The Sahara Desert, one of the driest and most desolate regions on Earth today, spans across 11 countries in North Africa and covers an area roughly equal to China or the United States. But this vast desert wasn’t always barren.
Between roughly 14,500 and 5,000 years ago, the Sahara experienced a dramatic transformation into a fertile savannah dotted with lakes and rich biodiversity. Now, DNA recovered from two individuals who lived around 7,000 years ago in what is now Libya has revealed that the region once supported a mysterious, genetically isolated human population.
Scientists analyzed the first ancient genomes from people who lived during this so-called “Green Sahara” period. The DNA was extracted from the remains of two women buried in the Takarkori rock shelter in remote southwestern Libya. Naturally preserved over millennia, these individuals represent the oldest-known examples of mummified human remains.
“At the time, Takarkori was a lush savannah with a nearby lake, unlike today’s arid desert landscape,” said Johannes Krause, an archaeogeneticist at the Max Planck Institute for Evolutionary Anthropology and one of the lead authors of the study, published this week in Nature.
The genomes showed that the individuals from Takarkori belonged to a unique and previously unknown human lineage, one that remained separate from both sub-Saharan and Eurasian populations for thousands of years.
“Interestingly, the Takarkori people show no significant genetic influence from sub-Saharan populations to the south or Near Eastern and prehistoric European groups to the north. This suggests they remained genetically isolated despite practicing animal husbandry — a cultural innovation that originated outside Africa,” Krause said.
Archaeological findings suggest that these people were herders, raising domesticated animals. Items uncovered at the site include tools crafted from stone, wood, and animal bones, as well as pottery, woven baskets, and carved figurines.
The ancestry of the two individuals traces back to a North African lineage that branched off from sub-Saharan populations around 50,000 years ago. That timing aligns with the period when other early human populations began migrating out of Africa into the Middle East, Europe, and Asia, becoming ancestors of modern non-African peoples.
“The Takarkori lineage likely represents a remnant of the genetic diversity present in northern Africa between 50,000 and 20,000 years ago,” Krause explained.
“From 20,000 years ago onward, genetic data indicates that new groups entered the region — first from the Eastern Mediterranean, then from Iberia and Sicily around 8,000 years ago. Yet for reasons still unknown, the Takarkori lineage managed to stay isolated far longer than expected. Since the Sahara only became habitable about 15,000 years ago, it’s unclear where this lineage originally came from,” Krause added.
This population remained genetically separate throughout most of its history, until the Sahara once again turned arid. Around 3,000 BC, the African Humid Period ended, and the region reverted to being the world’s largest hot desert.
As Homo sapiens spread beyond Africa, they encountered and mixed with Neanderthals in parts of Eurasia, leaving lasting genetic traces in present-day non-African populations. However, the people of the Green Sahara carried only minimal Neanderthal DNA, suggesting very limited contact with external groups.
While the Takarkori population disappeared roughly 5,000 years ago as the desert reemerged, their genetic imprint can still be detected among some North African populations today.
“Their genetic legacy offers a new perspective on the region’s deep history,” Krause said.
