Structure and ancestry patterns of Ethiopians in genome-wide autosomal DNA

Ethiopia is strategically located between Africa and Eurasia and has populations that speak languages belonging to Afroasiatic and Nilo-Saharan language families. Previous genetic studies of Ethiopians mainly used mitochondrial DNA and Y-chromosomes and led to different, even conflicting, conclusions about population relationships. More recent studies using ancestry informative markers (AIMs) provided better insights into the population structure and admixture patterns of Ethiopians, but did not fully capture the complexity of the genetic landscape in Ethiopia. Here, we studied autosomal DNA of 506 individuals from 12 Ethiopian populations as well as neighboring populations from Eritrea, Somalia, and Egypt using Illumina HumanOmni2.5 BeadChips and compared with North African, Middle Eastern, sub-Saharan African and European populations. We found that gene flow from non-Africans into the Cushitic-speaking populations of Ethiopia can be modeled as originating from Egypt, with possible ultimate ancestry from the Levant. The Omotic-speaking populations, however, lack this ancestry component and were found to be more similar to neighboring sub-Saharan populations. The Semitic-speaking Amhara and Tigray populations have additional European ancestry that could be linked to a Medieval migration event. Notably, the genetic structures inferred from the autosomal data were more consistent with the geographic distributions and linguistic relationships of the Ethiopian populations compared to conclusions from uniparental markers.