The Entwined African and Asian Genetic Roots of the Medieval Peoples of the Swahili Coast

The peoples of the Swahili coast of eastern Africa established a literate urban culture by the second millennium CE. They traded across eastern Africa and the Indian Ocean and were among the first sub-Saharan practitioners of Islam. An open question has been the extent to which these early interactions between Africans and non-Africans were accompanied by genetic admixture. We report ancient DNA data from 80 individuals deriving from six medieval and early modern (1300-1800 CE) coastal towns as well as from an inland town postdating 1650 CE. Many coastal individuals for whom we could perform high-resolution analysis had over half of their DNA derived from primarily female African ancestors, with large proportions and occasionally more than half coming from Asian ancestors. The Asian ancestry included both Persian-associated and Indian-associated components, with eighty to ninety percent deriving from Persian males and ten to twenty percent from Indian females. Peoples of African and Asian origins began to mix by around 1000 CE, a time when archaeological evidence documents changes on the coast that are often interpreted as marking the large-scale adoption of Islam. Before roughly 1500 CE, the Near Eastern ancestry detected in the individuals was mainly Persian-related, consistent with the narrative of the Kilwa Chronicle, the oldest history told by people of the Swahili coast. After this time, the sources of Near Eastern ancestry became increasingly Arabian, consistent with the archaeological and historical evidence of growing interactions between the Swahili coast and parts of southern Arabia. Subsequent interactions of Swahili coast peoples with Asian and African groups further changed the ancestry of present-day peoples relative to the ancient individuals whose DNA we sequenced.