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Massive “Basal Eurasian” back-migration”

In 2005 Dienekes Pontikos had a post up, The mitochondrial time depth of humanity:

It is common to distinguish between Africans and non-Africans, with the former being much more genetically diverse than the latter. But, the real “gap” in human origins seems to be between the really old Africans (“Paleoafricans”) and the rest (“Afrasians”).

The Paleoafrican element is entirely confined to Africa, while the Afrasian one is found in both Africa and Eurasia. Indeed, modern humans can be entirely split into two groups: (i) a group of “pure” Afrasians which includes all non-Africans, and (ii) a group of Afrasian-Paleoafricans which includes all non-Caucasoid Africans. Human groups of entirely Paleoafrican origin, unhybridized with the younger Afrasians are no longer in existence.

Today, a preprint with very sophisticated computational methods of data analysis was posted, Ancient admixture into Africa from the ancestors of non-Africans. The figure to the right shows the proportion of deep “Eurasian” admixture into each major Sub-Saharan African population. Basically this preprint very formally breaks down the high likelihood that Dienekes’ model outlined in the mid-aughts was correct. Even back in 2008, there was an mtDNA phylogeny and coalescence that aligned well with his hypothesis: The Dawn of Human Matrilineal Diversity. Finally, there is the fact Y haplogroup E is dominant among non-hunter-gatherers in Africa, and it is within the “Eurasian-clade” DE.

The abstract of the new preprint makes the genome-wide results pretty clearly in alignment with the older uniparental evidence, as well as some interesting twists that one can infer from population genomics:

Genetic diversity across human populations has been shaped by demographic history, making it possible to infer past demographic events from extant genomes. However, demographic inference in the ancient past is difficult, particularly around the out-of-Africa event in the Late Middle Paleolithic, a period of profound importance to our species’ history. Here we present SMCSMC, a Bayesian method for inference of time-varying population sizes and directional migration rates under the coalescent-with-recombination model, to study ancient demographic events. We find evidence for substantial migration from the ancestors of present-day Eurasians into African groups between 40 and 70 thousand years ago, predating the divergence of Eastern and Western Eurasian lineages. This event accounts for previously unexplained genetic diversity in African populations, and supports the existence of novel population substructure in the Late Middle Paleolithic. Our results indicate that our species’ demographic history around the out-of-Africa event is more complex than previously appreciated.

The reason I put “Basal Eurasian” in the headline is that this is the “ghost population” postulated by the Reich group researchers in the first half of the teens to account for the fact that Mesolithic European hunter-gatherers seem to share more genetically with people such as Oceanians and Han Chinese in some ways that European “first farmers.” More precisely, the early West Asian farmer groups seem to be a mix of a population that is distinct as the “first branch” of non-African humanity, “Basal Eurasians”, and people related to West Eurasian Mesolithic hunter-gatherers. The latter place West Asians in the clade with Pleistocene Europeans and early Siberians, as a “western” group, while the former means that West Asians have ancestry that is more distant to Papuans and Amerindians than Mesolithic European hunter-gatherers.

Another thing that notable about Basal Eurasians is there is some circumstantial evidence that this population did not undergo much admixture with Neanderthals. This is important because the authors above report that the dominant signal of admixture between “40 and 70 thousand years ago” didn’t contribute Neanderthal admixture. Additionally, there’s the symmetrical distance from Han and European, which means that the gene-flow predates that divergence. Europeans have some Basal Eurasian admixture, so the symmetry might imply that this admixture is even basal to the Basal Eurasians (a Lazaridis et al. preprint suggests that there might be such a thing), though I’m not sure they have the statistical power to ascertain this. Rather, whatever this back-migration was, it probably doesn’t extend to a population beyond the Near East, and, it was probably just a bit before the massive “Out of Africa” break that happened ~55,000 years ago and is synchronous with Neanderthal admixture that we currently detect.

