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.New SNP data for 64 YemeniContains the complete unfiltered new genotype data from 64 Yemeni samples in a binary PED (BED) file format (compatible with PLINK). These samples were collected by Connie Mulligan, Ali Al-Meeri, and Ryan Raaum in the spring of 2007 in Yemen with grant support from NSF BCS-0518530 to Connie Mulligan. These samples were genotyped on the Illumina Human CNV370-Quad V3.0 Beadchip. The chromosome and map location information in the bed map file are as provided in the Illumina documentation for this chip. As of April 22, 2014, Illumina has information on this chip at: http://support.illumina.com/downloads/humancnv370-quad_v30_product_files.ilmnyemen.zi