Data from: Early back-to-Africa migration into the Horn of Africa

Genetic studies have identified substantial non-African admixture in the Horn of Africa (HOA). In the most recent genomic studies, this non-African ancestry has been attributed to admixture with Middle Eastern populations during the last few thousand years. However, mitochondrial and Y chromosome data are suggestive of earlier episodes of admixture. To investigate this further, we generated new genome-wide SNP data for a Yemeni population sample and merged these new data with published genome-wide genetic data from the HOA and a broad selection of surrounding populations. We used multidimensional scaling and ADMIXTURE methods in an exploratory data analysis to develop hypotheses on admixture and population structure in HOA populations. These analyses suggested that there might be distinct, differentiated African and non-African ancestries in the HOA. After partitioning the SNP data into African and non-African origin chromosome segments, we found support for a distinct African (Ethiopic) ancestry and a distinct non-African (Ethio-Somali) ancestry in HOA populations. The African Ethiopic ancestry is tightly restricted to HOA populations and likely represents an autochthonous HOA population. The non-African ancestry in the HOA, which is primarily attributed to a novel Ethio-Somali inferred ancestry component, is significantly differentiated from all neighboring non-African ancestries in North Africa, the Levant, and Arabia. The Ethio-Somali ancestry is found in all admixed HOA ethnic groups, shows little inter-individual variance within these ethnic groups, is estimated to have diverged from all other non-African ancestries by at least 23 ka, and does not carry the unique Arabian lactase persistence allele that arose about 4 ka. Taking into account published mitochondrial, Y chromosome, paleoclimate, and archaeological data, we find that the time of the Ethio-Somali back-to-Africa migration is most likely pre-agricultural.

遗传学研究已在非洲之角（Horn of Africa, HOA）中发现了显著的非非洲裔混血现象。在最新的基因组学研究中，这类非非洲血统被归因于近数千年来与中东人群的混血事件。不过，线粒体DNA与Y染色体数据却暗示了更早的混血事件。为进一步探究该问题，本研究为也门人群样本生成了全新的全基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据，并将这些新数据与已发表的非洲之角人群全基因组遗传数据，以及涵盖周边多个群体的广泛遗传数据集进行整合。本研究通过多维标度（Multidimensional Scaling, MDS）与ADMIXTURE分析方法开展探索性数据分析，旨在构建非洲之角人群混血与群体结构相关的研究假说。这些分析结果表明，非洲之角人群中可能存在分化显著的非洲与非非洲血统。在将单核苷酸多态性数据划分为非洲起源与非非洲起源的染色体片段后，我们证实非洲之角人群中存在独立的非洲埃塞俄比亚型（Ethiopic）血统与非非洲埃塞俄比亚-索马里型（Ethio-Somali）血统。这类非洲埃塞俄比亚型血统仅局限于非洲之角人群，大概率代表了非洲之角的本土原生人群。非洲之角人群中的非非洲血统主要源自一个全新的埃塞俄比亚-索马里型推断血统组分，且该血统与北非、黎凡特及阿拉伯地区的所有邻近非非洲血统均存在显著分化。埃塞俄比亚-索马里型血统存在于所有混血的非洲之角族群中，在该类族群内部几乎不存在个体间差异；经估算，该血统与其他所有非非洲血统的分化时间至少可达2.3万年，且不携带约4千年前出现的阿拉伯地区特有乳糖耐受等位基因。结合已发表的线粒体DNA、Y染色体数据、古气候与考古学资料，本研究认为埃塞俄比亚-索马里型血统的非洲回迁事件大概率发生在农业起源之前。