There are some things to reflect on in light of these data. First, crazy ideas sometimes are true. Reading Dienekes’ 2005 post today is not that exciting. It is quite plausible, perhaps right even. But in 2005 it seemed crazy. The “dogma” of a tree-like phylogeny and explosive “Out-of-Africa” event all over the world was pretty strong then. It was a robust prior and hard to entertain alternative models. But science advances, so here we are.

Second, terms like “Eurasian” and “African” do a little too much work. The ancestral lineages that we are thinking of here may not have been geographically where we assume using the geographical term. There is a good amount of evidence that the ancestors of the non-African lineage went through a protracted bottleneck. But we don’t know where this bottleneck occurred. We call it “non-African,” but perhaps the bottleneck occurred in Kenya? We don’t know. The bottleneck includes Basal Eurasians, so it predated Neanderthal admixture, and the massive radiation ~55-60,000 years ago. The most likely region is probably the Levant and Arabia. Sub-Saharan Africa seems to be lacking the geographic barriers such as a mega-desert or bodies to water to sustain barriers to gene-flow for thousands of years. But “most likely” does not mean overwhelmingly likely.

Preprints like the one above fill in a lot of general dynamics, but I think ancient DNA is going to be necessary to nail down the model tightly.

What can we expect? Honestly, we don’t know, but here is my general sense of what ancient DNA + better methods + more compute time (look at all the simulations!) + non-genetic information (paleontology, paleoclimate, paleo-everything) might tell us. Below is my best guess outline…

  • Proto-modern humans diversified in Africa 100 to 200 thousand years ago.
  • One branch related to eastern modern humans becomes isolated from other populations 75 to 100 thousand years ago
  • This branch is ancestral “non-Africans.” They are probably located in the southern Near East
  • But, in southeast Asia, there are other earlier expansions of modern human-related groups, which have mixed with local hominins
  • The expansion of the primary non-African group means that most of the signal of earlier Asian “moderns” is gone, though perhaps some of them are responsible for the Denisovan and other archaic signals
  • At the same time that the non-basal non-Africans are pushing east, the basal non-Africans are pushing west. The admixture between Basal Eurasians and African hunter-gatherers of various sorts results in the emergence of what we term Africans qua Africans. My working assumption is that the non-African ancestry in hunter-gatherer populations is due to continuous gene-flow from the primary synthetic groups
  • Archaic admixture everywhere there were earlier human groups

As Iain Mathieson once said, the story of the last few hundred thousand years is the collapse of old structure.

82 thoughts on “Massive “Basal Eurasian” back-migration”

  1. @Obs
    “Tropical forests with their humid climate, flora and fauna, are a very different habitat than the one provided by the Sahara zone.”

    They are. But the non-ANA component of sub-Saharans native to the Savanna/Sahel regions (of proto-Niger-Congo and proto-Nilo-Saharan groups) would likely have been native/local to the savannas and (savanna-forest border zones and south sahel) rather than to the humid tropical forests further south (where other distinct groups such as the direct ancestors of Pygmies would have been found).

  2. @Obs
    “Tropical forests with their humid climate, flora and fauna, are a very different habitat than the one provided by the Sahara zone.”

    They are. That’s true. But the non-ANA component of sub-Saharans native to the Savanna/Sahel regions (of proto-Niger-Congo and proto-Nilo-Saharan groups) would likely have been native/local to the savannas and savannah border zones rather than to the humid humid tropical forests further south (where other distinct groups such as the direct ancestors of Pygmies would have been found).

    @Sally
    “…also had an ancient presence in the Levant. To assume they did not step into the Levant in their 70,000 years of existence is what I don’t agree with.”

    Some may have ranged into the Levant. But whether thise that did were the ones that migrated in to sub-Saharan Africa is a different proposition. It seems to me more likely that the group that made that migration into SSA was (for the most part at least) one (the part of the ANA-like population) that had remained in Africa. But it is as yet uncertain. It would thus make more sense to describe them as a (paleo) northeast African population rather than a Levantine one. Or perhaps they would be called something along the lines of a paleo-North African/paleo-Levanto-Arabian population continuum (?) that was basically native to Northern Africa and its margins/neighboring reagions.

