineages and the episodic type of rate variation are contributing to the large variance. The former is more significant to synonymous substitutions than to nonsynonymous substitutions. Isochore evolution may be similar to synonymous substitutions. The rate and pattern found here are consistent with the nearly neutral theory, such that the relative contributions of drift and selection differ between the two types of substitutions. The results are also consistent with Gillespie's episodic selection theory.
分子进化的近中性理论预测，同义替换比非同义替换具有更大的世代时间效应。通过计算哺乳动物星状系统发育树（啮齿目、偶蹄目和灵长目）中同义替换和非同义替换的平均值和方差，利用49个单拷贝基因的序列对这一预测进行了检验。49个基因的平均模式支持近中性理论的预测，但也有一些显著的例外。近中性理论还预测，进化速率的方差大于完全中性理论预测的值。通过检查离散指数（方差与均值之比）对这一预测进行了检验，该指数与平均替换数呈正相关。在按谱系效应加权后，这种相关性对于非同义替换几乎消失，但对于同义替换则并非完全如此。加权后，同义替换和非同义替换的离散指数仍然超过简单泊松过程下预期的值。结果表明，谱系间进化速率的系统偏差和速率变化的偶发性类型都导致了较大的方差。前者对同义替换的影响比对非同义替换的影响更大。等容线进化可能与同义替换相似。这里发现的速率和模式与近中性理论一致，因此两种类型替换中漂变和选择的相对贡献有所不同。结果也与吉莱斯皮的偶发性选择理论一致。
