A remarkable paper published in Nature in 2025 has provided the first genome-wide ancient DNA from human populations of the Central Sahara. The work, by Nada Salem and collaborators, is entitled “Ancient DNA from the Green Sahara reveals ancestral North African lineage.” Its implications are substantial because it gives direct genetic evidence for something that had previously been difficult to establish: North Africa possessed a deeply rooted indigenous population lineage of its own, neither reducible to recent Eurasian back-migration nor adequately describable as an extension of presently sampled sub-Saharan populations.
The result is particularly interesting because it also changes the interpretation of the famous 15,000-year-old Taforalt population from Morocco and clarifies the relationship between ancient North Africans, sub-Saharan African populations and the populations involved in the major Out-of-Africa expansion.
A Previously Unknown North-African Lineage
The central discovery is that the Takarkori individuals cannot be explained simply as descendants of Levantine farmers who moved into Africa with pastoralism.
Nor can their ancestry be adequately represented by Yoruba, Dinka, Mota or other presently sampled sub-Saharan populations.
Instead, the authors infer the existence of a deeply divergent ancestral North-African population.
Their best-fitting admixture graph gives approximately
Takarkori ≃ 93% deep North-African ancestry + 7% ancient Levantine-related ancestry.
The important statement is not the exact numerical precision of 93% and 7%, since admixture graphs are models rather than unique reconstructions of history. The robust qualitative conclusion is that the overwhelming majority of Takarkori ancestry derives from a previously unknown North-African lineage, with only a relatively small contribution from an Out-of-Africa-related Levantine population.
This immediately changes how one should imagine ancient North Africa.
The simple picture
North African = sub-Saharan African + Eurasian back-migration
is inadequate.
There appears instead to have existed an old North-African population with its own deep history inside Africa.
Another “Remain-in-Africa” Lineage
The most fascinating part concerns the position of this North-African lineage in the deeper human family tree.
The paper finds that Takarkori is genetically closer to the early Out-of-Africa lineage than the tested relatively unadmixed sub-Saharan populations are.
The authors use the approximately 45,000-year-old Zlatý kůň genome as a proxy for an early branch of the population that had left Africa.
Their admixture graph suggests approximately the following topology:
ancestral African Homo sapiens
→ an earlier branch represented by something like the Mota-related African lineage
→ another ancestral branch, which subsequently separates into
deep North-African lineage
and
Out-of-Africa lineage.
Thus the deep North-African population can be thought of, cautiously, as an African sister lineage relatively close to the population involved in the major Out-of-Africa expansion.
It is therefore useful to abandon the overly simple opposition
remain in Africa / leave Africa
and think instead in terms of several structured African populations.
One population lineage ultimately contributed to the major Out-of-Africa expansion.
Other lineages remained in Africa.
And among those that remained was apparently this distinctive North-African lineage, which was more closely related to the ancestral Out-of-Africa population than the Mota-like lineage used in the authors’ model.
This does not mean that North Africans were Eurasians who subsequently returned to Africa.
That alternative can be tested using Neanderthal ancestry.
The Neanderthal Test
Populations descended substantially from the major Out-of-Africa expansion normally carry Neanderthal ancestry because modern humans interbred with Neanderthals after leaving Africa.
Takarkori contains only about
0.15% detectable Neanderthal ancestry.
This is extremely low.
The corresponding values obtained in the study are roughly:
Takarkori: 0.15%
Taforalt and Neolithic Moroccan individuals: 0.6–0.9%
Typical Out-of-Africa populations examined in the study: 1.4–2.36%
The tested ancient and present-day sub-Saharan genomes contained essentially no detectable Neanderthal ancestry under the same analysis.
This is a crucial result.
If the dominant ancestry of Takarkori had come from a Eurasian population that left Africa, encountered Neanderthals and subsequently migrated back into North Africa, Takarkori should contain much more Neanderthal ancestry.
It does not.
The most economical interpretation is therefore that the major component of Takarkori ancestry comes from a population that remained in Africa, although it was closely related to the lineage that eventually participated in Out-of-Africa.
The small amount of Neanderthal ancestry can then be explained by the approximately 7% later Levantine-related contribution.
So two ideas that might initially appear contradictory can both be true:
The deep North-African lineage was closely related to the ancestral Out-of-Africa lineage.
It subsequently received a smaller amount of gene flow from populations that actually had participated in Out-of-Africa.
