Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data.
Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data.
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从果蝇种群基因组数据中检测硬和软选择性扫描。
DOI：
10.1371/journal.pgen.1009373
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发表时间：
2021-03
期刊：
影响因子：
4.5
通讯作者：
Petrov DA
中科院分区：
文献类型：
--
作者：
Garud NR;Messer PW;Petrov DA
是硬扫描还是软扫描主导了适应一直是一个有争议的问题。最近，我们开发了单倍型纯合性统计，（i）可以检测具有相似功率的硬扫描和软扫描，以及（ii）可以将检测到的扫描分类为硬扫描或软扫描。应用我们的方法，从自然种群的果蝇（DGRP）的人口基因组数据，使我们能够重新发现三个已知的情况下，适应在基因座Ace，Cyp6g1，和CHKov1已知的软扫描驱动，并检测到额外的候选基因座最近和强扫描。令人惊讶的是，所有前50名候选人都表现出与软扫描而不是硬扫描更加一致的模式。最近，Harris et al. 2018批评了这项工作，表明我们的单倍型统计检测到的所有候选基因座，包括阳性对照，根本不可能被扫描，相反，这些单倍型模式可以更容易地用复杂的中性人口统计模型来解释。他们还声称，这些中立的非扫描很可能是硬的，而不是软扫描。在这里，我们使用一系列复杂的混合人口统计模型重新分析DGRP数据，并重新确认我们最初发表的结果，表明大多数最近和强烈的扫描在D。首先，黑腹鱼很可能是真的扫掠，其次，它们确实看起来很柔软。此外，我们讨论了如何把这项工作向前推进，因为在这种分析中采用的大多数人口模型必然过于简单，无法捕捉到完整的人口复杂性，而更现实的模型是不太可能被正确推断，因为它们需要大量的自由参数。硬扫描和软扫描是否主导适应一直是一个有争议的问题。最近，我们提出了新的统计数据，可以识别和区分硬和软扫描，并发现软扫描是令人惊讶的普遍在北美果蝇。在我们排名最高的候选人中，有三个著名的软扫描位点Cyp6g1，Ace和CHKov1。最近，Harris等人（2018）声称，我们发现的选择性扫描是假阳性，更可能由混合人口统计学史解释。此外，他们声称，这些中立的非扫描更有可能是硬扫描，而不是软扫描。在这里，我们重新评估我们和哈里斯等人的工作，发现一个合理的拟合人口模型，软扫描是一个主导模式的适应在北美果蝇。
Whether hard sweeps or soft sweeps dominate adaptation has been a matter of much debate. Recently, we developed haplotype homozygosity statistics that (i) can detect both hard and soft sweeps with similar power and (ii) can classify the detected sweeps as hard or soft. The application of our method to population genomic data from a natural population of Drosophila melanogaster (DGRP) allowed us to rediscover three known cases of adaptation at the loci Ace, Cyp6g1, and CHKov1 known to be driven by soft sweeps, and detected additional candidate loci for recent and strong sweeps. Surprisingly, all of the top 50 candidates showed patterns much more consistent with soft rather than hard sweeps. Recently, Harris et al. 2018 criticized this work, suggesting that all the candidate loci detected by our haplotype statistics, including the positive controls, are unlikely to be sweeps at all and that instead these haplotype patterns can be more easily explained by complex neutral demographic models. They also claim that these neutral non-sweeps are likely to be hard instead of soft sweeps. Here, we reanalyze the DGRP data using a range of complex admixture demographic models and reconfirm our original published results suggesting that the majority of recent and strong sweeps in D. melanogaster are first likely to be true sweeps, and second, that they do appear to be soft. Furthermore, we discuss ways to take this work forward given that most demographic models employed in such analyses are necessarily too simple to capture the full demographic complexity, while more realistic models are unlikely to be inferred correctly because they require a large number of free parameters. Whether hard versus soft sweeps dominate adaptation has long been a matter of great debate. Recently, we proposed novel statistics that can identify and differentiate hard and soft sweeps and found that soft sweeps are surprisingly common in North American Drosophila melanogaster. Among our top ranking candidates are three well-known soft sweeps at the loci Cyp6g1, Ace, and CHKov1. Recently, Harris et al. 2018 have claimed that the selective sweeps we identified are false positives and are more likely to be explained by an admixture demographic history. Moreover, they claim that these neutral non-sweeps are more likely to be hard sweeps rather soft sweeps. Here we re-assess our and Harris et al’s work and find that given a reasonably well-fitting demographic model, soft sweeps are a dominant mode of adaptation in North American Drosophila melanogaster.
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