Gillespie John H
Section of Evolution and Ecology, University of California, Davis, California, 95616.
Evolution. 1994 Aug;48(4):1101-1113. doi: 10.1111/j.1558-5646.1994.tb05297.x.
Substitution processes are of two sorts: origination processes record the times at which nucleotide mutations that ultimately fix in the population first appear, and fixation processes record the times at which they actually fix. Substitution processes may be generated by combining models of population genetics-here the symmetrical-neutral, overdominance, underdominance, TIM, and SAS-CFF models-with the infinite-sites, no-recombination model of the gene. This paper is mainly concerned with a computer simulation study of these substitution processes. The rate of substitution is shown to be remarkably insensitive to the strength of selection for models with strong balancing selection caused by the genealogical drift of mutations through alleles held in the population by selection. The origination process is shown to be more regular than Poisson for the overdominance, TIM, and SAS-CFF models but more clustered for the underdominance model. A class of point processes called Sawyer processes is introduced to help explain these observations as well as the observation that the times between successive originations are nearly uncorrelated. Fixation processes are shown to be more complex than origination processes, with regularly spaced bursts of multiple fixations. An approximation to the fixation process is described. One important conclusion is that protein evolution is not easily reconciled with any of these models without adding perturbations that recur on a time scale that is commensurate with that of molecular evolution.
起源过程记录最终在群体中固定下来的核苷酸突变首次出现的时间，而固定过程记录它们实际固定的时间。替换过程可以通过将群体遗传学模型（这里是对称中性、超显性、亚显性、TIM和SAS - CFF模型）与基因的无限位点、无重组模型相结合来生成。本文主要关注这些替换过程的计算机模拟研究。对于由选择在群体中保留的等位基因上的突变的谱系漂移导致的具有强平衡选择的模型，替换率显示出对选择强度非常不敏感。对于超显性、TIM和SAS - CFF模型，起源过程显示比泊松过程更规则，但对于亚显性模型则更聚集。引入了一类称为索耶过程的点过程，以帮助解释这些观察结果以及连续起源之间的时间几乎不相关的观察结果。固定过程显示比起源过程更复杂，具有多个固定的规则间隔爆发。描述了固定过程的一种近似。一个重要的结论是，如果不添加在与分子进化相当的时间尺度上反复出现的扰动，蛋白质进化就不容易与这些模型中的任何一个相协调。