  3. “And regarding Senegalese (the large Wolof ethnic group for instance at least) have little to no Caucasian admixture and speak a Niger-Congo language (of the Atlantic branch) not an Afro-Asiatic one. Many gracile/non-robust types (as well as robust ones) can also be found among the various Niger-Congo (and Nilo-Saharan) peoples of the western (and central) Savanna and Sahel (among many Mande ethic groups in/around Mali for instance).”

    The interesting thing is that these kind of West Africans represent the best the component which deviates from the Pygmies the most. The further down you go, the more you have tendencies towards either Caucasoid proper in the North and East, pygmies in the forest zone or Khoisan in the South. They are, probably, closest to what the original core type looked like, but mixed nevertheless with the earlier layers.
    And concerning the non-ANA-like, more basal African lineages, they came from the North and East too, just they lived there far longer, adapted and probably mixed with local archaics as well. They might have lived in the borderzone, probably even the forest zone, for tens of thousands of years too.

  4. @Obs

    You wrote

    ”The interesting thing is that these kind of West Africans represent the best the component which deviates from the Pygmies the most. The further down you go, the more you have tendencies towards either Caucasoid proper in the North and East, pygmies in the forest zone or Khoisan in the South. They are, probably, closest to what the original core type looked like, but mixed nevertheless with the earlier layers.
    And concerning the non-ANA-like, more basal African lineages, they came from the North and East too, just they lived there far longer, adapted and probably mixed with local archaics as well. They might have lived in the borderzone, probably even the forest zone, for tens of thousands of years too.”

    Agreed, but I don’t agree with your earlier statements that these people who came from the North and East were strictly Caucasians. Remember, there were also different layers of ancient humans in Europe. Early Europeans of the C haplogroup were likely of a Melanesian looking stock (without the Denisovan admixture).

    These early Europeans were the ones migrating into Africa between 70,000-40,000 years ago. The last to arrive were the modern West Eurasian Caucasians. Early Europeans themselves were not homogeneously Caucasian.

    Southern Nigerian people (who carry the Y-DNA DE) would have been one of the first migrants that likely mixed with pygmies. However, there is nothing in their phenotype that screams ‘caucasian’.

  5. @Sally
    “These early Europeans were the ones migrating into Africa between 70,000-40,000 years ago.”

    I think I understand what you mean here. But those who migrated into Africa certainly were not Europeans (nor necessarily Eurasian). At most they would have been a pre/proto-Eurasian or Eurasian-related population or a native northeast African population that also ranged (or whose close relatives ranged) into the Middle Eastern edges of Western Eurasia near Africa. They may have been in some ways similar to the first H. sapiens (the first wave of proto-Aurignacians) to settle Europe or those who settled Melanesia or the Andamans, but would also have been distinct from them (not the same group; both ANA and BE were significantly more basal than those groups).

  6. @Jm8

    I am glad you understand what I am trying to say. Clearly, the use of the word ‘Eurasian’ and ‘African’ is what makes these genetic studies extremely misleading.

    When one hears the word ‘Eurasian’, they think of modern day Caucasians/Asians. But they forget that the ancient Europeans 70,000 years ago, were an entirely different people of a more Melanesian/Andaman-type appearance. These were the first wave of people coming back to Africa mixing with pygmies.

    Just because modern Europeans now occupy the region, it doesn’t mean the ancients resembled them. The whole ‘Eurasian’/ ‘African’ terminology is highly misleading. To put it simply, the Y-DNA DE carriers in Southern Nigeria looked NO different from their ancestors who migrated from Eurasia 70,000 years ago.

    The assumption that there were only two phenotypical layers of humans (from pygmy to Caucasian) is nothing short of narrow minded thinking. Many layers of humans existed in Europe and made their way back to Africa. Even in the Sahel region near Mali I have Tuareg Berbers with shiny straight hair and full blown Igbo phenotypical facial features.

    A good example is Brazil, where natives, blacks and European Caucasians live. The admixture with these 3 groups has created extremely diverse phenotypes.

