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

real expert

Regular Member
Reaction score
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 Africa1,2,3,4. 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.

Demographic transformations in the past approximately 5,000 years have fundamentally altered regional population structures and largely erased what was, by the Late Pleistocene, a well-established three-way cline of eastern-, southern- and central-African-related ancestry that extended across eastern and south-central Africa. Groups who historically forage have frequently been pushed to marginal environments and have experienced transformative demographic changes, making it difficult to learn about deep history from present-day DNA. Today, Africa houses the greatest human genetic diversity, but undersampling of both living and ancient individuals obscures the origins of this diversity40. We show that aDNA from tropical Africa can survive from the Pleistocene and reveal patterns that could not be inferred from populations that lived even a few millennia later, underscoring the breadth of African genetic diversity and the importance of eastern and south-central Africa as long-term reservoirs of human interaction and innovation.

Uniparental markers

All four newly reported males are similar to most published ancient foragers from this region of Africa in carrying the widely distributed Y chromosome haplogroup B2 (Extended Data Table 1). Among the 23 individuals in our dataset with known mtDNA haplogroups, up to 14—almost all from Kenya and Tanzania—have haplogroups that are today associated with eastern Africa (Extended Data Table 1 and Supplementary Table 6). Eight individuals—all from Malawi and Zambia—have haplogroups that are associated with some ancient and present-day southern African people, specifically groups for whom foraging is the main mode of subsistence17,18,19,20. Two individuals from Malawi (I19529 from Hora 1, dating to about 16 ka and carrying L5b, and I4426 from Fingira, dating to about 2.3 ka and carrying L0f/L0f3) have eastern-Africa-associated haplogroups, whereas a different individual from Malawi (I2967 from Hora 1, dating to about 8.2 ka with L0a2/L0a2b) and possibly one from Kenya (I8930 from White Rock Point with L2a4) belong to lineages that are characteristic of present-day central African foragers (such as Mbuti and Aka). These results show that eastern and south-central Africa was home to, and an area of interaction among, diverse ancient foraging groups, and also that several of these haplogroup lineages were formerly more widespread than they are today.

The study also reanalyzed published data from 28 individuals buried at sites across the continent, generating new and improved data for 15 of them. The result was an unprecedented dataset of DNA from ancient African foragers—people who hunted, gathered or fished. Their genetic legacy is difficult to reconstruct from present-day people because of the many population movements and mixtures that have occurred in the last few thousand years.


Fig. 2: Schematic of admixture graph results.

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


Branch lengths are not to scale. The arrows denote admixture events, with the three primary components of ancestry shown as dashed arrows, and other inferred gene flow as small solid arrows (with colours corresponding to related groups). Subclusters of ancient eastern and south-central African foragers reflect the inferred instances of excess relatedness among individuals, with internal branch lengths shown in genetic-drift units. Mixture proportions are shown in Fig. 3 and Supplementary Table 9 and the full results are shown in Extended Data Fig. 4. Individual laboratory numbers are shown at the bottom (Extended Data Table 1). N., north; W., west.

This thread has been viewed 1638 times.