来自三个基因组的欧亚人群中尼安德特人混合物的最大似然证据
Maximum likelihood evidence for Neandertal admixture in Eurasian populations from three genomes
摘要：
虽然一直有很大的兴趣，估计分歧和混合物的基因组数据，它已被证明很难区分基因流后，分歧的替代历史，涉及在祖先的人口结构。由于缺乏正式的测试来区分这些场景，最近引发了关于尼安德特人和欧亚大陆现代人之间杂交的可能性的争议。我们推导出突变配置的概率在非重组序列块下的分歧与混合物和祖先结构的替代历史。将基因组分成短块使得在两种模型下计算参数的最大似然估计成为可能。我们将这种方法应用于三胞胎的人类尼安德特人基因组和量化的相对支持模型的长期人口结构的祖先非洲人口和混合物从尼安德特人到欧亚人口后，他们的扩张出非洲。我们的分析使我们-第一次-正式拒绝了祖先人口结构的历史，而是显示了强有力的支持，从尼安德特人到欧亚人口的混合率（3.4%-7.9%）比以前建议的更高。
英文摘要：
Although there has been much interest in estimating divergence and admixture from genomic data, it has proven difficult to distinguish gene flow after divergence from alternative histories involving structure in the ancestral population. The lack of a formal test to distinguish these scenarios has sparked recent controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. We derive the probability of mutational configurations in non-recombining sequence blocks under alternative histories of divergence with admixture and ancestral structure. Dividing the genome into short blocks makes it possible to compute maximum likelihood estimates of parameters under both models. We apply this method to triplets of human Neandertal genomes and quantify the relative support for models of long-term population structure in the ancestral African popuation and admixture from Neandertals into Eurasian populations after their expansion out of Africa. Our analysis allows us -- for the first time -- to formally reject a history of ancestral population structure and instead reveals strong support for admixture from Neandertals into Eurasian populations at a higher rate (3.4%-7.9%) than suggested previously.
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