  7. @Jm8

    You wrote

    ”I think I understand what you mean here. But those who migrated into Africa certainly were not Europeans (nor necessarily Eurasian). At most they would have been a pre/proto-Eurasian or Eurasian-related population or a native northeast African population that also ranged (or whose close relatives ranged) into the Middle Eastern edges of Western Eurasia near Africa. They may have been in some ways similar to the first H. sapiens (the first wave of proto-Aurignacians) to settle Europe or those who settled Melanesia or the Andamans, but would also have been distinct from them (not the same group; both ANA and BE were significantly more basal than those groups).”

    Yes, I understand what you are saying. ANA was more basal than Melanesians, and way more basal than modern Europeans and Caucasians. In my opinion, ANA most likely were Hadza-like. And I bet they looked no different to modern Hadza. Funny enough, Hadza and Southern Nigerians look almost identical.

    It’s a no brainer for me. ANA were not Caucasians. There was certainly another layer, in-between Pygmies and Caucasians.

  8. @Sally
    “To put it simply, the Y-DNA DE carriers in Southern Nigeria looked NO different from their ancestors who migrated from Eurasia 70,000 years ago.”

    I agree that Nigerians and whatever H. sapiens lived in Eurasia at that time may have indeed looked fairly similar. But again, it is by no means certain (or even likely) that the ancestors of Nigerian DE carriers (or at least many of them) ever lived in Eurasia or migrated from there. They (of the bulk of them) may have migrated from northeast Africa (where DE and E may have originated – and CT, being at least as old as 100 kya is even more likely African. Though some BE or ANA-like peoples may have reached the Near East by that time, the likelyhood seem to be that Eurasians mainly descend from a ca 55-60 kya migration from northeast Africa and/ or its margins (whose people likely also resembled Melanesians, Andamanese and/or Sub-Saharan Africans more or less (in a general way).
    I agree with the rest of your comment.

    You also wrote:
    “In my opinion, ANA most likely were Hadza-like. And I bet they looked no different to modern Hadza. Funny enough, Hadza and Igbso almost look alike.”

    That seems very plausible, and in fact likely even, except that there are subtle differences between Igbo and Hadza, but many Hadza can pass for West African and vice versa.

  9. @Jm8

    Also, let’s not forget the Nuba people – extremely muscular, unlike the skinny Dinka. The Nuba are more muscular, are farmers and their facial features look very similar to Southern Nigerians. But they live close to Nilotic and speak a Niger-Kordofan language. Some even speak a Nilotic language. I’ve always assumed that it was the Nuba who migrated to West Africa and mixed with Pygmie, alongside the CT haplogroup.

    The diversity in Africa is immense. My assumption is that the Nuba are Nilotics who mixed with a Hadza-like people.

  10. We deal with largely unknown phenotypes on both ends of the spectrum with Senegal/Mali on one end and Pygmies on the other. Yet both groups mixed and adapted in meantime, are different from both ancestral components. How the original carriers looked like before that admixture and local adaptation is largely unknown.
    The Hadza are interesting as they have practically no basal or more extreme tropical traits and come closer to East Africans with West Eurasian admixture in a way.
    The typical West African core population has traits of its own which are quite specific and, considering the timing, should have been present before in the ANA-like people. I’m just curious, let’s hope they find samples which fit.

  11. @Razib Khan

    “Finally, there is the fact Y haplogroup E is dominant among non-hunter-gatherers in Africa, and it is within the “Eurasian-clade” DE.”

    Yet, it is notable that Nilotes/Nilo-Saharans, who generally lack E and DE (but are more dominated by A and B), seem to have more of this admixture than do Niger-Congo/Niger-Kordofanian peoples (who usually have mostly E).

  12. @ Jm8

    Nilotic peoples don’t lack E at all, they’re plenty loaded with E1b1b lineages, especially (maybe exclusively?) E-M78 and derivatives. So it’s not surpising at all that they would have more Eurasian ancestry than NC speakers given that they’ve received significantly more admixture from Eurasians within the past 10,000 years.

