Linking genetics with reality: Short hand analysis of African DNA under archaeological context.

So what’s going on?

Since as far as I can remember (2014) there has been an obsession with a particular set of people across the many layers of the bioanthropology community. Researchers and enthusiasts alike sought the means to properly identify and label this mysterious group as they hadn’t really been known by anyone prior. It’s been quite difficult as these people lived and died but hadn’t left behind any bones, culture or industry. They merely contributed to the genepool of those who’d go on to invent farming in the middle east. I’m referring to Basal-Eurasians. A population who weren’t African (“Sub-Saharan African”) but not quite Eurasian either. So who were they? Long story short, I don’t know and will continue to not know until something else can substantiate their existence, like say… an industry, burials or even culture. However I mentioned them to segue into a subjectively more interesting title of people, who’s existence was labeled by the same set of individuals who titled Basal-Eurasian. I’m speaking about Ancestral North Africans (ANA). Considering the fact that an argued point was that the previously mentioned Basal-Eurasians were resident North Africans, it felt appropriate to draw comparisons between the two hypothetical groups. Though the differences are more compelling, as the later group, Ancestral North African, might actually have bones, industries and a culture to tie them to. Some of which will be touched upon below. And like how Basal Eurasian is set to be ancestor shared by all modern day West Eurasians, ANA ancestry might be a component in virtually all Africans today.

What is ANA?

Ancestral North African (ANA) is supposedly a population which had diverged from an early east African population similar to the “pure” ancestors of Mota.¹⁠ They would hypothetically be the “pre-Basal Eurasians” or more descriptively, the “African Basal Eurasians.” However if this population existed, they would have contributed Admixture to the ancestors of not only present day North Africans but also to West and East Africans (and historical South Africans by extension).^1,2⁠ To put this into perspective, If the description holds true for this “Ghost” North African population, then the common genetic profile for Bantu speakers should accompany this ghost admixture. The Bantu expansion was said to be the largest migratory event in Africa. Their genetic influence also supersedes their cultural influence and language; having contributed to populations such as all African rain-forest hunter-gatherers,⁴⁰⁠ most south African hunter-gatherer groups and some East African Nilosaharan and Afroasiatic groups like the Masai⁴¹⁠ and Iraqw respectively.³⁠

North Africans by way of populations who prehistorically lived in North Africa, obviously harbors ANA ancestry.⁴⁠ And most East African populations who by way of North East African diffusion should also have this ancestry. As opposed to going down the copious list of populations in Africa who have ANA ancestry, we should instead focus on who doesn’t. A few groups of people come to mind when making such inquiries, all of whom primarily resides in East Africa. To summarize down to two: the Southern Sudanese Nilotic people and the historic Hunter-gatherer groups of the Great-Lakes and above like the Hadza. We can effectively dismiss the Latter as while they haven’t necessarily been linked to receiving ancestry from ANA, they’re effectively assigned to be related to the progenitors of ANA. This is why Mota a 4.5 thousand year old hunter-gatherer from Ethiopia, has and is currently being used to identify or serve as a proxy for Basal Eurasian and North African Ancestry. The Southern Sudanese groups however are a more interesting case. To date there hasn’t been a comprehensive look into if the Southern Sudanese Nilotic people have any ANA ancestry. And anecdotally, it’s been hard for even me to come across an admixture graph (qpGraph) which included certain ancient African samples and the aforementioned Nilotic groups. So for a more in depth look at Africa’s genetic landscape I went ahead and graphed an admixture chart.

Admixture Graph

ADNA is a recent advent however current acceptance of human population history haven’t changed much since it was first conceived with only extant DNA. For reference, most studies reiterated the same narrative with the branching-off of Africans based on the quadrant of the continent they currently reside. First, after reaching the stage of “Anatomically Modern Human” (AMH), the South African Hunter-Gathers branched off, then the West Africans, then the East Africans, and then after the Eurasians diversified.^5,6 North Africans were said to merely be a set of Eurasians that made it back to Africa and stayed near the coast or trickled down the Nile “corridor.”^7,8⁠ If that model was our most accepted view of African biological history, then it’d only be natural that future models will adhere closely to the concepts it suggested. So instead of a finding like that of Ballitobay’s Ancient Hunter-gatherers⁹⁠ urging researchers to rebuild the Human phyla from the ground up. We’ve either tried to figure out where they should fit on our current phyla, admixture graphs and pcas or ignored them all together in some subsequent genomics studies. It’s quite disappointing that that’s the workflow when it’s been shown how different our understanding of old movements within and out of Africa could be when considering these individuals. Furthermore, we’ve seen how a different narrative can be crafted when reassessing what we know to better reconcile with new found aDNA from Africa. For example, autosomal signals of South western Europe getting African admixture long before the islamic slave trade¹⁰⁠. And in that case, the aforementioned Ballitobay samples were useful in parsing elicit (non-North) African Ancestry in ancient Iberians.

