Two women buried roughly 7,000 years ago inside a rock shelter in southwestern Libya have yielded genome-wide ancient DNA that points to a previously undocumented North African genetic lineage component, according to a study published in Nature on April 2, 2025. The research, which the Natural History Museum says includes lead author Nada Salem, represents the first successful extraction of genome-wide genetic data from the ancient Sahara and adds new evidence about how populations may have moved across the region during a wetter, greener era. The finding adds to a growing push to better resolve the deep ancestry of North Africa, a region often described as a major blind spot in ancient DNA research.
A Hidden Lineage Beneath the Sahara
The two individuals were recovered from the Takarkori rock shelter, a site in the Tadrart Acacus mountains of southwestern Libya that served as a dwelling for pastoral communities during the African Humid Period. According to the Nature study, the majority of the ancestry of these approximately 7,000-year-old Pastoral Neolithic women derives from a genetic lineage that has no clear match among any modern or previously sequenced ancient populations. That distinction is what makes the result so striking: rather than slotting neatly into known branches of the human family tree, these genomes sit on their own branch, hinting at a wider and more complex population structure across the mid-Holocene Sahara than archaeologists had previously inferred from artifacts alone.
At the same time, the Takarkori individuals show a close relationship to ancestry first documented in approximately 15,000-year-old foragers from Taforalt cave in Morocco, as reported in a 2018 Science analysis that established genome-wide evidence for Late Pleistocene North African population structure and cross-region affinities between Near Eastern and sub-Saharan African populations. The tension between these two findings is real: the lineage is described as “previously unknown,” yet it shares deep roots with Taforalt ancestry separated by roughly 8,000 years and hundreds of miles. One way to reconcile this is that a broad North African population once stretched across the late Pleistocene and early Holocene landscape, diversifying into regional branches that later fragmented or disappeared from the modern gene pool. The Takarkori genomes may capture one such branch, preserving a snapshot of diversity that could have been reduced over time as the Sahara became drier and later population movements reshaped the region.
From Mitochondria to Full Genomes
The new Nature paper builds on a precursor study that first cracked the genetic code of these same two individuals at a smaller scale. That earlier work, published in Scientific Reports, produced the first mitochondrial sequences from the Sahara region, consisting of complete maternal genomes from the two approximately 7,000-year-old Takarkori individuals. The mitochondrial analysis identified an ancestral mutation motif linked to the haplogroup N root, often summarized as N*, a designation that signals a deep and unusual placement on the human maternal lineage tree. Haplogroup N is one of the two major branches descending from the mitochondrial “Eve” lineage that left Africa, so finding an ancient, unclassified variant of it in the Sahara raised immediate questions about back-migration from Eurasia into North Africa and about how early those returning lineages might have mixed with local groups.
Moving from mitochondrial DNA to genome-wide sequencing required a significant technical leap. The Nature study employed a capture approach involving enrichment at roughly 1.24 million single-nucleotide polymorphisms, a method informed by empirical comparisons of commercial Twist and Arbor assays that evaluated coverage, uniformity, allelic bias, and the effect of one versus two enrichment rounds. Those performance tests provided confidence that data pulled from badly degraded bone fragments in a hot desert environment could be trusted, despite the short fragment lengths and chemical damage typical of ancient DNA. Such benchmarking work helps researchers gauge how well enrichment performs on degraded material; in turn, it can bolster confidence in genome-wide results from challenging environments like the Sahara.
Challenging the Migration-or-Diffusion Debate
“This challenges our assumptions about how cultures and genes moved across the Sahara,” said lead author Nada Salem, according to the Natural History Museum’s news release. Salem’s comments point to a long-running debate in African archaeology: did the spread of pastoralism across the Sahara during the African Humid Period happen because people migrated with their herds, or because ideas and livestock management techniques diffused between neighboring groups who stayed put? Genetic data can help break that deadlock. If the Takarkori women carried a distinct lineage not found elsewhere, it suggests that at least some Saharan pastoral communities were genetically isolated enough to develop their own ancestry profile, rather than being recent offshoots of better-known populations from the Nile Valley or the Maghreb.
That finding complicates a popular narrative in which pastoralism radiated outward from a single origin point somewhere in Northeast Africa or the Near East. Instead, the genetic evidence suggests multiple populations with distinct ancestries coexisted during the green Sahara period, each potentially adopting herding independently or through limited cultural exchange rather than wholesale population replacement. Salem’s framing of cultural diffusion versus migration is not just academic shorthand; it shapes how researchers model the peopling of sub-Saharan Africa, because pastoral groups that later moved south into East Africa may have carried genetic signatures from these now-vanished Saharan lineages. Targeted ancient DNA sampling from mid-Holocene East African herder sites could test whether the Takarkori lineage, or something closely related, contributed to populations further south, offering a way to link archaeological evidence of cattle herding to specific ancestral components.
Why North Africa Remains a Genetic Blind Spot
One reason this discovery took so long is that ancient DNA preservation in hot, arid environments is notoriously poor. The Sahara’s extreme temperatures accelerate the chemical breakdown of DNA, leaving researchers with fragments too short and too damaged for standard sequencing. The Takarkori rock shelter offered a rare exception: its sheltered interior and the burial conditions of the two women preserved enough genetic material to work with, even if only a small fraction of the original genomes survived. Even so, the path from initial mitochondrial results to full genome-wide data took years of method development and careful screening of bone samples to identify those with the highest endogenous DNA content.
The broader North African region also poses logistical and political challenges that have slowed systematic sampling. Many key archaeological sites lie in remote desert zones or areas affected by conflict, limiting access for excavation and export of skeletal material. On top of that, ethical concerns about the treatment of human remains and the sharing of genetic data require close collaboration with local authorities and descendant communities. Large-scale reference datasets, such as those cataloged through NCBI resources, have historically underrepresented North African and Saharan groups, which makes it harder to place newly sequenced ancient individuals into a comparative framework. As more modern and ancient genomes from the region are added to public archives, researchers expect to refine the position of the Takarkori lineage and determine whether faint echoes of it persist in living populations.
Building a Framework for Future Research
The Takarkori study also highlights how infrastructure for managing genetic and bibliographic information is becoming integral to ancient DNA research. Scientists increasingly rely on personalized portals such as MyNCBI profiles to track relevant publications, manage alerts, and coordinate multi-author projects that span genetics, archaeology, and climate science. Curated bibliographies, including shared reference collections, help teams keep sight of rapidly expanding literature on Holocene climate shifts, Saharan rock art, and pastoral economies that provide context for interpreting genomic findings. In the case of Takarkori, synthesizing data from paleoenvironmental reconstructions, radiocarbon chronologies, and comparative skeletal analyses was essential for situating the genetic results within a coherent narrative of life in the green Sahara.
At the same time, the sensitivity of genetic data from small, ancient communities has pushed institutions to tighten oversight of how information is stored and shared. Researchers working with human remains are encouraged to review privacy and security options in tools like account settings associated with their data repositories, ensuring that raw sequences, metadata, and access permissions comply with consent agreements and local regulations. As more ancient North African genomes are generated, these governance frameworks will help balance open scientific inquiry with respect for the people whose remains are being studied. The Takarkori genomes thus serve not only as a window into a lost lineage beneath the Sahara, but also as a case study in how technical innovation, ethical reflection, and international collaboration must align to reconstruct the deep human past.
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*This article was researched with the help of AI, with human editors creating the final content.
