Versatile Detection of Diverse Selective Sweeps with Flex-Sweep.
Versatile Detection of Diverse Selective Sweeps with Flex-Sweep.
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DOI：
10.1093/molbev/msad139
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发表时间：
2023-06-01
影响因子：
10.7
通讯作者：
Enard, David
中科院分区：
文献类型：
--
作者：
Lauterbur, M. Elise;Munch, Kasper;Enard, David
理解选择压力对现代基因组多样性的影响是进化基因组学的一个主要目标。特别是，选择性扫描适应的贡献仍然是一个悬而未决的问题，与持续的统计局限性的功率和特异性扫描检测方法。具有微妙基因组信号的扫描对于检测特别具有挑战性。虽然许多现有的方法能够有效地检测特定类型的扫描和/或具有强信号的扫描，但它们的能力是以牺牲通用性为代价的。我们介绍了Flex-sweep，这是一种基于机器学习的工具，旨在检测具有各种细微信号的扫描，包括数千代的扫描。这是特别有价值的非模式生物，我们既没有期望的整体特征扫描或外群体与人口水平的测序，以方便检测非常古老的扫描。我们表明，Flex-sweep有能力检测扫描与微妙的信号，即使在面对人口统计模型的错误，重组率的异质性，和背景选择。Flex-sweep可检测最多0.125* 4 Ne代的扫描，包括弱、软和/或不完整的扫描;它还可以检测最多0.25* 4 Ne代的强、完整扫描。我们应用柔性扫描1000基因组约鲁巴数据集，除了恢复以前确定的扫描，扫描不成比例地发生在基因区域内，并接近监管区域。此外，我们发现，病毒相互作用蛋白（VIP）是非常丰富的选择性扫描，概括了以前的结果，证明了病毒作为人类适应性进化的驱动程序的重要性。
Understanding the impacts of selection pressures influencing modern-day genomic diversity is a major goal of evolutionary genomics. In particular, the contribution of selective sweeps to adaptation remains an open question, with persistent statistical limitations on the power and specificity of sweep detection methods. Sweeps with subtle genomic signals have been particularly challenging to detect. Although many existing methods powerfully detect specific types of sweeps and/or those with strong signals, their power comes at the expense of versatility. We present Flex-sweep, a machine learning–based tool designed to detect sweeps with a variety of subtle signals, including those thousands of generations old. It is especially valuable for nonmodel organisms, for which we have neither expectations about the overall characteristics of sweeps nor outgroups with population-level sequencing to otherwise facilitate detecting very old sweeps. We show that Flex-sweep has the power to detect sweeps with subtle signals, even in the face of demographic model misspecification, recombination rate heterogeneity, and background selection. Flex-sweep detects sweeps up to 0.125*4Ne generations old, including those that are weak, soft, and/or incomplete; it can also detect strong, complete sweeps up to 0.25*4Ne generations old. We apply Flex-sweep to the 1000 Genomes Yoruba data set and, in addition to recovering previously identified sweeps, show that sweeps disproportionately occur within genic regions and are close to regulatory regions. In addition, we show that virus-interacting proteins (VIPs) are strongly enriched for selective sweeps, recapitulating previous results that demonstrate the importance of viruses as a driver of adaptive evolution in humans.
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DOI：
10.1098/rstb.2019.0575
发表时间：
2020-11-23
期刊：
Philosophical transactions of the Royal Society of London. Series B, Biological sciences
影响因子：
--
作者：
Enard D;Petrov DA
通讯作者：
Petrov DA
影响因子：
6.6
作者：
Chen, Kuan-Yu;Marschall, Elizabeth A.;Ludsin, Stuart A.
通讯作者：
Ludsin, Stuart A.
影响因子：
7
作者：
Chen, Hua;Patterson, Nick;Reich, David
通讯作者：
Reich, David
影响因子：
9.8
作者：
Bersaglieri, T;Sabeti, PC;Hirschhorn, JN
通讯作者：
Hirschhorn, JN
影响因子：
30.8
作者：
Enattah, NS;Sahi, T;Järvelä, I
通讯作者：
Järvelä, I