The Ballitobay South African Hunter Gatherers were two individuals excavated from a shell midden near the Ballito bay shores. They lived about 2,000 years ago and were biologically most similar to modern Khoisan related groups of South Africa. ¹¹⁠Their autosomal make up was key to reassessing the age of anatomically modern humans due to their early divergence. The modern human age told by DNA had now been pushed from around 250,000 to 350,000 years ago.⁹⁠

With that being said I was careful in trying to model relationships between ancient individuals. For example the following chart was primarily composed of Ancient individuals for the purpose of avoiding much bias by modern interpretation when reconstructing the ancient human phylogeny. The goal was to build from the base up. Three populations I considered initially, was an individual from the Faroaskopp rockshelter in South Africa, Mota, and a group of individuals excavated from Shum Laka site. They each would be representative of the geographical quadrants of Africa mentioned prior; ancient South Africa, East Africa and West Africa respectively. And (not) to my surprise (After accounting for archaic hominids) all three of the “quadrants” seem to show evidence of them splitting around the same time. You can tell by the zero length drift from Anatomically modern humans to the fork that separates the ancient South African and Mota. This wouldn’t be the first publication showing such nuance through these means. Lipson (2020) showed the same relationship among Africans in the study that premiered the genomes Shum Laka’s individuals.²⁠

Predictions.

Graph alone, everything about the substructure within Africa going back to ancient times can’t be resolved. But it called my interest into who or what AWS and ANA could be. For AWS my initial thoughts were the “Ghost human” labeled by Lipson 2020 et al.²⁠ This line of ancestry was heavily represented by modern day West Africans in their schema. Furthermore, the requirement of it’s ancestry by Mota (29%) was also implied by their estimations when fitting Taforalt with west Africans and the Shum Laka samples. ANA however, is a bit more grounded due to it’s strong presence in the region of Africa which had garnered the most archaeological attention, the East. And as shown previously, West Africans for example, most likely require a source of admixture which had descended from the core ancestry of Mota.^1,2,21,22⁠ This model alone single-handedly makes this East African related group or ANA the leading single distributor of ancestry on the continent.

To further explore the impact of this group, I sought to calculate the amount of potential ANA-related ancestry in a select few populations. The process involved a (not so) complicated use of fstats to “prune” ancestry that’s both basal to Mota and shared drift with Eurasians. Essentially what that’ll be is shared drift with a group that diverged between Mota’s putative East African and Taforalts non-Eurasian. For more details see The Breakdown.

ANA Estimates

Up to the point this passage was written only a select few populations and individuals had been tested. As an ongoing experiment more people will be analyzed for this ANA component.

Outside of the stats.

Could the findings of ANA be a statistical anomaly? Perhaps. But such a conclusion is undermined by potential archaeological correspondences. Unlike Basal Eurasian²⁵⁠ per-say, ANA seems to have some cultural support based on it’s pattern of distribution. Be aware that their cultural identity as well as the genetic identity of cultures I will link them to is still theoretical. Further evidence is required to firmly place these people in their rightful context.

First and foremost if this population were to exist based on what we’ve theorized prior, they’d probably have had a long standing in East-Africa. This population must have expanded into North Africa sometime during or prior to the Late stone age in which they diverged and later mixed with West Eurasian hunter-gatherers there and in the Near-East. Some others could have likely remained in eastern Africa but expanded further during the last subpluvial. Some would have traveled west into the Sahara to form complex mixture with the descendants of Ancient West-Sudanic people and maybe some of the earlier West Eurasian Admixed populations of North Africa who had expanded south.

