Part 1: Deconstructing ideas of an Insular Middle East.

Overview: See below for detailed breakdown.

With Africa being the cradle of mankind it is home to over 3,000 ethnic groups with a great degree of diversity. But such diversity isn’t merely ontological, but biological as it’s been shown that the genetic diversity on the continent eclipses that of every individual outside of Africa combined.¹⁠ Such a reality is par for the course considering it being the birthplace of anatomically modern humans. With that said it is of importance to investigate Africa for insight to the origin of mankind. In doing so it is also advisable to give a deserved amount of attention to local groups who occupy the lands within, as more often than not, what is discovered through African history and prehistory gives context to all of us living. However, there are challenges in studying the region. Issues, such as political instability, lack of record keeping, and poor climate conditions for biological and anthropological preservation stand in the way of unearthing much. As a result there is an overwhelming disparity in artifacts recorded in and out of Africa, where, there are significantly more gathered and studied outside of the continent. With each discovery we must handle the issue delicately as a lot of assumptions must be made with gaps in knowledge. Here with the help of ancient DNA and the many archaeologist who came before, I look to piece the puzzle together with delicacy and attention to detail often over looked in modern day main-stream academia.

As predicted before in a series of technical reports, there are large blocks of mystery in the form of African substructure poorly accounted for ubiquitously. The people of the continent are generally accepted to be grouped in to about four quadrants; West African, East African, South African and North African. While such categories help us quickly associate geography with peopling, it holds together quite poorly when attempting to group people going further back into the past. For example, East Africans might not have been in East Africa during the paleolithic, the same for the North and West. Another highlight are the proto-historical and historical expansions of major ethnic groups. We have the unveiled Cushitic expansion of East Africans to the south^1,2⁠, The Bantu expansion from the West to the East and Southern regions^3–6 and the recorded Arab expansion from the Middle East to North Africa and some areas in East Africa.^7–10⁠ These relatively recent movements of people reshaped the peopling of the continent. Yet, perceived similarity in physical “types” and characteristics lend itself to another more adhesive categorization in distinctiveness; The dichotomy of North and “Sub-Saharan” African.

For some time, North Africans have been seen as ‘para-Eurasian’ due to the complex history some of which mentioned above. In the common era, the Arab expansion seen the spread of Islamic culture and people from the middle east. With that came the expected onset of mixing and settling. The overlapping culture as well as genetics from those of North Africa and people of the Middle East created the ‘Middle-East and North African’ ( MENA ) classification of peoples. As we periodically try to peel the layers back to further investigate, we learn that there were quite a few more interactions between Europe the Middle East and North Africa going back to the paleolithic. These include a late Iron-age expansion from a single lineage¹¹⁠, A neolithic expansion from Europe and then the Middle east,^12–14⁠ and a Paleolithic expansion from somewhere in West Eurasia. ^15–19⁠

On the flip-side it has been very hard to explain or quantify the degree Africans in general contributed to the settlements outside since the initial ‘Out of Africa’ expansion. The largest buffer is the lack of evidence we can garner from actual Africans going back in time. For instance, there’s only a fraction of samples from within Africa compared to what’s available elsewhere when observing ancient DNA. To add to the issues is the over simplified models in spite of potential African ancestry. A good example is the conclusion of a Basal Eurasian lineage to have contributed all outlying ancestry to non African populations of the middle east since the Upper-Paleolithic.^20,21⁠ Such models typically use modern populations from Africa as a sort of “negative-control” ( outgroup ) to statistically calculate how much an ancient Eurasian population relates to …an unknown hypothetical Eurasian population.

This example of ‘a lack of delicacy’ spills over into studying populations within the continent. For, if we know the mystery men of Eurasia are responsible for all of Eurasian diversity since OOA, then that diversity in Africa must be fully attributable to the Eurasians we have data for. While it might seem quite unscientific when stated in such a manner, it is in fact often the case when assessing any individual with overlapping types of DNA with Eurasians. It is so much so that even models with low statistical power are asserted to be true.^14,22–25⁠ It is simply the works of a biased field.

Though biased it is still fruitful. The same methods and procedures can be applied with a bit more care to get closer to the truth. What stood in the way for so long was the incomplete records and sampling in Africa. However, early 2025 marked the release and publication of two individuals from the Neolithic green Sahara. They along with previous samples from Africa’s interior allows us to breakdown African diversity in a way not fully achievable before. While I was able to calculate with accuracy what the Saharan ancestry would look like, I lacked the information to parse what other types of ancestry looked like going back in time. It took a lot of time and math, but it has been done, thanks to the research teams who excavated, unearthed, and genetically sequenced our ancient relatives.

The Story Once We Left Africa.

