Jagoda Evelyn, Lawson Daniel J, Wall Jeffrey D, Lambert David, Muller Craig, Westaway Michael, Leavesley Matthew, Capellini Terence D, Mirazón Lahr Marta, Gerbault Pascale, Thomas Mark G, Migliano Andrea Bamberg, Willerslev Eske, Metspalu Mait, Pagani Luca
Human Evolutionary Biology, Harvard University, Cambridge, MA.
Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom.
Mol Biol Evol. 2018 Mar 1;35(3):623-630. doi: 10.1093/molbev/msx314.
Recent studies have reported evidence suggesting that portions of contemporary human genomes introgressed from archaic hominin populations went to high frequencies due to positive selection. However, no study to date has specifically addressed the postintrogression population dynamics of these putative cases of adaptive introgression. Here, for the first time, we specifically define cases of immediate adaptive introgression (iAI) in which archaic haplotypes rose to high frequencies in humans as a result of a selective sweep that occurred shortly after the introgression event. We define these cases as distinct from instances of selection on standing introgressed variation (SI), in which an introgressed haplotype initially segregated neutrally and subsequently underwent positive selection. Using a geographically diverse data set, we report novel cases of selection on introgressed variation in living humans and shortlist among these cases those whose selective sweeps are more consistent with having been the product of iAI rather than SI. Many of these novel inferred iAI haplotypes have potential biological relevance, including three that contain immune-related genes in West Siberians, South Asians, and West Eurasians. Overall, our results suggest that iAI may not represent the full picture of positive selection on archaically introgressed haplotypes in humans and that more work needs to be done to analyze the role of SI in the archaic introgression landscape of living humans.
近期研究报告了一些证据，表明现代人类基因组中源自古老人类群体的渗入部分由于正选择而达到了高频率。然而，迄今为止尚无研究专门探讨这些假定的适应性渗入案例在渗入后的群体动态。在此，我们首次明确界定了即时适应性渗入（iAI）的案例，即古老单倍型在渗入事件后不久因选择性清除而在人类中升至高频率的情况。我们将这些案例定义为与对现存渗入变异的选择（SI）不同，在SI中，渗入的单倍型最初中性分离，随后经历正选择。利用一个地理分布多样的数据集，我们报告了现存人类中渗入变异选择的新案例，并在这些案例中筛选出那些选择性清除更符合是iAI而非SI产物的案例。许多这些新推断出的iAI单倍型具有潜在的生物学相关性，包括在西西伯利亚人、南亚人和西欧亚人中包含免疫相关基因的三个单倍型。总体而言，我们的结果表明，iAI可能并不代表人类中古老渗入单倍型正选择的全貌，并且需要开展更多工作来分析SI在现存人类古老渗入格局中的作用。
