In a study recently published, a conclusion said to be drawn was that the ancient women of Libyan Sahara had no Sub-Saharan African ancestry. At face value, it’s quite agreeable especially from my perspective. It’s always been quite simple, Sub-Saharan African as ill defined as it is, represents ancestry that incorporates many different cultures and peoples which lived throughout human prehistory. Some of which, very likely, had resided in Northern Africa until the African humid phase when the Sahara was green. However, the study did a bit more than prove the obvious (to some) as there seems to be an insinuation that the women had nothing to do with “Sub-Saharan African’s” at all, with the exception of maybe the Fulani. Such a sentiment is quite problematic as we’ve previously seen with a shortage of ancient African DNA, how even Paleolithic Moroccans can be used to infer ancestry of Sub-Saharan African groups. It was made quite obvious at least to us who have paid attention to the landscape that Takarkori (TK-RS) DNA should answer some serious questions about the origins of Africans in major. And upon careful analysis through various disciplines including the new study I can confirm their DNA does answer some major questions. So while I could possibly agree that the women were not “descendants of sub-Saharan Africans”, I can also jokingly point out that they’re as Sub-Saharan as a non Sub-Saharan can possibly get.

Understanding the landscape.

What is Sub-Saharan Africa? Sub-Saharan Africa is a now loaded term which initially meant to describe the non-arid geographical areas located south of the Sahara desert. ‘North Africa’ typically includes regions occupying the desert and further north so long as the area is within the boundaries of the African continent. Countries on the southern boundary but are essentially entirely within the Sahara region like, Mauritania, Chad, Mali, Niger and Burkina Faso are interchangeably referred to as Sub-Saharan or Saharan based on context and Sudan interestingly is nearly exclusively listed as Sub-Saharan. All of the countries just listed are Sahelian; meaning they host the region where the Sahara gradates to the tropics. Sub-Saharan ancestry refers to the DNA profile that is typical of those who occupy the aforementioned ‘Sub-Saharan’ region today. It is important to note that those who live in regions of the Sahel are considered Sub-Saharan. Inherently, therein lies conjecture when identifying ancestry by region when defining origins. Human being were privy to migration often moving from one area to the next. Also, not every population or individual who ever lived can be represented by contemporary groups or people. Mobility, population turn-over and genetic dead ends are just a few of the types of ways past human behavior or survival can trick us. For as we acknowledge wide spread events, such as the Bantu expansion, a degree of mindfulness needs to kept when associating geography with ancestry. After all, even when examining half of a centuries worth of continuity near the Bantu homeland, we’re still devoid of significant evidence that the Bantu were there.¹⁰ …On to Takarkori.

What do they look like… physically.

“It is worth noting, however, that when geometric morphometric analysis of the skull of TK RS H1 is compared with a large published dataset it shows closer affinities with sub-Saharan contests, such as Gobero in Niger whose occupation is dated from ~9.6–4.8 ka.”

Stefania Vai et. al., 2018. “Ancestral mitochondrial N lineage from the Neolithic ‘green’ Sahara“

“…relationships based on cranial metrical variables are expressed in Figure 5. The Neighbor Joining tree shows that the small sample from Takarkori takes relationships with the populations from Gobero in Niger, either coeval (Gobero B) or more ancient (Gobero A), thus with humans from sub-Saharan regions which are characterized by a wide morphological variation.“

Fabio Di Vincenzo et. al., 2015 “Modern Beams for Ancient Mummies …“

What do they look like…. Genetically.

At first glance when visualizing the data on Revoiye, we showed the sample H1 to resemble a two way mixture between East African hunter-gatherers¹⁰⁠ and the Capsian or Late North African hunter-gatherer^11,12⁠ at a ratio of about 2:1 respectively. Though not expanded upon to respect the eventual release of the study, the models were not definitive. As it turned out, reciprocal models between ancestries of Takarkori and early Moroccans can be explored as neither were overtly rejected. On one hand, TK-RS H1 could be modeled as having the majority of her ancestry being Sub-Saharan related yet on the other hand, a Near Eastern population (Natufian) said to have no Sub-Saharan ancestry³⁸ can be modeled with substantial ancestry from her. Furthermore an individual reported on in 2020 from Kakapeli rock shelter¹¹⁠ has an extremely similar ancestry profile to H1, owing around 81% of her heritage to TK-RS. This individual (KPL003), was previously shown to be 89% related to East African Nilotic pastoralists like the Nuer or Dink of Sudan and South Sudan.