The onset of the last ice age (LGM) likely pushed people who would have been a mixture of the aforementioned UP populations and local ancient East Asian-related people from North Asia (Modern day Russia) down into the Caucuses and further south. The degree to which these populations relate to the UP ancestors of Dzudzuana won’t be explored here, but this ancestry is core to explaining lower Caucuses and Zagros area people.^20,31,38⁠ These migrants could have mixed with more basal occupants related to the genetic isolates of the Andaman islands at the time; the people of the Baradostian. This modal ethos could have been the description of those who would be associated with the Mesolithic Trialetian cultures which are precursory to who are now considered genetically, Caucus Hunter-Gatherers.³⁹⁠ The same can be said for Mesolithic hunter gatherers of modern day Iran with the exception that they seem to show more of an affinity to Africans (see figure 6 and supplementary table S1). Archaeologically this can likely be explained by more direct influence of a Near eastern or source. This source would have probably had a greater degree of African ancestry than we have discovered genetically in the Natufians sampled so far. What is known is that in comparison to the Trialetian, the Zarzian, who are more directly related to later populations of the Zagros, has shown more direct cultural relatedness to Northeast Africans of the Mesolithic by proxy of Natufian predecessors³⁹⁠ (See; Microburin techniques, microlithic trapezes & lunates). The seemingly northward movements of these technologies associated with the M’lefaatian (Zarzian) could have played a part in birthing the CHG.

The Saharan profile within Africa was likely spawned from various degrees of African related ancestry. A case can be made that the Non-Eurasian portion of Iberomaurasian ancestry (Ancestral North African or ANA) was more widespread during the Middle Stone Age (MSA). Whatever the case it seems that a mixture between them and the East-African or Northeast African related population mentioned before lead to the Saharan profile seen in Takarkori. Though the samples from Southern Libya are quite young comparatively, evidence of their admixture dates to around the periods of the aforementioned East African expansion into the Middle East. Whether or not direct ancestry of the Saharan type made it’s way to the Zagros mountains remains to be seen but it its worth noting that there are minute cultural overlaps between earlier people of the Sahara and the middle east during pre-neolithic times.^40,41⁠ And judging by the non-admixed nature of the individuals of Takarkori, at least since the Pleistocene²³⁠, speculation of diffusion (from the Sahara) is warranted.

The Application of ‘Knowing’.

With the prehistory of the Middle east and Europe considered we can better evaluate ancestral components present in African populations. Deep ancestry shared between and African and non Africans will remain biased towards being represented as the latter. This is because Eurasians for all intent and purposes represent a subset of African diversity. The rough dichotomy between Sub-Saharan Africa and Eurasian (which unfortunately expanded to include north Africans) doesn’t help to unveil anything either. For one, enigmatic ancestries with clear links to modern day sub-Saharan populations can be overlooked in the grand scheme. It is so much so, that recently one of the most important samples for explaining African ancestry as a whole was considered irrelevant isolates loosely related to Eurasians and North Africans.²³⁠ Another example is the over representation of the the Natufian component in Africa, where instead of representing an ancient people of East Africa, we’re to consider populations such as those of the horn to be ‘half-African’. At the bear minimum such a characterization is misguided.

With being able to disentangle potential African ancestry in the ancient middle east comes the ability to statistically shape, to a wider scope, local or prehistoric sub-structure. Archaeological links will now become more apparent in conjunction with genetic studies. Oversimplified models which falsely grouped unrelated African populations won’t be the staple anymore. And to a better degree, we can categorize with accuracy the true sources of non African ancestry in relevant populations.

Ancestral Saharan Model Genotype. (Technical deep dive begins here)

With the successful genotyping of the ancient Saharan individual from Takarkori rock shelter we can now take a more nuanced approach to ascribing certain lineages and/or signatures vaguely associated with contemporary Sub-Saharan populations. Proposed signatures come in the forms of Ghost North African, Ghost Modern human, Ancestral North African and Basal Eurasian. The results of Salem et. al 2025 suggested that Takarkori was almost entirely Ancestral North African with minor (9-7%) ancestry related to Natufians. Interestingly, the subsequent and preparatory analysis done here shown that Takarkori was roughly 55-70% related to Sub-Saharan Africans and 30-45% Iberomaurasian related. But such simple models though speaking to parsimony isn’t enough to capture the real life nature and population history which produced this Saharan lineage. For one, Neanderthal estimates are disproportionately low for models of 30%+ Iberomaurasian ancestry as pointed out before. And secondly and more interestingly, by qpAdm, Takarkori’s SSA-related or ANA ancestry appears to be entirely downstream of East African diversity represented by Bayira (Ethiopian boy from Mota cave 4,500ya.)⁴²⁠ Ancestry of this type has never been captured in a single Sub-Saharan population before.

