Ancient DNA and deep population structure in sub-Saharan African foragers

Abstract from this paper from Nature

Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa1–4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations3,5. Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80–20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.

From commentary here:

Ancient DNA dating to between 16,000–18,000 years ago—the oldest human DNA to be extracted in Africa so far—reveals that populations of hunter-gatherers mixed and mingled 50,000 to 20,000 years ago, moving long distances across the continent. This supports the idea that demographic changes played a role in the transition from the Middle to the Later Stone Age, a time when new types of tools emerged and information was exchanged over long distances, a study published today (February 23) in Nature reports. 

The study presents genome-wide data from three individuals living in the Late Pleistocene, the period between 120,000 and 12,000 years ago. The researchers also analyzed the genomes of three people who lived in the Holocene, the period that began about 12,000 years ago

The researchers looked at the ancestry of the six newly sequenced individuals and 28 other individuals who had lived between 8,000 and 400 years ago in various parts of sub-Saharan Africa and whose genetic data had previously been published. Surprisingly, all 34 individuals were descended from the same three genetic lineages from eastern, southern, and central Africa. “The fact that all of these individuals are descended from the same three lines suggests that in the past, we had this big period of mixing and moving,” explains Sawchuk. “It was a tens of thousands of years process that involved many, many people moving over many, many generations­—it was a transformation in the way that hunter-gatherers were living in Africa.” 

Based on the genetics, the authors conclude that “this wasn’t just things moving, this was people moving long distances, taking eastern African ancestry all the way to the tip of South Africa, southern African ancestry to Ethiopia, and then central African ancestry throughout,” Sawchuk says. The only way this can be explained, she adds, is that people were moving long distances and finding partners far away from their birthplaces, creating what she calls “globalization,” and changing the genetic landscape. “We would have never seen this without DNA.” 

From the Blog’s POV:

This study illuminates the social structure of a previously unknown period from 80 to 20 thousand years ago. during that time their was diffuse interbreeding across the entire continent of Africa, and (from other sources) there is little (although not none) evidence of group violence during that time. So populations peacefully and actively interacted continent-wide during this period. By 20,000 years ago, populations became more regionalized, but still covered very large areas.

This dovetails with evidence presented in The Dawn of Everything that preceding the dynasties of Mesopotamia, Egypt, and in America, the Aztecs and Incas, all of which are characterized by monumental architecture, human sacrifice, and chronic war, there existed large settlements which interbred over wide-ranging areas, without evidence of hierarchy, with far-ranging intercourse and little evidence for war or violence. People could leave an abusive situation and expect hospitality over the entire far-flung settlement throughout which all considered themselves one people. These settlements were peaceful until, on the geographic fringes, charismatic politicians seized control of populations by intimidation via regular public killing of their retinue, which, in dynastic cultures became ritualized..

Tags: ancient DNA, human sacrifice, prehistoric Africa