In this new study the authors mainly used a collection of statistical tests (fstats) to explain the genetic composition of the Takarkori women. A way to test relatedness is to quantify the amount of drift between individuals. Shared genetic drift marks the frequency of shared genetic components in respects to the loss of genetic diversity due to factors like isolation, survival or selection. They were able to come to the conclusion that the only population(s) with significant results were Epipaleolithic and early Neolithic Moroccans. Other populations from Eurasia and Africa proper showed results unremarkable.

However upon examining the data TK-RS isn’t without affinity to modern populations. In fact, we can observe that the ancient women were consistently close to modern day African populations of the Sahel. Most notably, the Fulani of West Africa shows the closest draw to them in a few tests. In most of the principle component analysis (PCA), a test where variance is broken up into components to be visualized, we can see the aforementioned pattern (Figures 2., & S2.4-11. in linked study). In any which case the PCAs show that they plot intermediately between East and West Africans within the Sub-Saharan African cline. Note that these results alone aren’t indicative of Sub-Saharan ancestry, as the actual ancestors of TK-RS hasn’t been definitively distinguished. Also when dealing with individuals with unprecedented ancestral components, false overlaps can be seen in PCAs due to the metric of variance not accounting for outlying traits in the novel sample. This is especially true for aDNA samples for reasons I wont’ detail in this write-up, but the phenomena has been seen before. If we look at the PCA projection of Taforalt¹³⁠ for example, a conclusion that they’re most similar to the Ethiopian Afar can (falsely) be drawn. (see figure 7 below)

Figure 7. Taforalt’s placement when project on to a global PCA. As seen in Loosdrecht 2018

What do they look like…. (Continued.)

Another notable finding is that the women, considering their proposed relatedness to paleolithic North Africans, have disproportionately low amounts of Neanderthal DNA. This is even notable under the preliminary models done on Revoiye; being at least ~29% Paleolithic North African or Eurasian. It seems to be the case that they, as reported by (salem et. al., 2025), retained only a fractional amount of Non-African related ancestry. Roughly 7% to be precise. Furthermore, as opposed to being 29% Paleolithic North African (15-20% non-African), they’re likely related to or are of a substratum of ancestry which contributed to the likes of the Iberomaurasian. This idea coincides with the results from a series of statistical tests like those mentioned above to estimate ancestry proportions given a handful of potential doners. These tests were performed on here prior albeit with minor differences in setup. (See here.) Salem et. al. Found that TK-RS was likely the African ancestor responsible for the Sub-Saharan signals previously discovered in Paleolithic and Neolithic Maghrebi populations. This conclusion is indeed supported by the low amounts of neanderthal ancestry present in comparison to the amounts expected if TK-RS had 30% -15% Eurasian ancestry. (est. 0.66% – 0.19% Neanderthal.) For Neandethal ancestry is a hallmark of non-African ancestry.¹⁴⁠ This coupled with the fact that the women supposedly show no evidence of shared drift with modern day Sub-Saharan Africans, supports the idea that they weren’t descendant from a combination of any African populations we have data for to date. At best they can probably be seen as ancestral when analyzed in conjunction with modern day Sub-Saharan samples.

Lastly, there is one final pattern, a discrete “West African draw”, which wasn’t fully explored in the literature of the study, but prominent in a few data visualizations. In the supplementary figures (S.2.20.1-3) it is shown when the drift shared by all non-Africans is controlled for, Takarkori ancestry is most prominent in West African groups starting with Sahel populations like the Fulani and Songhai. In an ADMIXTURE¹⁵⁠ test, a test which breaks down ancestral components into clusters grouping DNA segments likely shared by common (K) ancestors, TK-RS retains a high West African component. This is important as it shows that even when paleolithic Moroccans form a tight cluster with Maghrebi populations^12,16⁠, the ancient Libyan women still exhibit a high amount of affinity towards Sub-Saharan Africans. These results in summary suggests the women at Takarkori rock shelter were statistically likely to share (or be) an ancestor with both early Maghreb populations and various Sub-Saharan populations.