To investigate and inadvertently simplify what we observe in the genotyping of the ancient Saharan I invoked a method to estimate ANA ancestry used before. To reiterate, this algorithm estimates the % of ancestry supposedly forming a clade within the diversity of the Iberomaurasians and Mota and to the exclusion of putative Eurasian admixture. This would be the genetic “hot spot” so to speak, if investigating ANA ancestry as described by previous authors.^22,23,43⁠⁠ Surprisingly this algorithm shows that Takarkori is only about 60.6% (+/-1.1%) ANA. This is less than the Dinka of South Sudan overall (73.2% ANA +/- 1.6%) by the same method of estimation. Even more important is the fact that all of Takarkori’s ANA is pretty much “downstream”, matching that of the Dinka’s (60% ANA +/- 0.8% non-deep ANA/shared with Taforalt.) Such a result shows that Takarkori has little to no extraneous ‘deep’ ancestry related to East, Central, and West Africans, which is in alignment with the results seen in the preliminary qpGraphs and in the results of Salem 2025. If we take into account the true estimates of Eurasian ancestry categorized by Neanderthal admixture we can deem a few things true.

1. No modern day Sub-Saharan composition serves as a true progenitor of the Saharan women, which is indicated by a lack of deep ANA ancestry not shared with Taforalt.

2. Takarkori women lack deep ghost African ancestry, whether it’s a West African ghost or a modern human ghost population as seen in Mota and most ancient African foragers of East-Central and Southern Africa.

3. Takarkori is related to or is a direct ancestor to the modern day Sub-Saharan populations for which they share drift. The West and East African signals in TK-RS is likely telling that as oppose to them having ancestry from a modern day Sub-Saharan source, gene flow was likely the other way around. The Dinka, for example, likely had an ancestor genetically similar to Takarkori and another ancestor harboring more deep ancestry on the ANA cline related to East Africans.

It is to be somewhat expected that the Saharan woman wouldn’t be derived as it relates to modern day populations. For one, she is over 7 thousand years old and such models are anachronistic to say the least. Another clue is their mitochondrial lineage (N*), being undiscovered until they were sequenced. This lineage is controversial in that it represents an extremely early off shoot to macro-haplogroup N, which went on to diversify and populate the majority of Eurasia and the Americas. However a degree of delicacy is required in this interpretation, for the likelihood that she is not of modern equatorial African decent can not be extrapolated to ancient times. The dynamics of African population movements and genetic substructure has not yet been comprehensively established or learned. Two-way admixture models between populations related to both North and Sub-Saharan groups do show substantial evidence of admixture in the forms of LD-decay and qpAdm tests. The most likely scenario is that the proto populations of the Sahel, North and Southern Africa, who’s biology as queued by morphological studies, reflect their own genetic nature. The modern components we heavily associate with geographical, cultural and even racial peopling haven’t yet developed and signatures with variable relatedness to different populations were present in some areas without gene-flow.

Nonetheless such results naturally begs the question; if TK-RS is mostly ANA, has minor Eurasian, and yet no deep African ancestry, what constitutes the rest of her genome? Given the nature of the equation used to calculate ANA ancestry and the results determined by published literature, mainly 2 scenarios or both can be true.^22,23⁠

a. Takarkori’s Deep ancestry is shared by all African populations used as references: The 2000 year old Southern Africans, the hunter gatherer populations of East-central Africa and Taforalt but not Mota.

b. Takarkori’s non ANA ancestry is related to Non-African populations, either by simply sharing drift from the Out of Africa expansion, representing Eurasian back migration or has contributed entirely to the ancestry of Non-Africans.

In either case it is worth investigating more carefully to get a correct picture of Africa’s distant past. For one, in the case of scenario a. these women would have been a gateway to grasping the complexity of deep substructure in Africa in a way unexpected. It could signify the ancient presence of a potential ghost or differentiated population which contributed to a wide geographic temporal space. In the case of scenario b. which is a bit more expected, due to the predicted Basal Eurasian, Takarkori could reveal the dept of which putative African ancestry differentiated by serving as a proxy for ANA.

Ancient African Lineages Reveals Widespread Distributions in Ancient West Eurasia.

Please note, that I will not be going too deep on archaeology of the middle east and Europe in this post as this series is geared towards revealing population structure and history of Africans. Supporting evidence by multidisciplinary means will be mentioned sparingly, but the focus is to better understand the genetic composition of people and like people whom contributed ancestry widely to African groups. With Takarkori H1 (TKRS) providing an ancestry which can be modeled primarily as ‘Ancestral North African’, we can some-what definitively identify proposed Ghost African lineages not only within African populations but also outside of Africa nearby. This is possible because of ANA’s phylogenetic position, having developed in parallel to major Sub-Saharan groups before contributing to their ancestry. Not only that, but unique affinity to pre-bottlenecked ‘Out of Africa’ populations as seen in the aforementioned phylogenetic positioning as well as potential categorical ‘Basal Eurasian’ ancestry in TKRS could pin down the presence and distribution of such ancestry.

