Ethiopian Genetic Diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool

Humans and their ancestors have traversed the Ethiopian landscape for millions of years and presentday Ethiopians show great cultural, linguistic and historic diversity, which makes them essential for understanding African variability and human origins. We genotyped 237 individuals from 10 Ethiopian and two neighboring (South Sudanese and Somali) populations on an Illumina Omni 1M chip. Genotypes were compared with published data from several African and non-African populations. PCA and STRUCTURE-like analyses confirmed substantial genetic diversity both within and between populations, and revealed a match between genetic data and linguistic affiliation. Using comparisons with African and non-African reference samples in 40-SNP genomic windows, we identified .African. and .non-African. haplotypic components for each Ethiopian individual. The non-African component, which includes the SLC24A5 allele associated with light skin pigmentation in Europeans, may represent gene flow into Africa, which we estimate to have occurred ~3 KYA. The African component was found to be more similar to populations inhabiting the Levant rather than the Arabian peninsula, but the principal route for the out-of-Africa expansion ~60 KYA remains unresolved. LD decay with genomic distance was less rapid in both the whole genome and the African component than in Southern African samples, suggesting a less ancient history for Ethiopian populations
Dataset of Pagani et al 2012