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How Good Are Predictions of the Effects of Selective Sweeps on Levels of Neutral Diversity?
GENETICS ( IF 3.3 ) Pub Date : 2020-10-26 , DOI: 10.1534/genetics.120.303734
Brian Charlesworth 1
Affiliation  

Selective sweeps are thought to play a significant role in shaping patterns of variability across genomes; accurate predictions of their effects are, therefore, important for understanding these patterns. A commonly used model of selective sweeps assumes that alleles sampled at the end of a sweep, and that fail to recombine with wild-type haplotypes during the sweep, coalesce instantaneously, leading to a simple expression for sweep effects on diversity. It is shown here that there can be a significant probability that a pair of alleles sampled at the end of a sweep coalesce during the sweep before a recombination event can occur, reducing their expected coalescent time below that given by the simple approximation. Expressions are derived for the expected reductions in pairwise neutral diversities caused by both single and recurrent sweeps in the presence of such within-sweep coalescence, although the effects of multiple recombination events during a sweep are only treated heuristically. The accuracies of the resulting expressions were checked against the results of simulations. For even moderate ratios of the recombination rate to the selection coefficient, the simple approximation can be substantially inaccurate. The selection model used here can be applied to favorable mutations with arbitrary dominance coefficients, to sex-linked loci with sex-specific selection coefficients, and to inbreeding populations. Using the results from this model, the expected differences between the levels of variability on X chromosomes and autosomes with selection at linked sites are discussed, and compared with data on a population of Drosophila melanogaster.

中文翻译:

选择性扫描对中性多样性水平影响的预测有多好?

选择性扫描被认为在塑造基因组变异模式方面发挥着重要作用。因此,准确预测其影响对于理解这些模式非常重要。选择性扫描的常用模型假设在扫描结束时采样的等位基因在扫描期间未能与野生型单倍型重组,从而立即合并,从而得到扫描对多样性影响的简单表达式。这里显示,在重组事件发生之前,在扫描结束时采样的一对等位基因在扫描期间合并的可能性很大,从而将它们的预期合并时间减少到简单近似给出的时间以下。推导了在存在这种扫描内合并的情况下由单次扫描和循环扫描引起的成对中性多样性的预期减少的表达式,尽管仅启发式地处理扫描期间多个重组事件的影响。根据模拟结果检查所得表达式的准确性。即使对于重组率与选择系数的中等比率,简单的近似也可能基本上不准确。这里使用的选择模型可以应用于具有任意显性系数的有利突变、具有性别特异性选择系数的性别连锁基因座以及近交群体。使用该模型的结果,讨论了 X 染色体和常染色体上的变异水平与连锁位点选择之间的预期差异,并与果蝇群体的数据进行了比较
更新日期:2020-10-31
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