Ideally there is a cultural phenomena that loosely corresponds with this trend. This would be the “Aqualithic culture”²⁶⁠ characterized by African barbed bone points and (dotted) wavy line pottery. Initially it had been suggested that this tradition followed the distribution of Nilosaharan languages.²⁶⁠ That assertion was also backed up when overlaying the sites where the bone points were discovered and nilosaharan languages²⁷⁠ This could speak to the association with the ANA component calculated above and Nilotic populations such as the Dinka. However Yellen (1998), who proposed that most barbed bone points in Africa bore enough similarity to be defined as derived from a common tradition²⁸⁠ concluded there was lack of a correlation between the usage of said tradition and any ethno-linguistic affiliation. He noted:

“..examination of barbed bone points in the broadest perspective permits several conclusions and speculations. First, the data clearly show that this tradition does not map on to any tightly defined linguistic or biological group and does not serve as a marker for any “cultural” entity as defined by common anthropological usage of the term. The northern Kalahari points are definitely associated with Khoisan peoples, the Ishangan with Nilotes or Nilote predecessors, and it is difficult to imagine a “culture” which extends from the central Sahara through the East African Lakes.”

-John Yellen, “Barbed bone points: Tradition and continuity in Saharan and Sub-Saharan Africa”

Yellen’s assessment is still fair when looking at the figure 3. from Drake (2011). Barbed bone points stretched as far north as Morocco and as far south as Botswana. This pattern might indeed out-range nilosaharan distribution. This gives more credence to the pattern we see when parsing ANA-related ancestry, as in this case, there is a strong biological affinity as opposed to a linguistic one to cover it’s distribution. Wavy line and dotted wavy line pottery follows a similar narrative, however more so to the exclusion of North and the more southern regions of Africa. Interestingly Wavy-line pottery though linked to the same early Holocene expansions might have it’s origins in western Africa unlike the observed barbed bone points which probably coalesced in east Africa before 20kya.²⁸⁠ As it appears, Sites in Niger for example uphold the oldest dates and nearby regions show non-derivative diversity in style not seen in Khartoum for example.^38,39⁠ However the true chronology of this cultures diffusion hasn’t been established yet, as discoveries within the Sahara and Sahel remains fragmented. More evidence and discussion regarding (dotted) wavy-line pottery and their potential genetic affiliates shall be explored in detail in a later publication.

Considering the fact that most of these events are dated towards the Holocene, association with North Africans needs further investigation. For one, Barbed bone points in North Africa were associated with the “Iberomaurasian” an industry which includes the Taforalt individuals.²⁸⁠ They were at most contemporaries with the Khartoum neolithic and would have predated Holocene expansions. So as described earlier these groups would have had to migrate northwest sometime between 30 thousand and 14 thousand years ago, prior to the interactions within the greened Sahara. Also the Biological Affinity measured by morphology or “morphometrics” disrupts patterns of continuity, even among the Africans who were found within or south of the Sahara. For instance, Iberomaurasians were given a morphological classification which separated them from most other Africans.^16,29–31⁠⁠ To further complicate matters certain groups within the contexts Eastern Africa were given biological association with the North African groups that included the Iberomaurasian. Some examples would be the Nubian A-group³⁰⁠, Nakuru or “Kenya Capsian,”^32,33⁠ and the Holocene Hora³⁴⁠. These North African biological affiliations would be to the exclusion of most Africans associated with the Aqualithic traditions or Becker’s (2011) Saharo-Nilotic complex.³⁰⁠ ⁠

Just like the prehistoric inhabitants of the Wadi Howar, the Early and Middle Holocene population of the Malian Sahara and the Late Pleistocene Jebel Sahaba/Tushka population belonged to the Saharo-Nilotic population complex. None of these biologically sub-Saharan groups shared any direct ancestors with prehistoric North Africans. The A-Group, on the other hand, was not part of the Saharo-Nilotic population complex.

– Erik Becker, “The prehistoric inhabitants of the Wadi Howar”

My thoughts

It can be proposed that among ANA there was substructure most likely molded by temporal distribution and interactions with other Africans and maybe west Eurasians. “Pure” ANA ancestry had probably been long gone before even the Iberomaurasian in North Africa. In any case the most pristine ANA population could have been populations of the nile not exposed to West-Eurasian admixture. These would have been the Mesolithic Nubians mentioned earlier, such as Tushka or Jebel Sahaba. Regardless if the previous statement is true or not it remains that the aforementioned groups were not the progenitors of LSA north Africans, but probably adjacent descendants of a common east African ancestor. In which an assertion like the one made in pendergast, (2019) where North East African ancestry is on a cline from being South Sudanese related (by way of Mesolithic Nubians) to Near East related (By way of biological North Africans) is probably close to reality.³⁵⁠ Populations like the Dinka could have been a combination of the mysterious west Sudanic group (AWS) and an ANA population who formed a complex culture in the Sahara. Then as described in Becker (2011), had recombined with the people who showed continuity from Mesolithic Nubian in the Nile.³⁰⁠ West Africans could have been descendant of the Saharans mentioned but who instead recombined with AWS people, west. Biological similarities with North Africans in East Africans (and to a lesser extent west Africa³⁶⁠), could have been a result of North Africans who had penetrated the Sahara or traveled up the Nile deep into more southern regions³⁰⁠.

