Abstract
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.
Highlights
The timing and extent of migration and admixture are questions that are central to the entire scope of human evolutionary history from the origin of our species to the present day
Historical, and linguistic evidence for contact with nonAfrican populations beginning about 3,000 years ago, it has often been assumed that the non-African ancestry in Horn of Africa (HOA) populations dates to this time
We find that the genetic composition of non-African ancestry in the HOA is distinct from the genetic composition of current populations in North Africa and the Middle East
Summary
The timing and extent of migration and admixture are questions that are central to the entire scope of human evolutionary history from the origin of our species to the present day. The most important event underlying human population structure is the origin of anatomically modern humans in Africa and their subsequent migration around the globe [1,2,3]. Beginning around 11 ka (thousand years ago), the switch to reliance on domesticated plants and animals is associated with major population and language expansions from multiple centers of domestication around the world [8,9,10]. Migration and admixture accelerated during the last few thousand years with increasing international trade, including the trade in slaves and the transplantation and shuffling of populations in the colonial era, culminating in the modern era of high international migration.
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