Here we present first genome-wide data obtained from the same two approximately 7,000-year-old Saharan herders, recovered from the Takarkori rock shelter in the Central Sahara.... suggesting a long-standing and stable population in North Africa before the AHP (14,500–5,000 bp). Plausibly, this ancestry was present in large parts of Northern Africa after the OoA event,...Furthermore, the Takarkori individuals exhibit a close genetic affinity to Northwestern African foragers but no substantial ties with sub-Saharan African lineages, implying no detectable genetic exchange across the Green Sahara during the AHP from sub-Saharan to northern Africa.
This pattern suggests that no substantial genetic exchanges across the Green Sahara occurred during the AHP [ African Humid Period (AHP) between 14,500 and 5,000 years ]or other humid periods preceding the Later Pleistocene. The Sahara, spanning around 9 million km2 and housing diverse biomes, such as grasslands, wetlands, woodlands, lakes, mountains and savannas55,56, probably saw fragmented habitats impacting human gene flow. These ecological barriers, combined with social and cultural barriers, spatial structuring of populations, and the selective adoption of specific practices, may have facilitated the widespread dissemination of similar archaeological features57,58, while limiting extensive genetic admixture. This genetic discontinuity is consistent with modern data, which show substantial genetic differentiation across the Sahara beyond just a geographical gap59. Our findings suggest that sporadic Green Sahara events, particularly before pastoralism, were insufficient to allow for considerable genetic exchange, mirroring the Sahara’s persistent role in limiting human genetic flow, as reflected in both ancient and modern population structures.
https://www.nature.com/articles/s41586-025-08793-7
t ancient genomic data from the Central Sahara, obtained from two approximately 7,000-year-old Pastoral Neolithic female individuals buried in the Takarkori rock shelter in southwestern Libya. The majority of Takarkori individuals’ ancestry stems from a previously unknown North African genetic lineage that diverged from sub-Saharan African lineages around the same time as present-day humans outside Africa and remained isolated throughout most of its existence.
Both Takarkori individuals are closely related to ancestry first documented in 15,000-year-old foragers from Taforalt Cave, Morocco2, associated with the Iberomaurusian lithic industry and predating the AHP. Takarkori and Iberomaurusian-associated individuals are equally distantly related to sub-Saharan lineages, suggesting limited gene flow from sub-Saharan to Northern Africa during the AHP. In contrast to Taforalt individuals, who have half the Neanderthal admixture of non-Africans, Takarkori shows ten times less Neanderthal ancestry than Levantine farmers, yet significantly more than contemporary sub-Saharan genomes.
Ancient DNA data from northwestern Africa points to a stable and isolated genetic population from at least 15,000 to 7,500 years ago2,8.
This stability was disrupted by the arrival of early farming groups from southwestern Europe between 7,500 and 5,700 years ago who marked the beginning of the Neolithic in the Maghreb by introducing farming practices to the local foragers9. The earliest herders with their livestock entered Africa probably along the Sinai and the Red Sea routes, after which they rapidly spread into northeastern Africa and reached the Central Sahara around 8,300 years ago10. By 6,400 years ago, further gene flow occurred with the appearance of ancestry associated with Neolithic groups from the Levant, whose archaeological signatures are visible in the Eastern Sahara9,11,12.
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