Homo sapiens migrated out of Africa roughly 50,000 years ago, but scientists have now discovered that some chose to remain—revealing a previously unknown lineage that stayed isolated for millennia.
While North Africa’s Sahara Desert is an arid expanse today, the region was once a verdant landscape crossed by rivers 15,000 to 5,000 years ago. Genetic researchers are now analyzing skeletons recovered from the Takarkori rock shelter in present-day Libya to learn more about this ancient, secluded population.
An Unknown Population
Nada Salem, a PhD student with the Max Planck Institute for Evolutionary Anthropology, led the study, shedding light on a new chapter of the human story. Ancient DNA reveals a group that survived in northern Africa for tens of thousands of years in isolation, previously unknown to science. While other Homo sapiens leaving Africa were intermingling with human populations and related species across the globe, this group remained genetically distinct.
It wasn’t until the Sahara transformed into a savannah around 14,500 years ago that this long-isolated population began receiving immigrants from Asia and other parts of Africa.
“Our research challenges previous assumptions about North African population history and highlights the existence of a deeply rooted and long-isolated genetic lineage,” Nada says. “This discovery reveals how pastoralism spread across the green Sahara, likely through cultural exchange rather than large-scale migration.”
Dr Savino di Lernia, the study’s senior author, adds, “The study highlights the importance of ancient DNA for reconstructing human history in regions like Central Northern Africa, providing independent support to archaeological hypotheses.”
Desert Challenges
While DNA research has significantly advanced our understanding of human evolution, warmer regions like deserts and rainforests pose unique challenges, as high temperatures degrade DNA more quickly than in colder climates. Fortunately, natural formations such as caves and rock shelters provide cooler conditions that help preserve ancient remains. The Takarkori rock shelter is one such site, protecting the remains of 15 women and children buried between 8,900 and 4,800 years ago—just as the Sahara’s green era was drawing to a close.
Salem’s project is not the first to investigate these remains. Previous studies examined mitochondrial DNA, which is passed down maternally. This latest research differs by analyzing nuclear DNA from the teeth and bones of two individuals, offering deeper insights into ancestry and population dynamics. The findings indicate that the Takarkori individuals descended from a group that branched off from other humans around 50,000 years ago, just as others began migrating out of Africa.
This population remained genetically stable, showing little change for tens of thousands of years. At the time, they inhabited a lush environment—similar to modern-day Kenya—rich with rivers, grasslands, woods, and wildlife. Despite such a hospitable setting, DNA evidence suggests they remained cut off, with no signs of genetic intermixing.
Change Eventually Arrives in Africa
That isolation would eventually come to an end. According to current understanding, some of the original out-of-Africa descendants returned via the Sinai Peninsula around 8,000 years ago—completing a circular migration that had taken more than 40,000 years. A millennium later, groups from southwestern Europe also returned to Africa. These arrivals finally mixed with the long-isolated Takarkori population, ending their genetic seclusion. This mixing introduced 0.15% Neanderthal DNA into the Takarkori genome—a level absent or significantly lower in populations purely descended from Africans.
In addition to genetic exchange, cultural practices began to shift as well. Around 6,400 years ago, the Takarkori adopted a pastoral lifestyle, grazing livestock across vast landscapes and learning from Mediterranean farmers. Interestingly, while the groups influenced each other culturally, they did not significantly intermingle genetically.
The research team hopes that continued fossil discoveries will help fill the genetic gaps in humanity’s history. Such insights are vital to understanding human origins and evolution.
The paper “Ancient DNA from the Green Sahara Reveals Ancestral North African Lineage” appeared in Nature on April 2, 2025.
Ryan Whalen covers science and technology for The Debrief. He holds an MA in History and a Master of Library and Information Science with a certificate in Data Science. He can be contacted at ryan@thedebrief.org, and follow him on Twitter @mdntwvlf.