Being that the vast majority of post-Pleistocene back-migrated populations were shown to harbor varying degrees of Basal Eurasian, it is worth investigating how exactly they related to older African populations in light of these new genomes. For one, in 2016, it was put forth by lazaridis’ et al that the Natufian could haave received ancestry from a source likely from East Africa in a pre-print.⁴⁴⁠ As you will see soon, such predictions were likely correct. However, upon publication, the reviewed article denied the Natufians of having any affinity or affiliation with Sub-Saharan Africans.²⁰⁠ Instead, it has been widely accepted that they received considerable amounts of ancestry from an unspecified ‘Basal Eurasian’ lineage. That was done on the basis of pair-wise fst scores which showed drastic differentiation from modern Sub-Saharan groups, as well as the result of testing Neanderthal ancestry which was diluted by a population said to lack such introgression (like Africans). From there, academia has not turned back despite the growing contradictory evidence. And such fallacious practices continued to manifest itself till 2025 where Salem concluded a lack of relatedness between Sub-Saharan Africans and Takarkori.²³⁠ Here we show clear evidence via formal stats ie, qpAdm that not only does TKRS have heavy Sub-Saharan African signatures, but so does the Natufians albeit to a lower magnitude, from an ANA proxy. Moreover, these discrete signatures were present in other ancient Near Eastern populations since the Pleistocene and possibly older in extinct forms.

Firstly in order to better understand the landscape outside of Africa we must address signatures by age. The oldest contributors to found lineages must be characterized in a manner definitive or at least suggestive of something tangible or meaningful. Being that the oldest culture of Africa of which we have genetic evidence for is the Iberomaurasian (Taforalt and Afalou) it is fair to start there. Once sequenced the Taforalt genomes exposed a generalized affinity to both Natufians and Sub-Saharan populations of west Africa; being about 66% and 33% respectively.¹⁶⁠ Further tests rather convincingly if not conclusively shown that they as well as the later sequenced Afalou and Early Neolithic North African agriculturalists and hunter-gatherers were not composed of any two way admixture for which we have genetic samples for.²²⁠ Investigations by various means shown that instead, both Sub-Saharan Africans like the Yoruba of ibadan and the Natufians received ancestry from sources similar to the Iberomaurasian.^22,43⁠ This (reversal of admixing direction) is a theme that is repeated as we discover more samples and perform in-depth analysis. It’s often rather likely that such conclusions are the case where the novel sample is older than the samples necessary to model them. In this instance, the Iberomaurasian burials predated both the Natufian and any other African sample we’ve gathered DNA from to date. Here we’re able to supply more evidence via qpAdm that North African hunter-gathers associated with the Iberomaurasian material culture received their non-African ancestry from a population hitherto-unknown. Furthermore this population, likely the carriers of mitochondrial dna super-lineage U, specifically U6, likely did not contribute a meaningful amount of ancestry to any putative Eurasian population prior to the Iberomaurasian timeline. Rather, they, ultimately by descent, had presence in various African population gene pools and served as a marker of African mediated gene flow within the continent and outwards since the Epipaleolithic. This is evidenced by the failure of any two way admixture result of statistical significance, even with the ANA derived Takarkori individuals in the dataset, as well as a relaxed qpAdm algorithm. Also when the putative African ancestry is adequately accounted for, no two-way three-way or four-way admixture models found success in modeling ancestry of the North African hunter gatherers. Note; Takarkori failed to show a single feasible admixture combination to any significance when testing via this method. These results are in alignment with published literature when adequate African populations are used in the reference set.^16,22,45⁠

Further east at the dawn of the Epipaleolithic, the Natufian farmers show significant evidence of admixture. The source of ancestry in the farmers seems to be in-part related to Western Hunter Gathers on one end and on the other, Saharan and North Africans. Where as, ~25-33% of their genome can be convincingly traced to Saharan Africans. Another interesting phenomena appeared in a replication of the findings in a 2017 pre-print where Lazaridis and co. were able to sequence and analyze a 20+kya individual from Dzudzuana cave Georgia.²²⁠ In place of that sample, here I used an Epi-Paleolithic sample from ancient Turkey whom likely forms a tight clade with them.⁴⁶⁠ Throughout the results it seems the Turkey, Pinarbaşi-like ancestry was widespread through out west Eurasia and Anatolia. This ancestry makes up the bulk of Near Eastern Farmer (early European farmer, EEF) ancestry which mediated the spread of agriculture throughout the western world. The degree to which of such a radical expansion is curious, but credence to such models won’t be explored here. So far our results are in alignment with that of published literature and like Dzudzuana, it seems Pinarbaşi and Natufians are on a cline of WHG and North-African ancestry. ²²⁠ The best Ancestral models for the Epipaleolithic Anatolian involved a mixture of Natufian and WHG (2-way: 40% Natufian x 60% Locshbour. P-val 0.015.) All of the best significant 3-way models for Pinarbaşi involved Locshbour and either Natufians, CHG or both. Trace amounts of East-Asian related ancestry is often picked up when CHG is not in the analysis and deep ancestry can be adequately accounted for by either of the two (Natufian, CHG) late Epipaleolithic candidates.