It remains to be seen if the bulk of ANA ancestry had resided in geographical North East Africa in it’s entirety and what it’ll mean for concepts such as Basal Eurasian. Pagani in 2019 reviewed the landscape and written on the possibility of bottle-necked group of Africans who’d remained in North Africa after around 60,Kya. He explained the necessity of such ancestry being widespread in every African in order for North Africans to be uniquely North African. But the contexts weren’t in lieu of African ancestry and diversity but instead Eurasian.³⁷⁠ When speaking on regions of deep ancestry shared between North Africans and West Eurasians who harbor said ancestry he stated:

“If these regions are simply reflecting shared ancestry between any African and any Eurasian population, rather than the presence of a Natufian-like genetic leaking across the Green Sahara, then they should be equally present in all African populations and the resulting population split estimates should not be affected by the masking procedure.”

-Luca Pagani, “What is Africa? A human perspective.”

He went on to even state that North Africans would have needed to be biologically Eurasian at the time in order to explain continuity.³⁷⁠ Such extreme scenarios are not necessary to explain the relationship between the ancient individuals in question. We don’t yet know to which extent North Africans had been bottle-necked or contributed to/received contributions from neighboring Eurasian populations in order to make such assertions on the requirements of their genetic history. However put, there is a case to be made that regardless of the importance of actual Eurasian admixture in North Africa, there was an indigenous presence outside of the diversity that categorizes Non-African populations.

Nonetheless it is ironic that the question as to “who is responsible for the bulk of ‘Sub-Saharan’ ancestry, is reliant on Saharan and North African population history. On top of the evidence mentioned, there are quite a few industries and genetic factors that contributes to the departmentalization of Northern and Southern Africa. What was mentioned so far was only the beginning of what’s to be unveiled here. This is a call to action for people who share an interest in human population history to take a deeper, and more comprehensive look into African archaeology and bio-anthropology. If admissible such a finding like this shared ANA component would have been buried under preconceived notions and sociopolitical views on the history of Africans and what makes them Africans.

References

1. Lazaridis, I., Belfer-cohen, A., Mallick, S. & Patterson, N. Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry.

2. Lipson, M. et al. Ancient West African foragers in the context of African population history. Nature 1–6 (2020) doi:10.1038/s41586-020-1929-1.

3. Tishkoff, S. A. et al. The Genetic Structure and History of Africans and African Americans. Science (80-. ). 324, 1035–1044 (2009).

4. Fregel, R., Méndez, F. L., Bokbot, Y., Martín-socas, D. & Camalich-massieu, M. D. Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe. (2018) doi:10.1073/pnas.1800851115.

5. Schlebusch, C. M. & Jakobsson, M. Tales of Human Migration, Admixture, and Selection in Africa. Annu. Rev. Genomics Hum. Genet. 19, 405–428 (2018).

6. Bergström, A., Stringer, C., Hajdinjak, M., Scerri, E. M. L. & Skoglund, P. Origins of modern human ancestry. Nature 590, 229–237 (2021).

7. Henn, B. M. et al. Genomic ancestry of North Africans supports back-to-Africa migrations. PLoS Genet. 8, (2012).

8. Olivieri, A. et al. The mtDNA legacy of the Levantine early Upper Palaeolithic in Africa. Science (80-. ). 314, 1767–1770 (2006).

9. Schlebusch, C. M. et al. Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago. bioRxiv 655, 652–655 (2017).

10. González-Fortes, G. et al. A western route of prehistoric human migration from Africa into the Iberian Peninsula. Proc. R. Soc. B Biol. Sci. 286, 20182288 (2019).

11. Ribot, I., Sealy, J., Morris, A. G. & Maggs, T. Population history and economic change in the last 2000 years in KwaZulu-Natal, RSA. South. African Humanit. 22, 89–112 (2010).

