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Genetic evidence for archaic admixture in Africa

机译：非洲古混合气的遗传证据

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A long-debated question concerns the fate of archaic forms of the genus Homo: did they go extinct without interbreeding with anatomically modern humans, or are their genes present in contemporary populations? This question is typically focused on the genetic contribution of archaic forms outside of Africa. Here we use DNA sequence data gathered from 61 noncoding autosomal regions in a sample of three sub-Saharan African populations (Mandenka, Biaka, and San) to test models of African archaic admixture. We use two complementary approximate-likelihood approaches and a model of human evolution that involves recent population structure, with and without gene flow from an archaic population. Extensive simulation results reject the null model of no admixture and allow us to infer that contemporary African populations contain a small proportion of genetic material (=2%) that introgressed =35 kya from an archaic population that split from the ancestors of anatomically modern humans =700 kya. Three candidate regions showing deep haplotype divergence, unusual patterns of linkage disequilibrium, and small basal clade size are identified and the distributions of introgressive haplotypes surveyed in a sample of populations from across sub-Saharan Africa. One candidate locus with an unusual segment of DNA that extends for >31 kb on chromosome 4 seems to have introgressed into modern Africans from a now-extinct taxon that may have lived in central Africa. Taken together our results suggest that polymorphisms present in extant populations introgressed via relatively recent interbreeding with hominin forms that diverged from the ancestors of modern humans in the Lower-Middle Pleistocene.
机译：一个长期争论的问题是人类的古老形式的命运：它们是在没有与现代解剖学人类杂交的情况下灭绝的，还是它们的基因存在于当代人群中？这个问题通常集中在非洲以外的古形式的遗传贡献。在这里，我们使用从三个撒哈拉以南非洲人口（曼登卡，比亚卡和圣桑）的样本中的61个非编码常染色体区域收集的DNA序列数据来测试非洲古混合物的模型。我们使用两种互补的近似似然方法和一种人类进化模型，该模型涉及到最近的种群结构，有无古细菌的基因流。大量的模拟结果拒绝了没有混合的零模型，并允许我们推断当代非洲人口包含一小部分的遗传物质（= 2％），该遗传物质来自与解剖现代人类祖先分开的古种群= 35 kya。 700千确定了三个候选区域，这些区域显示出很强的单倍型差异，连锁不平衡的异常模式和小的基部进化枝大小，并且在整个撒哈拉以南非洲地区的人口样本中调查了渐渗单倍型的分布。一个候选基因座的一个不寻常的DNA片段在第4号染色体上延伸了> 31 kb，似乎已经从一个可能已经生活在非洲中部的现已灭绝的分类单元渗入了现代非洲人的视野。综上所述，我们的研究结果表明，现存种群中存在的多态性是通过相对较近的人糖蛋白形式与现代中下更新世祖先的人源杂交而渗入的。

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