Figure 8. ADMIXTURE visual for Takarkor H9 (top row) and H1 (bottom row), K clusters 3 – 9. As Seen in Salem 2025

Thoughts by Revoiye.

As you probably can tell already while reading this, there are some issues with the study. Most of which came in the form of interpretation. A few claims made by the authors were either unfounded or contradicted by their own data. Other claims and postulations find themselves at odds with archaeology and common sense logic. This reading from this point onward will get a slight bit technical as I will detail many of the flaws in either methodology, logic and or interpretation. Read with caution.

Breakdown in analysis (bare with me)

Firstly, the bold claim announced on paper and in public, that the Sahara hadn’t serve as a bridge but more so as a barrier ‘even when it was green’ is contradicted by a mountain of evidence,^3,7,17–25 some of which is provided by their own study. Simply hypothesizing that the ancient Libyan women weren’t of a ‘sub-Saharan ethnogenesis’ given limited analysis doesn’t disprove trans-Saharan mobility. For one, these women could have very well likely been progenitors of a group of Africans who emigrated south within the last 7,000 years. And while I agree and hold the same hypothesis that TK-RS were likely of Northern descent, it is to be acknowledged that the evidence of that notion provided by (Salem et. al., 2025) and Revoiye is insufficient. Trans Saharan contacts have been shown quite consistently over the course of about a century by archaeology and later on genetic anthropology. Such a statement provided by Salem and co. as well as other assertions emphasized a slue of other logical and technical inconsistencies.

Inappropriate and Confusing f₄ Equation(s).

An interesting but jarring issue was the logic behind the formal stats as well as the conclusions drawn from them. The most problematic being: f₄(chimpanzee, Zlatý kůň; X, Takarkori). The Zlatý kůň specimen, female cranium discovered in the Czech Republic, was chosen for they yielded some of the oldest non-African DNA, revealing a population basal to later European lineages.²⁶⁠ After applying the aforementioned problem to Africans in their data-set they came to the conclusion that Zlatý kůň was somewhat of a ‘genetic intermediate’ between Takarkori and Sub-Saharan Africans. The logic is that if the equation yields a positive Z score, then Takarkori must share more alleles and therefore more common ancestry with Zlatý kůň than other Africans. This takes the official use of the problem f₄(A, B; X, O) where the difference in shared alleles between population A and B is being compared to X and O. Without being too technical, I’ll break this down.

Salem et al., 2025. Discussion; 10.1038/s41586-025-08793-7

If the alleles not shared between A and B are the same as those not shared between X and O, then the Z score will be driven to a more positive integer if: A shares more alleles with X, and or if B shares more unique alleles with O. On the other hand if A shares more unique alleles with O, or if B does with X, then the score will be driven in a more negative direction. The less unique any alleles are in this problem the more close to 0 the score will be. This (f₄) is a powerful method to test or confirm ancestral relationships, but it isn’t without flaw. One major flaw is tendency toward incorrect application and faulty interpretation, both of which were on full display by (Salem et. al., 2025.)

For one; When testing for shared ancestry, it is advisable for the problem to find the difference between either the test or the controlled population and an outgroup. (test = x, Outgroup = O.) This is because it is to be assumed that all populations should have comparable levels of drift compared to the Outgroup. With this practice we are ensuring that the alleles to be compared isn’t hampered by excess overlap between populations on both sides of the equation. In (Salem’s et, al., 2025) equation, they had both potential test populations on the same side of the problem. This essentially served the purpose of treating Zlatý kůň as the test group rather, since the difference is initially being calculated from most diverged population (Chimp). This makes their equation; f₄(O, X ; A, B). From there on a positive Z score will inform the observer that Zlatý kůň is closer to population B and a negative score will show they’re closer to A. This does not indicate that Takarkori(B) shares more unique alleles with Zlatý kůň(X) than any test population(A).

