Ancient Subsaharan African DNA

Not so long ago there was doubt that we'd every get ancient DNA from Sub-Saharan Africa. A new open access paper with a score of new samples (many quite old) discusses almost all of the African ancient DNA data currently available (85 samples), which, while not abundant, is enough to clarify (and add mystery to) the population genetic history of Africa. The abstract of the paper in Science Advances is as follows:

Africa hosts the greatest human genetic diversity globally, but legacies of ancient population interactions and dispersals across the continent remain understudied. Here, we report genome-wide data from 20 ancient sub-Saharan African individuals, including the first reported ancient DNA from the DRC, Uganda, and Botswana. These data demonstrate the contraction of diverse, once contiguous hunter-gatherer populations, and suggest the resistance to interaction with incoming pastoralists of delayed-return foragers in aquatic environments. We refine models for the spread of food producers into eastern and southern Africa, demonstrating more complex trajectories of admixture than previously suggested. In Botswana, we show that Bantu ancestry post-dates admixture between pastoralists and foragers, suggesting an earlier spread of pastoralism than farming to southern Africa. Our findings demonstrate how processes of migration and admixture have markedly reshaped the genetic map of sub-Saharan Africa in the past few millennia and highlight the utility of combined archaeological and archaeogenetic approaches.

For reference purposes, Bantu expansion is generally consider an "Iron Age" event.

Bernard's Blog discusses a new sub-Saharan African ancient DNA paper (translation via Google), and I quote from Bernard below. It will take considerably greater analysis to fit this into the paradigm to see where it supports it, and where it supposed different narratives. 

Ke Wang and his colleagues have just published a paper entitled: Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa . They sequenced the genomes of twenty skeletons from Kenya (10 in red below), Congo (5 in blue), Uganda (1 in orange) and Botswana (4 in green) dated between 3900 and 150 years old:

The Principal Component Analysis:

Admixture data:

The figure above shows in particular that if the Levantine ancestry (in red) is fairly constant between 30 and 40% among pastoralists in East Africa the two other components: hunter-gatherer (in light blue) and Dinka (in dark blue) vary greatly from one individual to another. In addition, estimates of the dating of genetic mixtures suggest that genetic mixtures between pastors and hunter-gatherers have occurred regularly in Kenya. It is therefore likely that communities of hunter-gatherers and pastoralists have lived in parallel in the region for a long time. Furthermore, if there is indeed a flow of genes from hunter-gatherer populations to pastoralists, the reverse is not verified.

Two individuals from the Iron Age Kakapel archaeological site in Kenya dated 900 and 300 years show strong Dinka ancestry in the figure above and strong Bantu affinity on the PCA. In addition, one of the two individuals has a small proportion of Levantine ancestry, thus suggesting the complexity of the interactions that took place in the Iron Age in Africa. In addition, an individual from the Congo dated 750 years has a very high proportion of hunter-gatherer ancestry and adds to the complexity of the different interactions. Finally, the 500-year-old Ugandan individual shows a strong affinity with Bantu farmers. Several different livelihood groups entered East Africa during this period.

The four genomes of Botswana make it possible to investigate the arrival of agriculture in South Africa. Their position on the PCA highlights the high proportion of Bantu ancestry they have. These results are confirmed by the figure indicating the proportions of ancestry above. However, Botswana individuals have between 10 and 40% hunter-gatherer ancestry from South Africa. However, the best determined model shows that the South African source is not the same according to the individuals of Botswana. If the source corresponds to a hunter-gatherer of 2000 years for certain individuals, it corresponds to a hunter-gatherer of 1200 years for others. This latter ancestry is actually the result of a genetic mix between hunter-gatherers of South Africa and the pastors of East Africa. This thus suggests a first dissemination of pastors in South Africa followed by the dissemination of Bantu farmers. These results are also reflected in the archaeological evidence in South Africa which shows great diversity. Different and specific interactions between populations have taken place depending on the region.