12. Fu, Q. et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445–9 (2014).

13. Yang, M. A. et al. 40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia. Curr. Biol. 27, 3202-3208.e9 (2017).

14. Sikora, M. et al. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science (80-. ). 358, 659–662 (2017).

15. van de Loosdrecht, M. et al. Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations. Science (80-. ). 8380, eaar8380 (2018).

16. Irish, J. D. The Iberomaurusian enigma: North African progenitor or dead end? J. Hum. Evol. 39, 393–410 (2000).

17. Lazaridis, I., Nadel, D., Rollefson, G., Merrett, D. C. & Rohland, N. The genetic structure of the world ’ s first farmers. (2016) doi:https://doi.org/10.1101/059311.

18. Bar-Yosef, O. & Belfer-Cohen, A. The Levantine Upper Palaeolithic and Epipalaeolithic. South-eastern Mediterr. peoples between 130,000 10,000 years ago 144–167 (2010).

19. Skov, L. et al. Extreme selective sweeps displaced archaic admixture across the human X chromosome around 50,000 years ago. bioRxiv 503995 (2018).

20. McColl, H. et al. The prehistoric peopling of Southeast Asia. Science (80-. ). 361, 88–92 (2018).

21. Schlebusch, C. M. et al. Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago. bioRxiv (2017).

22. Skoglund, P. et al. Reconstructing Prehistoric African Population Structure. Cell 171, 59-71.e21 (2017).

23. Rodríguez-Varela, R. et al. Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans. Curr. Biol. 27, 3396-3402.e5 (2017).

24. Wang, K. et al. Ancient genomes reveal complex patterns of population movement , interaction , and replacement in sub-Saharan Africa. 1–15 (2020).

25. Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Fig S3 Pre-Revised. Chart 14 doi:10.1101/001552.

26. Sutton, J. E. G. The Aquatic Civilization of Middle Africa. J. Afr. Hist. 15, 527–546 (1974).

27. Drake, N. A., Blench, R. M., Armitage, S. J., Bristow, C. S. & White, K. H. Ancient watercourses and biogeography of the Sahara explain the peopling of the desert. Proc. Natl. Acad. Sci. U. S. A. 108, 458–462 (2011).

28. Yellen, J. E. Barbed bone points: Tradition and continuity in Saharan and Sub-Saharan Africa. African Archaeol. Rev. 15, 173–198 (1998).

29. Vermeersch, P. M. Palaeolithic Quarrying Sites in Upper and Middle Egypt. Egypt. Prehistory Monogr. (2002).

30. Becker, E. The prehistoric inhabitants of the Wadi Howar. (2011).

31. Holliday, T. W. Population Affinities of the Jebel Sahaba Skeletal Sample: Limb Proportion Evidence. Int. J. Osteoarchaeol. 25, 466–476 (2015).

32. Correia, M. et al. Who were the Nataruk people ? Mandibular morphology among late Pleistocene and early Holocene fi sher-forager populations of West Aur e. 2018, (2018).

33. Cole, S. The Prehistory of East Africa. Am. Anthropol. 56, 1026–1050 (1954).

34. Tobias, P. V. The men who came before Malawian history. (1972).

35. Prendergast, M. E. et al. Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa. Science (80-. ). 12, eaaw6275 (2019).

36. Groves, C. & Thorne, A. The terminal Pleistocence and early Holocene populations of northern Africa. (1999).

37. Pagani, L. & Crevecoeur, I. What is Africa? A human perspective. Mod. Hum. Orig. Dispersal 15–24 (2019).

38. Garcea, E. A. A. From early Khartoum to the Saharan neolithic : Ceramics in comparison. Cah. Rech. l’Institut Papyrol. d’Egyptologie Lille 17, 91–104 (1998).

39. Mohammed-Ali, A. S. & Khabir, A.-R. M. The wavy line and the dotted wavy line pottery in the prehistory of the Central Nile and the Sahara-Sahel belt. African Archaeol. Rev. 20, 25–58 (2003).

40. Busby, G. B. et al. Admixture into and within sub-Saharan Africa. Elife 5, e15266 (2016).

41. Pickrell, J. K. et al. Ancient west Eurasian ancestry in southern and eastern Africa. Proc. Natl. Acad. Sci. U. S. A. 111, 2632–7 (2014).