About 7,000 years ago, the Sahara desert was green, and now we know who lived there

About 7,000 years ago, two women were laid to rest in a rocky shelter in today’s southwestern Libya. Their remains have now yielded the first ancient human genomes ever recovered from the central Sahara.

An international study finds that these women carried a long isolated North African lineage now erased as a separate group. Their DNA also helps redraw the map of how people moved, or did not move, across a greener Sahara.

Takarkori rock shelter revelations

The work was led by Nada Salem, a geneticist at the Max Planck Institute for Evolutionary Anthropology (MPIEA) in Germany. Her research focuses on using ancient DNA, genetic material recovered from long dead organisms, to reconstruct population history in Africa.

Pollen and lake records show that between roughly 14,500 and 5,000 years ago, northern Africa was much wetter than today. Researchers call this the African Humid Period.

The Takarkori rock shelter sits in the Tadrart Acacus Mountains, overlooking what used to be a lush savanna dotted with small lakes.

Excavations there trace human activity from mobile foragers more than 10,000 years ago through to herders who relied on cattle and goats.

Today this part of the Sahara is hyper arid, so heat and dryness usually destroy DNA before scientists can read it. The natural mummification at Takarkori kept enough tissue intact to extract whole genomes and glimpse a population that would otherwise be invisible.

Meet the Takarkori herders

By the time these women lived, people at Takarkori were keeping cattle, sheep, and goats instead of relying only on wild game.

Archaeologists call these communities pastoralists, herders whose livelihoods center on domesticated animals rather than crops.

Most burials from the shelter belong to women, children, and teenagers, suggesting a settled community rather than a small traveling band.

Chemical analysis of tooth enamel, which tracks local geology in the water people drank, indicates that these individuals grew up near Takarkori.

In the lab, researchers powdered a tooth and leg bones, then used capture methods to pull out specific stretches of human DNA. These methods target single nucleotide polymorphisms, short DNA changes used to track shared ancestry.

Even with this careful work, the DNA fragments were short and scarce, so each genome covers only part of the full sequence.

That partial view is still powerful enough to compare these women with hundreds of ancient and present day genomes across Africa and Eurasia.

Lost North African lineage

Genetic analysis shows that most of the Takarkori ancestry comes from an unknown North African lineage, a group of people sharing inherited history.

This branch appears to have split from sub Saharan Africans around the time other humans expanded out of Africa, roughly 50,000 years ago.

Over thousands of years, later migrations diluted this ancient ancestry, so no one today carries it in a pure form. Even so, the genetic signal from Takarkori and related groups remains a major component of many present day North African populations.

A genomic study of 15,000 year old skeletons from Taforalt Cave in Morocco identified a distinctive North African ancestry. The new Takarkori genomes fall within that same cluster, linking pastoralists in Libya to much older foragers on the Atlantic side of North Africa.

Genetic tests show that both Takarkori and Taforalt are about equally distant from sub Saharan Africans, even during periods when the Sahara was wetter.

That pattern suggests that rivers and lakes formed natural corridors for culture and trade but did not erase long standing north south genetic differences.

Pastoralism without mass migration

Archaeological work at Takarkori shows that herders brought livestock into this part of the Sahara from the northeast about 8,300 years ago.

Genetic evidence supports this view by revealing only a small Levant related component in the Takarkori genomes, not a population replacement.

“This discovery reveals how pastoralism spread across the Green Sahara, likely through cultural exchange rather than large-scale migration,” said Nada Salem. That pattern suggests that local groups adopted livestock while largely staying in place.

Recent genomic work on Fulani herders shows ancestry tied to North African groups, a finding that aligns with the Takarkori results. It indicates that traces of this old Saharan ancestry extend into the Sahel today.

Analysis of matching DNA segments points to a group size of around 1,000 people, which was large enough to limit close inbreeding but still relatively small.

Lessons from Takarkori

Genetic analysis shows that most non-Africans carry 1 to 2 percent DNA inherited from Neanderthals. Neanderthals are an extinct human group from Eurasia, and the Takarkori women have 0.15 percent of that ancestry, higher than in sub Saharan Africans.

That pattern suggests a trickle of gene flow from Eurasian groups into North Africa, overlaying a much older local ancestry without overwhelming it.

It contrasts with places like Morocco and East Africa, where later farmers from the Levant and Europe left a far stronger genetic imprint.

Viewed over tens of thousands of years, the Sahara comes across as a stubborn barrier, even during wetter phases when lakes and grasslands expanded.

The new genomes fit this picture by showing distinct northern ancestry that stayed separate from sub Saharan lineages despite changes in climate and lifestyle.

As techniques for recovering fragile DNA keep improving, more buried individuals from the Green Sahara and surrounding regions may finally have their stories read.

Each new genome adds clues to how people adapted to shifting landscapes, and how ancient diversity shapes the genetic mosaic of Africa today.

The study is published in Nature.

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