群体遗传学模拟中缩放的正确与错误
The rights and wrongs of rescaling in population genetics simulations
AI总结：
本文探讨了群体遗传学模拟中缩放方法的理论基础及其应用，指出某些统计量可缩放而另一些不可，同时指出在模拟大染色体区域、复杂性状选择及部分自交或无性繁殖种群时可能出现问题。
摘要：
计算机模拟复杂群体遗传模型是解读单物种多个基因组序列大规模数据集的关键工具。为减少计算时间，常通过使用选择系数和突变率等参数来模拟远小于自然种群的群体，这种做法称为缩放，其理论依据是有限种群遗传学。然而，近期对这一做法的批评揭示了其可能导致错误结论的场合。本文回顾了缩放的理论基础，并将其与当前群体遗传学模拟实践联系起来。文章指出某些群体遗传统计量可缩放而另一些不可。此外，模拟大染色体区域时，由于核苷酸位点间物理距离与重组频率之间非线性关系，缩放可能会出现问题。其他缩放问题可能出现在复杂性状选择模拟以及部分自交或无性繁殖种群的模拟中。本文提出了若干关于缩放良好实践的建议。
英文摘要：
Computer simulations of complex population genetic models are an essential tool for making sense of the large-scale datasets of multiple genome sequences from a single species that are becoming increasingly available. A widely used approach for reducing computing time is to simulate populations that are much smaller than the natural populations that they are intended to represent, by using parameters such as selection coefficients and mutation rates whose products with the population size correspond to those of the natural populations. This approach has come to be known as rescaling, and is justified by the theory of the genetics of finite populations. Recently, however, there have been criticisms of this practice, which have brought to light situations in which it can lead to erroneous conclusions. This paper reviews the theoretical basis for rescaling, and relates it to current practice in population genetics simulations. It shows that some population genetic statistics are scaleable while others are not. Additionally, it shows that there are likely to be problems with rescaling when simulating large chromosomal regions, due to the non-linear relation between the physical distance between a pair of separate nucleotide sites and the frequency of recombination between them. Other difficulties with rescaling can arise in connection with simulations of selection on complex traits, and with populations that reproduce partly by self-fertilization or asexual reproduction. A number of recommendations are made for good practice in relation to rescaling.
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