Similarly, CHG is best modeled with Natufian ancestry, but in place of WHG/Loschbour, and ANE best matches their Hunter-gatherer component. However all 2 and three way models are of a low confidence being that the p-values are less than 0.01. (2-way: 42% Natufian x 58% Mal’ta1 Hunter-Gatherer. P-val 3.0e-04. 3-way: 43% Natufian x 51% Mal’ta1 Hunter-Gatherer x 6% Jomon. P-val 1.5e-03.) Instead, They’re modeled best by a four way mixture of late-ANE, Takarkori, East-Asian-related and Pinarbasi, where as, interestingly, the bulk of their ancestry was contributed to by the latter every run. Lastly of these populations were those of Mesolithic and Neolithic Iran. I took the individuals from the Belt caves (Hotu IIIb)^20,47⁠ and the Neolithic individual from Ganj Dareh³⁸⁠ as representatives. Remarkably but not entirely surprisingly was their higher affinity for African ancestry both Saharan and possibly Sub-Saharan. Like the CHG, their Eurasian hunter-gatherer profile is most similar to ANE, however, instead of Natufians providing the basal ancestry, Takarkori yields the most significant two way result though p-val <0.01. (2-way: 20% Takarkori, 80% Mal’ta1 Hunter-Gatherer, P-val 3.1e-0.3.) Best 3 and 4-way estimates continued to show African affinity with high p-vals, sometimes showing models involving 2 African groups along with the added ANE and broad Epipaleolithic or Basal East-Asian signatures.

Interpretations of qpAdm results.

Relationship between Epipaleolithic North Africans and Eurasians.

With the African test populations of the initial runs failing to produce any meaningful models statistically, it seems so far that available samples including the unreleased Dzuduana were not involved in UP migrations into Africa. There might have been overlap in ancestry though, which is why samples like those found at Ifri Ouberrid and Taforalt can be modeled simply, though not significantly. When excluding derived ancestry from being potential contributors, the Mesolithic North African samples can be modeled as WHG, Ust Ishim and Takarkori, though still, insignificantly. While over half of their genome is Takarkori related, the remaining ancestry is split between the IUP and WHG samples. The only 4-way model was similar with the exception of the IUP being split into a component related to China’s TianYuan man and Russia’s Sunghir 3. This seems to suggest that the people or individuals of West Eurasian decent which back migrated was of a distinct early lineage and not derived WHG. Relatedness to Villabruna as pointed out by a few publications ^17,22⁠ was possibly amplified by the nature of the Villabruna cluster. Simply put, this could be caused by transcontinental contacts between Europe and North Africa. The Villabruna sample while not showing significant evidence of contributing ancestry to the tested African samples, showed evidence of receiving marginal ancestry from almost all African populations in the reference group. This can explain the discrepancy of the Villabruna cline in relation to Western Hunter Gatherers like Loschbour. Early populations of the middle east were likely derived of the western portion of the UP expansion 37kya to which the ancestors of the WHG were also a apart^26,48–50Western Hunter gatherers per-say have distinct ancestry due to high levels of drift coming in and out of the LGM and were more or less unrelated to the contemporaneous populations of the middle east and Africa. However, the Villabruna individual forms a cline with “Basal Eurasian” enriched populations likely because he himself harbor deep or African ancestry. Such findings of genetic relatedness is not in isolation as post cranial metric traits have shown the Villabruna individuals to fall closer to more tropically adapted populations than expected.³²⁠

Argument for Diffusion from Egypt to the Near East before and during the Early Neolithic.

While credited earlier as possibly being a major source of ancestry in Takarkori and populations of the Middle East, Basal Eurasian is merely a place holder due to a nature of uncertainty. What I put forth here is what can be mislabeled as “Basal Eurasian” is divergent East African ancestry, some of which partially drifted towards OOA populations. This East-African related ancestry could have became an early part of West Eurasian ancestry after meeting and mixing with Aurignacian-related populations of the middle east or within North Africa represented by U6 migrants. This gene flow was likely captured in the Upper Paleolithic peopling of the Trans-caucuses region 35-26kya, and represented the deep ancestry in Dzudzuana C. Another interesting fact to consider is the ability to model Basal Eurasian without the need of an African outgroup, reference or proximate donor. If Basal Eurasian lies within the OOA population diversity, defined by the extreme bottleneck, then we can effectively approximate Basal Ancestry with Neanderthals as an outgroup. The sample representing the earliest dispersion into Eurasia, Zlaty Kun, of Czechia can serve as a proxy so long as Neanderthal ancestry is masked by the outgroup. Furthermore, IUP samples like Ust Ishim have already shown evidence to have received ancestry from a population which is, by the definition placed forth in 2014, Basal Eurasian-related.^21,26,51⁠ Patterns of extreme selection in genetic regions which lacked neanderthal segments suggested that Upper-Paleolithic settlers received gene-flow possibly in Asia from a non-Neanderthal admixed group 45-50kya.⁵²⁠ As opposed to the Yoruba, Mbuti or Mota serving as either or both Basal Eurasian proxies and Outgroups, Ust-Ishim and Zlaty-Kun can be used when Neanderthal segments are masked ( Outgroup; Neandethal & Denisovan ). A control and experimental qpADM run involving the Epipaleolithic sample, Pinarbasi (AHG) shows that while deep ancestry can effectively be approximated by Zlaty Kun ( and to a greater extent Ust Ishim, though less statistically significant ) the presence of a single African reference group drastically reduces the scores of any model not including The Saharan or a north African donor. This suggests that some of AHG’s ancestry lies outside of the range of the Eurasian pool we have available.