The first is a deep genealogical relationship.
The second is later admixture.
They should not be confused.
The Extraordinary Connection with Taforalt
The part of the paper that I find particularly striking concerns Taforalt Cave in Morocco. The Taforalt individuals are about 15,000 years old, approximately 8,000 years older than Takarkori.
An earlier ancient-DNA study had modeled Taforalt approximately as
63.5% Natufian-related ancestry + 36.5% broadly “sub-Saharan African” ancestry.
But the supposed African component could not be identified with any specific known sub-Saharan population. The Takarkori genomes now provide a much better proxy for this missing component, giving approximately
Taforalt ≃ 60.8% Natufian-related + 39.2% Takarkori-related North-African ancestry.
Since Takarkori is younger than Taforalt, this obviously does not mean that Taforalt descended from Takarkori. Rather, Takarkori is the best available representative of a still older unsampled North-African lineage inherited by both populations.
Calling this deeper lineage A and the Levantine-related component L, the approximate picture is
Takarkori ≃ 0.93 A + 0.07 L,
Taforalt ≃ 0.40 A + 0.60 L.
The apparently counter-intuitive fact that younger Takarkori preserves much more of A is therefore explained by geography and isolation rather than chronology: northwestern North Africa had already experienced substantial Levantine-related gene flow by the time of Taforalt, whereas the Saharan Takarkori population remained much more isolated.
This also shows why Takarkori cannot simply be modeled as Taforalt + Natufian. Since Taforalt itself contains only about 40% of A, adding further Natufian-related ancestry can only decrease that fraction, whereas Takarkori requires approximately 93%.
Thus the Takarkori genomes reveal something that Taforalt alone could not expose: evidence for a deeper North-African population that existed before both Taforalt and Takarkori.
The Mitochondrial Haplogroup N
Both Takarkori women carried a very basal branch of mitochondrial haplogroup N, one of the major maternal lineages associated with populations outside Africa. Its estimated split around 61,000 years ago is close to the period of the major Out-of-Africa expansion.
This is consistent with the possibility that a population closely related to the ancestral Out-of-Africa population remained in North Africa. But mtDNA traces only one maternal lineage, so this result is supportive rather than decisive. The stronger evidence comes from the autosomal genome, admixture modeling and Neanderthal ancestry.
What the Paper Does Not Show
The study is based on only two individuals, with most high-resolution inference coming from one genome, so the admixture percentages should be treated as model-dependent estimates rather than exact historical proportions.
Nor does the paper show that modern North Africans are simply 93% Takarkori-like. Thousands of years of later migration and admixture separate Takarkori from present-day Maghrebi populations.
What the study establishes is the existence of a deep indigenous North-African lineage. Determining how widespread it was and how much of it survives today will require many more ancient genomes from across North Africa and the Sahara.
The Larger Historical Picture
The deepest significance of this work is that it makes the old binary picture of North Africa as simply
sub-Saharan African + Eurasian
increasingly untenable.
Instead, early Africa contained several deeply differentiated populations. Among them was apparently a North-African lineage that remained in Africa but was more closely related to the ancestral Out-of-Africa population than the sampled sub-Saharan lineages were.
Takarkori therefore represents something conceptually important: another “remain-in-Africa” lineage—deeply African, distinct from the sampled sub-Saharan populations, yet unusually close to the lineage that later participated in the Out-of-Africa expansion. It subsequently received limited gene flow from descendants of populations that had actually left Africa.
This also changes the interpretation of Taforalt. The older shorthand
Taforalt ≃ 60% Near Eastern + 40% sub-Saharan African
is better replaced by
Taforalt ≃ 60% Natufian-related + 40% deep North-African ancestry.
Thus Takarkori appears to preserve evidence of an ancestral North-African population that existed before both Takarkori and Taforalt.
For me, this is the central result: a deep indigenous North-African lineage existed early in modern-human history, remained largely within Africa, was closely related to the ancestral Out-of-Africa lineage, and later received limited admixture from its descendants.
What had previously been, for me, largely a historical and metaphysical intuition has now acquired substantive genomic evidence.
The result does not close the history of North Africa. It opens it.
Reference: Nada Salem, Marieke S. van de Loosdrecht, Arev Pelin Sümer et al., “Ancient DNA from the Green Sahara reveals ancestral North African lineage,” Nature 641, 144–150 (2025), DOI: 10.1038/s41586-025-08793-7.
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