Medieval DNA from Soqotra points to Eurasian origins of an isolated population at the crossroads of Africa and Arabia

Abstract

Soqotra, an island situated at the mouth of the Gulf of Aden in the northwest Indian Ocean between African and Arabia, is home to ~60,000 people subsisting through fishing and semi-nomadic pastoralism who speak a Modern South Arabian language. Most of what is known about Soqotri history derives from writings of foreign travelers who provided little detail about local people, and the geographic origins and genetic affinities of early Soqotri people has not yet been investigated directly. We report genome-wide data from 39 individuals who lived between ~650–1750 CE at six locations across the island and document strong genetic connections between Soqotra and the similarly isolated Hadramawt region of coastal South Arabia that likely reflects a source for the peopling of Soqotra. Medieval Soqotri can be modeled as deriving ~86% of their ancestry from a population like that found in the Hadramawt today, with the remaining ~14% best proxied by an Iranian-related source with up to 2% ancestry from the Indian sub-continent, possibly reflecting genetic exchanges that occurred along with archaeologically documented trade from these regions. In contrast to all other genotyped populations of the Arabian Peninsula, genome-level analysis of the medieval Soqotri is consistent with no sub-Saharan African admixture dating to the Holocene. The deep ancestry of people from medieval Soqotra and the Hadramawt is also unique in deriving less from early Holocene Levantine farmers and more from groups like Late Pleistocene hunter-gatherers from the Levant (Natufians) than other mainland Arabians. This attests to migrations by early farmers having less impact in southernmost Arabia and Soqotra and provides compelling evidence that there has not been complete population replacement between the Pleistocene and Holocene throughout the Arabian Peninsula. Medieval Soqotra harbored a small population that exhibited qualitatively different marriage practices from modern Soqotri, with first-cousin unions occurring significantly less frequently than today.