African ancestry in the Mesolithic near east was more pronounced in the dataset through observers such as the Natufian and Iranian/Iraqi samples of the neolithic and earlier. Material data shown clear influences in pre-Natufian cultures as well as the Natufian biological affinities. These include the lithic transition in the late Kebaran and Mushabian industry and the skeletal morphology of Natufian samples from Shuqba^36,53–57 The samples sequenced and available as of this writing were from a site previously un-published with no skeletal morphological data to reference.²⁰⁠ It is also the case that the sequenced samples were associated with a site (Raqefet) which lacked cultural practices of their contemporaries adopted from African customs.⁷² This allows for speculation of variability in relatedness to contributing populations. In this case being that the Natufians available from Raqefet Cave, can be as much as roughly 24.5% (Saharan Pastoral) to 30% (Morrocan HG + East African HG) putative African. The relatively high levels of Saharan related ancestry ( 19.4% ) in Mesolithic Iran can probably attest to Natufian groups of greater African heritage. It was noted that a sparse implementation of microburin techniques featuring key traits likely invented by those of the Silsilian and developed by Sibilian cultures located in Upper Egypt and Sudan was a key signature of the Zarzian for a short period.^39,53,58,59⁠ Such influences fit with the metrics discovered in Mesolithic Iran at the discovery of the Belt Cave’s HotuIII, who’s Natufian-like cranial traits stand out.⁶⁰⁠ These cultural links were probably facilitated by diffusion from aforementioned admixed populations who were stationed near Sinai. More perplexing is the genesis of the CHG genetic cluster. The CHG is heavily shifted toward Early Iranian, Iraq and Mesolithic Iran people genetically but show different levels of affinity to other populations.^31,61⁠ While the Iranians show clear affinity with Africans the CHG samples seem to be more related to Asians with deep ancestry, such as the Natufians and Dzudzuana/AHG. However what remains consistent is the ANE and Basal East Asian (or SEAHG) ancestry prevalent in both the CHG and early Zagros settlers. Considering the best working models for CHG involves the Saharan, ANE, and SEAHG along with AHG, with the former three proportionate to the ancestry in Hotu III, a Zagros region hunter-gatherer, I postulate CHG might be of a Zarzian + Transcaucus origin (AHG + Hotu/Iran_M/N).

Transitioning to Neolithic era.

Following up the large scale migrations of the pre-neolithic (PPN), were more fine-tuned movements of people in that window of time until the late neolithic. All samples appear to be more related to each other than their elder geographical counterparts. For example, while the closest sample to PPN samples of Turkey is the AHG by far, all Neolithic populations show evidence of gene flow from elsewhere in the Middle East. The least prominent region seems to have been the Levant and Africa during this time, where as, the majority of African related alleles where likely passed around by Zarzian or other early “Transcaucasian” surrogates. Among early Mesopotamian (Nemrik and Mardin PPN) samples⁶²⁠ the core genetic component was that of the CHG as seen in previous studies.^62,63⁠ A similar trend though to less amplitude is seen among other samples of the Middle Eastern PPN period, as individuals of AşıklıHöyük and Boncuklu have moderate affinity to CHG ( 20% and 0-25% respectively. ) As expected Anatolian and Mediterranean populations show elevated relatedness to AHG and Natufian-like ancestry spread moderate to negligibly. An interesting discovery was that of Bestansur, who solely shows more affinity towards Africans than Ganj Dareh of Neolithic Iran. From the greater Levant area there seems not to be an all encompassing set model. No two or three-way model for them in aggregate yields a significant p-Val. Though, regardless , the best model includes their predecessors, Iran Neolithic and AHG, where the bulk of their ancestry can be seen as coming from the latter. (34.4% Natufian, 15.3% Zagros Neolithic and 50.3% AHG. P-val = 0.0133).

Concurrent Neolithic Back Migration.

