About 7,000 years ago, in the Sahara, two women were buried in a rock shelter in what is now southwestern Libya. At the time, it was not a desert but a savanna. Their remains, preserved by the dry air, have now yielded a treasure trove of ancient DNA — and with it, an unexpected twist in the story of our species.
Scientists have recovered the first genome-wide data from humans who lived in the so-called Green Sahara, revealing the existence of a long-isolated, previously unknown North African lineage. Their findings, published in Nature, suggest that this group was genetically distinct from sub-Saharan Africans, shared deep roots with some of the earliest known North Africans, and barely mingled with populations beyond the Sahara for millennia.
“It’s incredible,” Johannes Krause, a geneticist at the Max Planck Institute for Evolutionary Anthropology and senior author of the study told Science Focus. “At the time when they were alive, these people were almost like living fossils—like something that shouldn’t be there. If you’d told me these genomes were 40,000 years old, I would have believed it.”
A Hidden Lineage in the Heart of the Sahara
The Takarkori rock shelter sits within the Tadrart Acacus Mountains in Libya’s Southwestern desert. During the latest African Humid Period, which stretched from about 14,500 to 5,000 years ago, this region was dotted with lakes, grasslands, and trees. It supported fishing, herding, and some of the earliest pastoral societies in Africa.
Excavations at Takarkori unearthed 15 human burials from this time. Among them were two naturally mummified adult women, dated to between 6,800 and 7,200 years ago. Scientists extracted DNA from their bones with painstaking care. Despite the challenging preservation conditions, the team retrieved hundreds of thousands of genetic markers — enough to analyze their ancestry in detail.
“These samples come from some of the oldest mummies in the world,” Krause noted. “That we could sequence their entire genomes is a small miracle.”
The results stunned the researchers. Despite living during a time when the Sahara was green and passable, the Takarkori women carried a genetic signature unlike any other known population, ancient or modern. Their closest relatives were not nearby North Africans, but rather 15,000-year-old hunter-gatherers from Taforalt in Morocco—and even a 45,000-year-old individual from what is now the Czech Republic.
Isolated but Connected
Archaeologists had long suspected that the spread of herding in the Sahara—around 8,000 years ago—was driven by migration from the Near East. After all, the domestication of animals like sheep and goats originated there. But the genomes of the Takarkori women suggest something different.
“We know now that they were isolated in terms of genetics, but not in cultural terms,” Savino di Lernia, an archaeologist at Sapienza University of Rome who coauthored the study told CNN. “There’s a lot of networks that we know from several parts of the continent, because we have pottery coming from sub-Saharan Africa. We have pottery coming from the Nile Valley and the like.”
In other words, while the Takarkori people shared ideas and technologies with neighbors, their bloodlines remained largely untouched for thousands of years. This challenges previous assumptions that the “Green Sahara” acted as a bridge between North and sub-Saharan Africa. Instead, it may have been more of an island.
Even their genetic connection to Neanderthals was sparse—only about one-tenth the amount found in modern non-African populations. Yet it was higher than in sub-Saharan Africans, hinting at a North African origin for this group, possibly from populations that had already mingled with Neanderthals before settling the region.
The answer may lie in the very environment that allowed them to thrive. When the African Humid Period ended and monsoon rains withdrew, the Sahara once again turned to desert. Water sources vanished. Communities were forced to migrate—or perish. The Takarkori lineage seems to have vanished with the drying of the land.
Revising the Story of the Sahara
The new findings help clarify an older puzzle: the ancestry of the Taforalt people.
Previous studies suggested that the Taforalt foragers carried a blend of Natufian (Levantine) and some undefined “sub-Saharan” ancestry. But the current study shows that the latter likely came from a Takarkori-like population — not from groups living further south.
“This lineage was probably widespread during the late Pleistocene,” the researchers write. But as the Sahara dried out again, human groups splintered, migrated, or vanished.
The discovery has also stirred memories of the enigmatic “Cave of the Swimmers,” a site in Egypt’s Libyan Desert popularized by the explorer Lászlo Almásy. On its walls, ancient artists painted people swimming—an image that made little sense in the middle of a desert until now. These were depictions of a lost world.
“This gives a more realistic a, who lived in an ecosystem that no longer exists,” Carles Lalueza-Fox, a geneticist at the Spanish National Research Council told El Pais. “They uncover a previously unknown lineage that appears to have separated from other African ancestry for almost 50,000 years.”
The Takarkori people did not survive the return of the desert, allegedly. But fragments of their DNA still persist in modern North African populations, a silent genetic whisper from a vanished civilization.
For some scientists, the study’s sample size—just two individuals—invites caution. “Even two individuals can change our conception of the past,” wrote Mary Prendergast, an anthropologist at Rice University. “But more data will be crucial to confirming the story this study tells.”
For now, the findings open new doors into one of the least understood chapters of human prehistory: the lives of people who flourished in a green Sahara, then disappeared.
