The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA.
The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Cell. 2020 Feb 20;180(4):677-687.e16. doi: 10.1016/j.cell.2020.01.012. Epub 2020 Jan 30.
Admixture has played a prominent role in shaping patterns of human genomic variation, including gene flow with now-extinct hominins like Neanderthals and Denisovans. Here, we describe a novel probabilistic method called IBDmix to identify introgressed hominin sequences, which, unlike existing approaches, does not use a modern reference population. We applied IBDmix to 2,504 individuals from geographically diverse populations to identify and analyze Neanderthal sequences segregating in modern humans. Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date.
混合在塑造人类基因组变异模式方面发挥了重要作用，包括与现已灭绝的人类如尼安德特人和丹尼索瓦人之间的基因流。在这里，我们描述了一种称为 IBDmix 的新概率方法来识别渐渗的人类序列，与现有方法不同，它不使用现代参考人群。我们将 IBDmix 应用于来自地理上多样化的人群的 2504 个人，以识别和分析在现代人类中分离的尼安德特人序列。引人注目的是，我们发现非洲个体携带的尼安德特人遗传信号比以前认为的要强。我们表明，这可以用由于迁徙回非洲的真正的尼安德特人遗传来解释，主要是来自祖先的欧洲人，以及从非洲早期扩散的人类群体向尼安德特人的基因流。我们的结果细化了我们对非洲和非非洲人群中尼安德特人遗传的理解，并表明迄今为止研究过的每一个现代人类群体中都存在尼安德特人基因组的残余。