With the precedent of modeling up-stream populations set, I set forth to initially estimate which populations the Eurasian portion of admixed African are most like. A general trend can be summarized from the collection of data I present here. It appears likely that a possible hunter-gatherer or premature neolithic settlement from the Anatolia area found it’s way towards the Levant. These people would have been responsible for the bulk of the ancestry in the PPN Levant as well as of those moving into Africa. This is evidenced by the presence of mitochondrial haplogroups deep within Kenya during the pastoral neolithic period at-least about 6 thousand years ago being likely of AHG origin (Macrohaplogroup K, AHG is K2b, Kenya Pastoral neolithic is K1a²⁠.) The spread of this ancestry in the middle east between the Levant and Anatolia is interesting in that it seems some-what bidirectional. In this case, the migratory pattern was likely mostly southward if we take into account admixture proportions and the presence of major haplogroups and their frequency. Though it is quite interesting that since early neolithic times the macrohaplogoup distribution appears relatively sex biased, where mitochondrial haplogroups moving south and westward prevailed.^49,64⁠ Whether or not it’s simply due to higher diversity among female lineages in relation to males during this time is yet to be fully investigated, but such patterns are worth noting. Said migrations south in the middle east likely would have been before or in avoidance of CHG expansions as Levant PPN as well as Earlier African admixed samples tend to lack excess relatedness to CHG. Another facet which will be investigated here at a later date is the affinity towards Neolithic Zagros samples and more specifically, affinity for the Bestansur PPN sample prevalent in North Africa.

Logical Procedure & Methods.

Samples used in the multi-analysis above were taken from a various repositories as stated before. A subset of samples related to the neolithic and earlier with the exception of a couple of East Africans (Mota, and Dynastic Egyptian of Nuerat) were extracted for the explicit purposes of modeling ancestry. The goal was to use simple and repeated methods to disentangle ancestral components in a novel way. The core of the analysis was done using formal stats. The precedent set for which to assume models was taken from previous archeological and genetic sources cited. With the bulk of this analysis I employed the Admixtools2 package.⁶⁵⁠

The idea that the ancient Saharan of Takarkori rock shelter would serve as a sort of ‘keystone’ population was hinted at with previous models of their type of ancestry prior to their genetic discovery. Upon genetic sequencing and open availability, it was imperative to follow through and check for certain how the Takarkori sample fit in to the genetic landscape. With that as a focus I used an old method for inferring ‘Ancestral North African’ ancestry. The method uses a collection of f₄ stats to essentially filter out ancestry that would either be considered Eurasian or deeply Sub-Saharan. Though the algorithm wasn’t change over-all, a different approach to ancestry modeling was taken. In this analysis the populations relied upon was Mota of Ethiopia and the high quality ancient Moroccan sample of Ifri Oberrid.⁶⁶⁠ Also, as opposed to having multiple output’s for which to report variable estimates, I looked to gather the mean and average variances per sample. The controlled ancient Eurasian groups were; the ancient Jomon of Japan, 40kya sample from TianYuan China, Initial Upper paleolithic sample Zlaty Kun and slightly later Ust Ishim, and a grouped sample of the Andamanese Onge with Hoabinhian samples of Laos and Malaysia (SEAHG). Grouping the Onge and Hoabinhian samples were strategic in that the samlples form a clade which hasn’t been elaborated in common core East Asian ancestry, but serves as a basal clade. This grouping also allowed for more snps to be grafted into the analysis from that basal East Eurasian sector. These stats were calculated using qpDstat in f4 mode of the original Admixtools software.⁶⁷⁠

The bulk of the models provided in this publication required the usage of qpAdm. Due to the large amount of iterations required for such an analysis, Admixtools2 was the better package. I took a two step approach to running admixture models. First I ran admixtool’s bulk algorithim ‘qpAdm_multi’ on all unique 2-way, 3-way and 4-way combinations of possible donors. This run served as a preliminary run to highlight all feasible models. In between steps one and two, admixture models with a p-value of less than 1e*-4 where flagged as unfit and removed from the analysis. This was done only to the exception of models of samples that lacked any significant results but have feasible models. In those cases only the single most significant model proceeded to step 2. The second step was a straight forward case of running all models carried over from step 1 to get accurate p-values and ancestry coefficients. The function ‘qpAdm’ was ran on each model with arguments and parameters set to mimic results that would have been made via the classical qpAdm program of admixtools (allsnps = TRUE, fudge_twice = TRUE). In the end the top nine models based on p-Value were reported.

