Genomes From The Green Sahara

New genetics reveal an unknown divergent North African population

It’s probably common enough knowledge by now that the Sahara Desert was not always a desert. Between roughly 14-11,000 and 5,000 years ago the region was humid, full of lakes and rivers, shifting forest cover and open landscapes. Prior to this, during the peak of the ice age - the Last Glacial Maximum - the Sahara Desert had actually been much larger, extending further south. Africa was much colder and drier, and evidence for people living in the most arid areas is almost non-existent. As the temperature rose and the desert shrank, people began moving into the interior, taking advantage of new opportunities for food and river-based mobility.

The human composition of Africa at this time, and even before, is still unclear. Fossil evidence is very rare outside of the driest regions, and internal migrations have dramatically altered the picture from the time of the Green Sahara. What we do know is that the ancestral proto-Khoisan people split first from the main group of Homo sapiens around 250-200,000 years ago. Then the ancestral Pygmy or central African hunter-gatherers split around 150-100,000 years ago. Another branch sometimes called ‘basal West African hunter-gatherers’ adds a third layer to the puzzle, and of course the rest of us non-Africans all descend from those people who left Africa, who possess genetic signatures of mixing with other human species such as Neanderthals and Denisovans.

a, Timeline of climate phases and subsistence strategies during the late Pleistocene and the Holocene in North-East Africa and Central Sahara. The radiocarbon dates for both Takarkori individuals are given by the black diamond and circle. b,c, The distribution of ecozones in Northern Africa in the Green Sahara period during the early Holocene 9,000 years ago (b) and in recent times (1901–1930) (c) using the dynamic vegetation model Carbon Assimilation in the Biosphere (CARAIB). The location of the Takarkori rock shelter site is marked with a black square. The maps are adapted from refs. ²⁰ and ⁶⁰ under a Creative Commons licence CC BY 4.0.

The above image is taken from a new paper which examines several new genomes from “two approximately 7,000-year-old Pastoral Neolithic female individuals buried in the Takarkori rock shelter in southwestern Libya”. This paper, entitled Ancient DNA from the Green Sahara reveals ancestral North African lineage, proposes another African population which split very early and remained largely isolated until the introduction of pastoralism.

Exactly how much of a barrier the Sahara Desert was during prehistory has been debated. A paper published in 2018 sequenced the genomes of several stone age individuals (15,000 years old), from Taforalt in eastern Morocco. The authors detected a strong sub-Saharan African signal, around a third of the genome, however - they could not find a good contemporary sub-Saharan African (SSA) group to fit this model. Ancient population turnovers in SSA did occur, as seen by the Shum Laka genomes from Cameroon. These four child burials revealed two distinct dates of internment (8,000 years ago and 3,000 years ago). Genetically they possessed the oldest known male Y-chromosome haplogroup (A00), but had no relation to the later Bantu-speaking farmers who would eventually sweep across SSA down to the tip of the Cape and across the Indian Ocean.

The new Takarkori genomes in this 2025 paper revealed that they possessed the maternal haplogroup N, which is a very old group, and descends from the oldest mitochondrial haplogroup within the sapien species - L. Although the N clade is more often found outside Africa, even in Australia and North America, it does not appear in SSA, except very rarely. This indicates that the ancestral Takarkori population split very early, much like the Khoisan and Pygmies. Their genomes showed no evidence of admixture with sub-Saharan Africans. However, they do show ancestral relations with the Moroccan Taforalt foragers, as well as individuals from Ifri Ouberrid and Ifri n’Amr o’Moussa. In the words of the researchers:

The individuals from the Takarkori rock shelter predominantly carry an ancestral African lineage, representing an ancestry profile that has not been previously described. They share the most genetic drift with Epipalaeolithic and Early Neolithic individuals from Ifri Ouberrid and Ifri n’Amr o’Moussa, as well as the 15,000-year-old foragers from the Taforalt Cave in Morocco, 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, and the Takarkori individuals inherited it from the group that inhabited the area during the final period of the Late Acacus (10,200–8,000 cal. bp). In Southwestern Libya, this period preceded the arrival of domesticates and is characterized by cultural advancements within those hunter–gatherer groups

The colour gradient from blue to green indicates the genetic proximity to Takarkori, with the bluer colours representing closer genetic relationships.

The nearby Natufians have an important role to play in the story of the later Green Sahara. These are the Levantine people who were the first to domesticate cereal grains, leading to the beginning of agriculture in the Near East and beyond. They also helped spread cattle and other domesticate pastoralism south into Africa, down the Nile at first and then outwards west and south. The introduction of cattle into Africa had a momentous legacy, including on the formation of the Nilotic, Cushitic and Khoi people. The Takarkori genomes show a small amount of genetic admixture with Levantine Natufians, who also brought trace amounts of Neanderthal DNA with them. However, the amounts are so small that the authors argue it points to pastoralism spreading as an economic model, rather than through an invasion of peoples.

We found that individuals from Takarkori exhibit only a marginal amount of genetic admixture from Levantine groups, suggesting that the emergence of pastoralism in the Sahara was primarily driven by the dissemination of cultural practices rather than through large-scale human migration, as suggested on archaeological basis¹⁰. Material culture at the onset of the earliest pastoral period shows both continuity and change, reflecting possibly complex assimilation dynamics during socioeconomic transitions^10,19. These patterns may further suggest gradual cultural transformations rather than abrupt population replacement. This interpretation is further supported by the comparatively lower levels of Neanderthal genetic admixture found in the Takarkori individuals.

Through this analysis of just two individual genomes, we now know that North Africa likely had a highly divergent population of hunter-gatherers who did not leave the continent, but remained and spread out to the coastlines. After the Ice Age ended and the desert shrank, these people came back to the central regions and eventually adopted pastoralism as a way of life. Despite the opportunities the Green Sahara offered, the Takarkori people showed no signs of mixing with other people to their south, but rather looked northeast to the Nile and the new cattle-breeding cultures which came out of the Natufian-Afroasiatic zone.