  13. @Mick

    Nilotic peoples that have Cushitic admixture (such as the Maassai and others from that general region) have Eurasian ancestry (and significant rates of E1b1b. But unmixed Nilotes such as those found in South Sudan (like the Dinka, who are often used as a Nilotic sample in these studies) do not tend to have much E, and little if any Eurasian admixture from the last 10,000 years.

  14. (Cont.) There are low rates of E1b1b in some (South Sudanese Nilotes), possibly from minor and relatively recent North African admiture, but A and B are generally dominant.

  15. That’s more or less what I was referring to (but I will try ro find better and mire recent haplogroup data on Sudanese Nilites). Core Southern Sudanese Nilotes have about 10-17% E1b1b and the rest mostly A and B. E1b1b is generally associated with heavily Eurasian or Eurasian admixture-bearing Near Easterners, North Africans, or Horn Africans. But South Sudanese Nilotes seem to have very little Eurasian autosomal ancestry (at least from the last 10,000 years). See here (several tables with Eurasian admixture estimates for various African ethnic groups):

    http://anthromadness.blogspot.com/2016/01/the-mota-mistake.html?m=1

    Their minor but not significant rate of E1b1b compared to their very/much lower amounts of Eurasian autosomal dna could perhaps be explained by bottlenecking (hard to say). But nonetheless, E is in the minority aming most South Sudanese Nilotic (and some other Nilo-Saharan) groups.

  16. Edit: Should be:

    “Their minor but not insignificant rate of E1b1b compared…”

  17. As far as phenotype is concerned. I really don’t know about large early populations but there was a cromagnid skull from south Africa from 36,000 years ago. The extremely basal rich IBM and Hotu cave people were also cromagnid. I think that races like Caucasians and Negroids are recent evolutes out of older cromagnid and paleo Africans.

  18. IIRC the Iberomaurusian paper concluded that population was dark in terms of skin color. This isn’t surprising, considering the Natufians (and hell, WHG) were also apparently dark-skinned. I do believe they had the “European” variant of a gene associated with straighter hair however, meaning they would not have looked straight-up SSA however. Of course, the Iberomaurusians were themselves an admixed population, and the straighter hair texture may indeed have come from Natufians (I can’t find any references to Natufian hair texture online).

    The presence of various genetically East Eurasian populations (Andaman Islanders, some Papuans, etc) who – when missing any other admixture – can pass for Sub-Saharan African does strongly suggest that medium-dark brown skin with kinky black hair was a basal trait for the OOA population – meaning it was likely the original phenotype for Ancient North Africans and Basal Eurasians as well (though drift and selection likely changed trait expression across tens of thousands of years).

  19. @DaThang

    Cromagnons (in the classical sense) were an early Western Eurasian type (that began to develop in Western Eurasia/Europe sometime around the 30,000s BC or later), but even in their early stage, still retained many “racially undifferentiated” tendencies shared by other humans in sub-Saharan Africa and elsewhere in Eurasia.

    Eastern Eurasians and Oceanians/Andamanese/Australo-Melanesians do not derive from cromagnons (nor do sub-Saharan Africans) but from earlier more basal types. And the Basal Eurasians and ANA (being yet more basal) would not have belonged to it (the cromagnon type) or derived from it.

    An early skull from ca 55,000 years ago found in the Levant (Manot Cave,Isreal) was found to resemble those of recent (sub-Saharan) Africans, as well as, in some respects, those of the earliest Upper Paleolithic modern humans of Europe (who were still somewhat undifferentiated and had not yet diverged fully into the (later/classic) cromagnon type), but it was not found to be similar to modern European/Western Eurasian skulls (beyond being clearly modern human).
    The skull could have belonged to a Basal Eurasian (or partly Basal Eurasian individual) or it could have been from an early non-Basal Eurasian (early ancestral “crown Eurasian”) ancestral to other Eurasian populations (or even possibly an individual with sone ANA ancestry). Either way, being early (if early Eurasian), as an early Eurasian, it still retained many pre-OOA African/African-like traits and tendencies.

    https://www.nature.com/articles/nature14134?draft=collection

    @Karl Zimmerman

    That (your reasoning regarding likely OOA, ANA, and Basal Eurasian phenotype tendencies) indeed makes sense. And I would agree.

