Oldest Human DNA from Africa Illuminates Complex Migrations
Ancient DNA f from East Africa reveals migrations from Central Africa 50,000 years ago
A new paper in Nature1 was published today and the study is remarkable on several accounts.
The study analyzed ancient DNA from six individuals, two adults and four infants, buried across three different Subsaharan sites. The most impressive feat is that the authors were able to extract DNA from samples as old as 18,000 years old. This was possible because five of the remains contained the inner ear bones which are dense and preserve DNA well in unformidable climates.
This makes this study the oldest human DNA to date from Subsaharan Africa by over 9,000 years2!
Next, the authors analyzed the six ancient genomes to 28 others previously reported from across the continent. In total, their sample demonstrated these 34 people were derived from three major source populations. We could surmise that the northeastern and southern African roots are not as novel as these samples came from sites in modern-day Malawi, Tanzania, and Zambia. But the third population, which likely came from nomadic hunter-gatherers from Central Africa, came as a surprise and is another of the remarkable findings.
These ancestral populations had distinct genomes, suggesting isolation from one another before coming together. In fact, the authors were able to calculate that they were clearly separate 200,000 years ago and maybe 80,000 to 50,000 years ago they mixed. Around 20,000 years ago they diverged.
This is where the paper brings another remarkable line of evidence, the archaeological record, as the genetic commingling matches developments in material culture. See, stone tools found in their rock shelters take on a local flair around 20,000 years ago. Which is a finding covered in this newsletter, three months ago. Suggesting these people stayed close to home and did not exchange genes or material culture like they were doing before.
Overall, this is a high-quality study that demonstrates the successful extraction of the oldest ancient DNA to date from Subsaharan Africa, comparative genomic analysis, and integrates the archaeological record to bring multiple lines of evidence to their conclusion. While their conclusion fits with previous ancient and modern African DNA studies suggesting that mating among widespread human groups began 200,000 years ago or more3. I for one welcome the thorough approach they have taken.
What keeps me interested is that the authors leave a cliffhanger; hints of a “ghost” human population unknown from any fossils, but which contributed to the ancestry of ancient eastern Africans, also emerged in this new study which is something that has been suggested before4.
Lipson, M., Sawchuk, E.A., Thompson, J.C. et al. Ancient DNA and deep population structure in sub-Saharan African foragers. Nature (2022). https://doi.org/10.1038/s41586-022-04430-9
Skoglund, P., Thompson, J. C., Prendergast, M. E., Mittnik, A., Sirak, K., Hajdinjak, M., Salie, T., Rohland, N., Mallick, S., Peltzer, A., Heinze, A., Olalde, I., Ferry, M., Harney, E., Michel, M., Stewardson, K., Cerezo-Román, J. I., Chiumia, C., Crowther, A., … Reich, D. (2017). Reconstructing prehistoric African population structure. Cell, 171(1), 59-71.e21. https://doi.org/10.1016/j.cell.2017.08.049
Lipson, M., Ribot, I., Mallick, S. et al. Ancient West African foragers in the context of African population history. Nature 577, 665–670 (2020). https://doi.org/10.1038/s41586-020-1929-1
Durvasula, A., & Sankararaman, S. (2020). Recovering signals of ghost archaic introgression in African populations. Science Advances, 6(7), eaax5097. https://doi.org/10.1126/sciadv.aax5097