Ancient South African DNA

A new paper on South African ancient DNA isn't paradigm shifting but does pin down more precisely when outsiders from different places began to admix with local hunter-gatherers and the extent to which that mixture involved mostly male outsiders who replaced a significant share of local hunter-gatherer men in the gene pool. 

Most admixture between South African hunter-gatherers, West African derived Bantus, and East African herders, took place starting around roughly 900 CE to 1500 CE (i.e. during the European Middle Ages). European admixture with Southern Africans begins in earnest around 1800 CE. All of this admixture with outsiders was male outsider dominated.

Joscha Gretzinger, et al., "9,000 years of genetic continuity in southernmost Africa demonstrated at Oakhurst rockshelter" (October 2024) provides ancient DNA from 10,000 to 1,300 years old (based upon radiocarbon dates) from the Southern tip of South Africa. (Hat tip to Bernard).

The Khoi-San hunter-gatherers of Southern Africa have largely been forced into the Kalahari desert to the north, but still have a north-south cline genetically, and these ancient DNA samples are towards the southern edge of that cline, although not at the actual bottom of it, as one might expect, with the greatest similarity to the Khomani San (who are part of the Tuu linguistic family).

Bernard recounts from the paper (as translated from the French by Google) that:

None of these individuals have any genetic affinity with other African populations, even the most recent dated 1300 years ago, suggesting that the non-San component arrived in South Africa more recently than 1300 years ago. On the other hand, all the ancient Oakhurst individuals older than 4000 years ago as well as the other ancient South Africans from St. Helena, Faraoskop and Ballito Bay, dated between 2200 and 1300 years ago, are genetically indistinguishable. 

Then the authors highlighted a genetic discontinuity between 1300 and 400 years ago relative to the arrival of populations from northeastern Africa in South Africa. All these results suggest a very strong genetic continuity between 10,000 and 1300 years ago in South Africa, while the Oakhurst population does not show any sign of particular isolation as shown by the analysis of heterozygous segments.

The authors then investigated recent genetic admixtures in South Africa with the Northeast and West African components. To do this, they used the qpAdm software on contemporary San, Khoe and Bantu individuals with no European ancestry. They thus highlighted the older arrival of the Northeast African component (1068 years on average) compared to the arrival of the West African component (808 years on average among Bantu populations and 578 years among San and Khoe populations). This last result suggests the arrival of several waves of Bantu migration in South Africa, or a continuous flow of arrival of this population over several centuries:

On the other hand, the authors highlighted a sexual bias in these genetic admixture events. Thus, the San, Khoe and Bantu populations have more South African components in the X chromosome than in the autosomes, suggesting that there are more San women than men among the ancestors of contemporary populations, and therefore more men than women from Northeast Africa or West Africa. The ratio of the number of San women to the number of San men among the ancestors of current populations is estimated at 1.4 for the Damara population, 2.28 for the Hoan population, 4 for the Shua population, 5.2 for the Haiom population and 2.1 for the Bantu population of South Africa.

Finally, the authors highlighted a recent sexual bias corresponding to the arrival of men from Northwestern Europe in South Africa dated on average 199 years ago.

As another recent paper demonstrated, Southern African hunter-gatherers were genetically isolated from other modern humans for about 300,000 years (until about 1,100 years ago as indicated by this paper).