VolcanoFinder: Genomic scans for adaptive introgression
VolcanoFinder: Genomic scans for adaptive introgression
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DOI：
10.1371/journal.pgen.1008867
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发表时间：
2019-07
期刊：
影响因子：
4.5
通讯作者：
D. Setter;S. Mousset;Xiaoheng Cheng;R. Nielsen;Michael Degiorgio;J. Hermisson
中科院分区：
文献类型：
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作者：
D. Setter;S. Mousset;Xiaoheng Cheng;R. Nielsen;Michael Degiorgio;J. Hermisson
最近的研究表明，近缘物种之间的渐渗是一个重要的适应性等位基因的广泛类群的来源。通常，从基因组数据检测适应性渐渗依赖于比较分析，其需要来自受体和供体物种的序列数据。然而，在许多情况下，捐助者是未知的或目前没有数据。在这里，我们介绍了一个基因组扫描方法火山-检测最近的事件，适应性基因渗入，仅使用多态性数据从受体物种。火山爆发检测自适应渐渗扫描从他们在基因组的侧翼区域产生的多余的中频多态性的模式，一个模式，这似乎是一个火山形状的成对遗传多样性。使用聚结理论，我们得到这些模式的分析预测。基于这些结果，我们开发了一种复合似然检验来检测相对于基因组背景的自适应渐渗的签名。模拟结果表明，火山有很高的统计能力来检测这些签名，即使是旧的扫描和软扫描发起的多个移民单倍型。最后，我们实现了Volcanosimplex来检测欧洲和撒哈拉以南非洲人群中的古老基因渗入，并在这两个人群中发现了有趣的候选人，例如欧洲人的TSHR和非洲人的TCHH-RPTN。我们讨论了它们的生物学意义，并提供指导方针，以识别和规避人为的信号在火山的实证应用。将有益的等位基因从一个密切相关的物种引入一个物种的过程被称为适应性渐渗。我们提出了一个易于分析的模型，适应性渐渗对非适应性遗传变异的影响，在基因组区域周围的有益等位基因。我们描述的结果是一个特征性的火山形模式，其变异性增加，出现在阳性选择的位点周围，我们引入了一种开源方法Volcanosit来检测基因组数据中的这种信号。重要的是，火山是一种基于种群遗传可能性的方法，而不是一种比较基因组方法，因此可以探测来自单个种群的基因组变异数据，以寻找适应性渐渗的足迹，甚至是来自先验未知和可能灭绝的供体物种。
Recent research shows that introgression between closely-related species is an important source of adaptive alleles for a wide range of taxa. Typically, detection of adaptive introgression from genomic data relies on comparative analyses that require sequence data from both the recipient and the donor species. However, in many cases, the donor is unknown or the data is not currently available. Here, we introduce a genome-scan method—VolcanoFinder—to detect recent events of adaptive introgression using polymorphism data from the recipient species only. VolcanoFinder detects adaptive introgression sweeps from the pattern of excess intermediate-frequency polymorphism they produce in the flanking region of the genome, a pattern which appears as a volcano-shape in pairwise genetic diversity. Using coalescent theory, we derive analytical predictions for these patterns. Based on these results, we develop a composite-likelihood test to detect signatures of adaptive introgression relative to the genomic background. Simulation results show that VolcanoFinder has high statistical power to detect these signatures, even for older sweeps and for soft sweeps initiated by multiple migrant haplotypes. Finally, we implement VolcanoFinder to detect archaic introgression in European and sub-Saharan African human populations, and uncovered interesting candidates in both populations, such as TSHR in Europeans and TCHH-RPTN in Africans. We discuss their biological implications and provide guidelines for identifying and circumventing artifactual signals during empirical applications of VolcanoFinder. Author summary The process by which beneficial alleles are introduced into a species from a closely-related species is termed adaptive introgression. We present an analytically-tractable model for the effects of adaptive introgression on non-adaptive genetic variation in the genomic region surrounding the beneficial allele. The result we describe is a characteristic volcano-shaped pattern of increased variability that arises around the positively-selected site, and we introduce an open-source method VolcanoFinder to detect this signal in genomic data. Importantly, VolcanoFinder is a population-genetic likelihood-based approach, rather than a comparative-genomic approach, and can therefore probe genomic variation data from a single population for footprints of adaptive introgression, even from a priori unknown and possibly extinct donor species.