Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups. The Vaalkrans man

Previous studies show that the indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting ~400 years ago and their descendants are today mixed with Europeans and Asians. To gain insight on the occupants of the shelter, we investigated the genetic make-up of an individual who lived about 200 years ago on the southernmost tip of Africa. We further contextualize the genetic ancestry of this individual among prehistoric and current groups.We sequenced and analyze the genome (1.01 times coverage) of a Later Stone Age individual, who lived about 200 years ago, obtained from a hair sample excavated at Vaalkrans Shelter, southern Cape, South Africa. We analyzed this genome, along with genetic data from 10 ancient, pre-colonial individuals from southern Africa spanning the last 2000 years.We show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter-gatherer populations, and ~20% to a mixed East African-Eurasian source. This genetic make-up is similar to modern-day Khoekhoe individuals from the Northern Cape Province (South Africa) and Namibia, but in the southern Cape, the Vaalkrans man’s descendants have likely been assimilated into mixed-ancestry ‘Coloured’ groups.The Vaalkrans man’s genome reveals that Khoekhoe pastoralist groups lived in the southern Cape as late as 200 years ago, without mixing with non-African colonists or Bantu-speaking farmers. It is also consistent with the model of a Holocene pastoralist migration, originating in Eastern Africa, shaping the genomic landscape of historic and current southern African populations..