Interestingly, on the flip side, when the equation was done with Africans of varying relatedness to non-African groups mostly due to a history of mixing, the results were consistently negative. The authors concluded that a negative Z score in that context was suggestive of the mixed African populations being closer the Zlatý kůň than Takarkori. Once again, such conclusions are not admissible by this equation. What the results should inform us is that Zlatý kůň shares more unique alleles with those Africans than they do Takarkori. Disappointing as it may be, it turns out that the conclusions of the authors, based on this problem, were not only dubious but completely contradictory. For one, if both a negative and a positive Z-score, either of the two realistic binary results, would yield a conclusion which would differentiate TK-RS from Africans, then there’s no point to the test. Secondly, and most damning is that If Zlatý kůň shares more alleles with almost every admixed Sub-Saharan African group regardless of the ancestry composition, then Takarkori is inadvertently firmly placed within the Sub-Saharan substrata as just minor non-African ancestry is enough to shift the Z score to negative. As touched on earlier, this is because Eurasians share extreme drift due to the Out-of Africa bottleneck and Zlatý kůň given their age and genetics represents deep ancestry relating to some of the first Eurasians.^27,28⁠ North Africans, even those of the Epipaleolithic, share this drift to some degree due to their complex history.^12,29–31⁠ And a problem like f₄(chimpanzee, Zlatý kůň; admixed-African, Taforalt) will more often than not yield a positive Z-score.

Incomplete Analysis on Ancestry Modeling.

Another odd logical choice was how the modeling of ancestry estimates were handled. To put it simply, Takarkori was inferred to be almost purely ancestral north African. Ancestral North African (ANA) as explained before on this site was inferred when trying to model Paleolithic Maghrebi populations.^32,33⁠ The ANA population was said to contribute at least 45% to 55% of the ancestry discovered in Taforalt, and this would be in conjunction with Epipaleolithic samples from the Caucuses contributing a near equivalent amount of ancestry.³²⁠ When the Taforalt genome was first discovered however, the only plausible two way model was that of a combination between a Sub-Saharan African population (Yoruba of Nigeria) and the earliest Near eastern population we have DNA for (The Natufian of Raqefet.)¹³⁠ That model was rejected by the same authors who proposed the two-way model, and was further rejected again when ‘ANA’ ancestry was hypothesized. The simpler two-way Sub-Saharan + Natufian model was discarded for a lack of statistical and prehistoric significance.^32,33⁠ Furthermore it has been explicitly stated and corroborated over a handful of studies, that ANA ancestry, if existed, was passed to Natufians by a population related to the Early Maghrebi Hunter-Gatherers, like Taforalt.^32,34⁠ In (Salem et. al., 2025), the mentioned rejected two way model was further prefaced and utilized. It seemed the intent was to definitively show that modern day Sub-Saharan Africans were not the the contributors of such signals in 15,000 year old samples of Morocco. And in their place the Takartori women could suffice. They shared results showing that when modeled in conjunction with Natufians, the Takarkori women show a statistical contribution of ~39% to the Paleolithic Moroccan ancestry. These estimates are reminiscent of what’s to be expected when using Sub-Saharan Africans as a stand-in (33-38%). This admixture pattern if statistically significant only wedges Takarkori in the unique place of being Sub-Saharan African-like. Moreover, if the authors are to issue the postulation that the grand majority of Takarkori’s ancestry(~93%) is Ghost North African or ANA, then their models should also investigate via qpAdm if the combination of TK-RS + Epi-Paleolithic Caucuses (or Villabruna) yields a statistical fit for Epi-Paleolithic Moroccans. If done, Salem et al. could have established proof that these new physical remains were what was statistically modeled 7 years ago.³²⁠ Or as a researcher, at least corroborate or adjust the equations that predicted the ancestry type claimed to be unveiled in the study as homage. Overall, this concern highlights a missed opportunity in understanding the genetic landscape of not only African populations but also West Eurasian populations proper. More specifically those West-Eurasian populations who are theorized to have ancestry currently undefined outside of the statistical realm. As seen prior in a simple preliminary look into the Takarkori (TK-RS H1) genome, it was shown here that models involving Takarkori as ancestral to various ancient Middle Eastern, North African and Sub-Saharan populations can be explored.