With this first post of the series being focused on better understanding ancient Near-Eastern ancestry, I followed the logical path of going down the line chronologically. The focus of this series is Africa so the upper limit was somewhat restricted to North Africa, as the oldest ancestry composition sequenced is from there (Iberomaurasian.¹⁶⁠) Previous work has attempted to show that ancestry in North Africa was related to Dzudzuana a ~26kya sample from the Caucuses, Georgia.²²⁠ Therefore I tackled this type of ancestry using samples available, then meticulously followed up with samples closer to an modern African epicenter both chronologically and geographically. The analysis started primarily with trying to model Takarkori and the Iberomaurasian cluster along with relevant Mesolithic and Epipaleolithic samples of West Eurasia. For reference populations (right pops) I aimed to use samples which were older or not uniquely involved in the epigenesis of any test populations or donors. The heuristic approach done in other studies were repeated here were I cycled out in iterations, individuals of the reference set (with the exception of the out-group; South Africa 2000bp). I also limited the right pops to 4 ancient Africans including the out group, who in total accounts for most of the diversity expressed in modern day populations. This is essentially a the rotating method with temporal stratification with Africans contributing in the run as proxies (proximal competition protocol.)^68–70⁠ Right pops (BEL_GoyetQ116_1, Cameroon_SMA.DG, China_Tianyuan, Ethiopia_4500BP.DG, Japan_Jomon.SG, LIB_Takarkori_RS_PN.DG, Luxembourg_Loschbour.DG, Papuan.DG, RUS_Kostenki14, RUS_MA1_HG, Russia_Sunghir3.SG, SEAHG, South_Africa_2000BP, Ust_Ishim.DG.)

The potential donors (left pops) included samples in the right as well as novel and more derived individuals. Left pops (BEL_GoyetQ116_1, Cameroon_SMA.DG, China_Tianyuan, Ethiopia_4500BP.DG, Georgia_CHG, Ifri_Ouberrid_EpiP.DG, Iran_Ganj_Dareh_N, Japan_Jomon.SG, LIB_Takarkori_RS_PN.DG, Luxembourg_Loschbour.DG, Malawi_Hora_9000BP_all, NaqadaI_Gebelein, Natufian_Raqefet_Cave, Papuan.DG, RUS_AfontovaGora3, RUS_Kostenki14, RUS_MA1_HG, Russia_Sunghir3.SG, SEAHG, TUR_Pınarbaşı_EpiP, Ust_Ishim.DG)

As reported above, no population combination gave significant results for either Takarkori or Ifri Ouberrid, the latter of which was shown explicitly to be the case when at least one African is included in the reference set (right pops.) I also took note of the fact that many of the population combinations were overlapping, (Natufian ancestry in AHG and AHG in Natufian,) So I took to the protocol another time where I systematically removed Eurasian populations younger than the test populations (theoretical admixing dates.) and included Villabruna as a potential donor. African populations were left as is due to the lack of ancient representatives. This was called the ‘NOCHG’ set. In the second pass, I looked to model early Neolithic (PPN) and pastoral Neolithic samples of West Eurasia and Africa. The potential donors would be those of the Mesolithic and Epipaleolithic and Africans represented in the Right populations. The right pops were expanded to include those of known ancestry types from the first couple of runs excluding the Ganj Dareh sample due to age and extraneous SSA/Saharan related ancestry. Right pops ( BEL_GoyetQ116_1, Cameroon_SMA.DG, China_Tianyuan, Ethiopia_4500BP.DG, Georgia_CHG, Japan_Jomon.SG, LIB_Takarkori_RS_PN.DG, Luxembourg_Loschbour.DG, Natufian_Raqefet_Cave, Papuan.DG, RUS_Kostenki14, RUS_MA1_HG, Russia_Sunghir3.SG, SEAHG, South_Africa_2000BP, TUR_Pinarbasi_EpiP, Ust_Ishim.DG )

The third pass held on to the logic of the second, however was a collective test of admixed African samples from the early Pastoral Neolithic phase to the Bronze age. Also, potential donor populations opened up to include Eurasian test populations of the previous step (PPN individuals). This is to get a clear chronological basis of how certain Eurasian elements trickled down into Africa. The fourth pass was simply a test to get best fitting modules of the ancient African samples using all samples tested so far in the Analysis as potential donors. This run serves to set up the basis of comparison for which I’ll reference later in the series when we deconstruct African ancestry of all types.

Table 1. two & three way ancestry models of various admixed ancient East and North Africans. Full dataset can be downloaded here.

Simple 3-way graphing.

Three way admixture estimates were determined using the sample Right pops in passes 2, 3 and 4. The potential donors (left pops) however were limited to Hotu, Takarkori, and AHG. Mesolithic and paleolithic samples in figure 6a used three and four way estimates of the NOCHG set. And proportions not of a unique type of ancestry was reported in aggregate. (example; in 4-way: Ethiopia, TKRS, Pinarbasi, ANE, African-related = TKRS + Ethiopia_4500bp.)

The 2-way ancestry of Takarkori was measured by different means as their ancestry estimates fell outside of the range of variation provided by the samples in the collection of left and right populations. Therefore, I took the approach of using an ancient sample which shown evidence of clustering along a cline of Nilo Saharan East African ancestry and general West African ancestry. That was sample KPL002, of Kakapeli Rock shelter only 300 years ago.⁷¹⁠

Download QP ADM tables below!! (tables S1 – S6)

Part 2: Deconstruction and Demystification of “Ghost” Populations and Un-Linked Industries in Africa.

To be continued.

.Stay tuned…

⁠Don’t Be Afraid to Comment, Like and or Share!

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