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.

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关于选择性扫描对中立多样性水平的影响的预测效果如何？

选择性扫描被认为在塑造整个基因组变异的模式中起着重要作用。因此，对其效果的准确预测对于理解这些模式很重要。常用的选择性扫描模型假定等位基因在扫描结束时进行采样，并且在扫描过程中未能与野生型单倍型重组，因此会瞬间合并，从而导致简单地表达扫描对多样性的影响。此处显示，在重组事件发生之前，在扫频期间在扫频结束时采样的一对等位基因可能会出现合并的显着概率，从而将它们的预期合并时间减少到简单近似给出的以下。对于在这种内部扫频合并的情况下，由单次扫频和循环扫频导致的成对中性多样性的预期减少，可以得出表达式，尽管扫频过程中多次重组事件的影响只能通过试探来解决。对照模拟结果检查了所得表达式的准确性。对于什至适度的重组率与选择系数的比率，简单的近似可能实质上是不准确的。这里使用的选择模型可以应用于具有任意优势系数的有利突变，具有特定性别选择系数的性连锁基因座以及近交种群。使用该模型的结果，