Something else raised by the authors which I find a bit obscure was the interpretation and importance given to their f₃ calculations. Through such calculations ( f₃(Takarkori, X; Outgroup) ) It was determined that TK-RS’ drift was excessively shared with the isolated individuals of the paleolithic Maghreb and their kin. The authors reconcile with this discovery by crediting long standing homogeneity and continuity in the Northern reaches of Africa. The issue is that there was poor investigation into whether such claim could be survive scrutiny. In fact, the supplementary data shows evidence and dating of a Sub-Saharan + Middle Eastern admixture event(s). Such evidence provided by linkage disequilibrium analysis of their own submission exemplified admixture from potential relevant sources dating to a time post-dating the Iberomaurasian period. It can be implied that the strong signals of drift shared could be a direct result of admixture and not necessarily population continuity. This phenomena has been unveiled before with testing of the Epi-Paleolithic North African samples, where as, a considerable amount of drift is seemingly shared with more contemporary north African groups despite their population history due to Iberomaurasian introgression.¹⁶⁠ Additionally by the author’s admission, (see figure 10) the ancient Libyans showed evidence of sharing unique ancestry with modern day west African groups via f₃. They further elaborated that Sahelian groups tend to share the greatest amount of drift with them among modern populations. However, this is despite the fact that the Fulani, who were previously shown to have ancestry distinctly related to Early Neolithic Moroccans,^34,35⁠ were highlighted in this study as ‘possibly the only Sub-Saharan population to have significant related ancestry’. Signaling out the Fulani in this context is quite odd when considering the diversity in populations which show similarities to the Libyan women according to multiple calculations. For example, such variance can be seen within the f₃ analysis’ themselves when the results are fed into a cluster algorithm. (see figure 11.) TK-RS shows evidence of clustering with many Sub-Saharan populations of the Sahel and east Africa. Even when grouped with northern Africans, TK-RS clusters at a basal position to horn Africans with higher levels of Sub-Saharan ancestry respectively. Further test’s in the face of this much contradicting evidence is needed to solidify claims that the Fulani are unique in their relatedness to TK-RS; For which, in this case a simple test to model their (Fulani) ancestry via qpAdm would have sufficed.³⁶

⁠En Closing ~Final Statement

All in all the discovery and genetic sequencing of these samples mark a milestone in genetic anthropology. As technology advances and scientists become more clever, us enthusiasts and researchers are becoming more well fed with information. Africa had been at the tails of the genetic frontier for reasons often due to climate and poor conditions for DNA preservation and studies. A sample analyzed from the Sahara is a blessing as every little piece of data matters in the advent of scarcity. However it seems that history often repeats itself when it comes to African studies. Figures tend to be lack luster, creativity is subpar, logic becomes half-witted, and conclusions tend to be dubious in comparison to analysis done on material from elsewhere around the world. Salem et. al., sadly contributes to that pattern. Ironically, such work is quite familiar to what (almost) was released back in 2017. Fregel et. al. were to publish a study which sought to introduce the genetic legacy of Early Neolithic Moroccan samples of Ifri n Amer Moussa.¹⁶⁠ That study, despite the coverage and relevance or lack thereof to down stream coastal north Africans, mainly focused on middle neolithic samples who shown signs of arriving from southern Europe (Iberia.) In their pre-print, the newly excavated and sequenced Ifri n Amer Moussa individuals were said to share more alleles with Eurasian populations and showed “no evidence of Sub-Saharan admixture or relatedness”. Fortunately, shortly after Loosdrecth et al. in 2018 released a comprehensive and detailed study exploring the then, novel Iberomaurasian ancestry which reshaped the approach by Fregel et. al. and gave way to understanding depth of African population history through aDNA. This is an example of how interpretation can create a stark difference in how data is perceived by others. just in the span of a few months, the perception of prehistoric North Africa shifted in the academic world. With biases overly unscientific and possibly social in nature comes a perspective that is not necessarily rooted in fact, logic or even discovery. I hope that such strange biases in this field can peter out as more research is done to tackle the gaps in knowledge we have on African population genetics. As far as keen identification or understanding of who the Takarkori women are, I’d imagine that the best conclusion to draw from Salem 2025 is that their ancestry composition is unresolved.

Source³⁷

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