Two women buried 7,000 years ago in a Libyan rock shelter have no business being genetically mysterious. They lived during the African Humid Period, a stretch of millennia when the Sahara Desert transformed into a green savannah with lakes, rivers, and grasslands that supported human settlements, fishing, and livestock herding across what is now one of Earth’s most arid regions.
Yet their DNA, extracted from naturally mummified remains at the Takarkori rock shelter, tells a story that contradicts what researchers expected to find. The genomes show these pastoralist herders belonged to a previously unknown North African lineage that remained isolated for tens of thousands of years, showing no meaningful genetic influence from sub-Saharan populations to the south or from Near Eastern and European groups to the north.
View from the Takarkori rock shelter in Southern Libya. © Archaeological Mission in the Sahara, Sapienza University of Rome
The finding, detailed in a new study published in the journal Nature, upends the long-held assumption that the Green Sahara served as a migration corridor connecting African populations. “This suggests they remained genetically isolated despite practicing animal husbandry, a cultural innovation that originated outside Africa,” Johannes Krause, a geneticist at the Max Planck Institute for Evolutionary Anthropology and senior author of the study, told Reuters.
A Lineage Frozen in Time
The Takarkori individuals carry ancestry that diverged from sub-Saharan African populations roughly 50,000 years ago. That split occurred around the same time that modern human lineages began spreading beyond Africa into the Middle East, Europe, and Asia.
Krause described the genomes as “almost like living fossils” in an interview with BBC Science Focus. “If you’d told me these genomes were 40,000 years old, I would have believed it,” he said. The official press release from the Max Planck Institute noted that the newly described lineage remained isolated, revealing deep genetic continuity in North Africa during the late Ice Age.
7,000-year-old natural mummy found at the Takarkori rock shelter (Individual H1) in Southern Libya. © Archaeological Mission in the Sahara, Sapienza University of Rome
The genetic isolation preserved in these two women, both in their 40s when they died, appears to have persisted throughout their lineage’s existence. When researchers analyzed their Neanderthal ancestry, they found only trace amounts, approximately 0.15 percent of the genome.
That figure is ten times lower than what appears in Levantine farmers and other populations outside Africa. It is, however, measurably higher than what contemporary sub-Saharan African genomes contain, suggesting ancient but extremely limited contact with groups beyond North Africa.
Herders Who Learned Rather Than Migrated
Archaeological work at the site, located in the Tadrart Acacus Mountains of southwestern Libya near the Algerian border, has uncovered a rich record of human occupation. The rock shelter contains 15 burials spanning from Late Acacus hunter-gatherer-fishers around 10,200 years ago through a long Pastoral Neolithic period that ended approximately 4,200 years ago.
The two women selected for ancient DNA analysis came from the Middle Pastoral Period. Their remains were naturally mummified, with skin, ligaments, and tissues still intact. Excavators also recovered stone tools, wooden implements, animal bone artifacts, pottery, woven baskets, and carved figurines from the shelter.
Anotherview of the Takarkori rock shelter in Southern Libya. © Archaeological Mission in the Sahara, Sapienza University of Rome
The genetic findings answer a question archaeologists have debated for years: Did pastoralism spread across the Green Sahara through migrating herders or through cultural transmission? The Takarkori genomes point decisively toward cultural diffusion. Local populations adopted livestock herding techniques, including the management of goats and sheep, without being genetically replaced by outside groups.
Nada Salem, a researcher at the Max Planck Institute for Evolutionary Anthropology and first author of the study, said the discovery “reveals how pastoralism spread across the Green Sahara, likely through cultural exchange rather than large-scale migration.”
Rewriting the Taforalt Equation
The Takarkori genomes also clarify the ancestry of a much older North African population. The 15,000-year-old foragers from Taforalt Cave in Morocco, associated with the Iberomaurusian lithic industry, have long puzzled geneticists. Previous research modeled Taforalt ancestry as roughly 63.5 percent Natufian from the Levant and 36.5 percent from an unidentified sub-Saharan African source.
The new analysis replaces that unknown component. The African ancestry in Taforalt individuals now appears to derive from a Takarkori-like North African lineage rather than any sub-Saharan population. The revised model estimates Taforalt ancestry at approximately 60 percent Natufian and 40 percent Takarkori-related.
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. © Nature/Creative Commons
Both the Takarkori and Taforalt groups stand equally distant from sub-Saharan African lineages. This genetic distance suggests that even when the Sahara bloomed with vegetation and water, substantial gene flow between North African and sub-Saharan populations did not occur. The desert’s greening did not translate into a human migration highway.
Traces That Survived the Desert’s Return
The Takarkori lineage itself vanished around 5,000 years ago. The African Humid Period ended, the Sahara resumed its arid state, and the isolated population disappeared from the archaeological record. But their genetic signature did not vanish completely.
Modern North African groups still carry traces of this ancestry. The study also detected increased genetic affinity between the Takarkori lineage and certain Sahelian populations, including Fulani herders from multiple countries. This connection aligns with archaeological evidence showing pastoralist groups moved southward from the Central Sahara as the region dried. The researchers were surprised by the lack of gene flow, as many had theorized the Green Sahara was a human migration corridor.
Mary Prendergast, an anthropologist at Rice University who was not involved with the research, wrote in an accompanying commentary that studies like this are “just beginning to reveal Africa’s complex population history, uncovering lineages barely detectable in the genomes of present-day people.” She noted that “even small sample numbers can shape our understanding of the past.”
The human remains from Takarkori are curated at the Museum of Anthropology of the University of Rome, La Sapienza.