  20. @Jm8

    Can’t access the full text in your link. Here is the Hofmeyr skull paper:

    https://web.archive.org/web/20090605030704/https://www.eva.mpg.de/evolution/pdf/Grine_et_al_2007.pdf

    Closer to EUP than the rest, though it is not the exact same thing.

    Looking briefly at the titled paper on researchgate, the Manot skull also overlaps with the Australians. Similarity to them doesn’t necessarily preclude the result from the 2007 paper and what I said earlier- that both Caucasoids and Negroids (addendum: more so the former than the latter) are recent byproducts of much older populations. A lot of the old cromagnid skulls also were in the African-Australian intersection, but there are large parts of the African and Australian sections outside of the range of these ancient skulls- maybe recent changes kind of like how European and Asian sections are even more outside of the zones of the range of these skulls. The older populations were most likely a mish-mash of cro magnids + proto-Australoids and Paleo-Africans. Modern Africans and Australians likely better retained the older traits.

  21. @karl zimmerman

    >medium-dark brown skin with kinky black hair was a basal trait for the OOA population

    Razib said something about the hair- in reference to Australian aboriginals having wavy hair as opposed to kinky hair.

    https://www.gnxp.com/WordPress/2019/02/24/ancestral-proto-eurasians-may-have-had-wavy-hair/

    “Hair form is a polygenic trait. It is not unreasonable to think that the humans moving out of Africa would carry standing variation, and that selection for curlier hair in some tropical climates would result in convergent evolution. The ancestors of Papuans and Negritos then may have had wavy hair, and Australian Aboriginals simply maintained this.”

    Maybe a mix of kinky hair and curly hair.

  22. @DaThang

    A mix of kinky and curly may be plausible, but kinky hair/a predominance of kinky hair seems most likely (for the aforementioned basal/common ancestor groups). Several (not especially closely related) populations in Oceania and southern Eurasia have kinky hair (or tend to, especially when unmixed). Papuans and Negritos have it, and so do most Melanesians (esp. those with little Austronesian admixture), as well as Andamanese, and Tasmanian Aboriginals also did.

    The various widely disparate and divergent Sub-Saharan populations also have kinky hair pretty consistently (excluding those with significant known/recent Eurasian admixture like those of much of the Horn of Africa, who, unsurprisingly, due to admixture, have a wider range of hair types – including sometimes kinky).

  23. Cont.: …and Tasmania is not an especially tropical climate (also perhaps suggesting the retention of the trait or tendency of kinky hair in the Tasmanians from an earlier period, and its loss in most of the Native groups of mainland Australia and elsewhere – Australia also may have recieved more than one wave of settlement, including some in which many had lost the trait/tendency).

  24. @DaThang

    I also made some comments to this effect – re possible ancestral hair textures (perhaps better explained there than here) in the comments section of the page/entry you linked in your last comment.

  25. This is a bit of an aside, but it’s always interested me why humans developed kinky hair to begin with. There are many hypotheses that are given for how it made us better adapted to the savanna environment, but the key issue with a lot of them is that other animals in the same environment do not develop kinky hair. Indeed, as far as I am aware, curly hair in non-human mammals only occurs in domestics, which suggests that it’s actively selected against in general – which makes sense, because of the risk of matted hair interfering with shedding, contributing potentially to infections, etc.

    My own best guess is it had something to do with the unique traits of humans – limited body hair and copious sweating. The former meant that there really wasn’t that much of a risk of tangling, other than on the head. In terms of the latter, kinky hair is less likely to hold sweat in a sopping mess. Since the whole point of sweat is evaporative cooling, it’s better that the sweat drip down the scalp onto exposed skin on the face and neck than get absorbed into the hair and drip off the strands onto the ground.

    I’m not that knowledgeable about the genetics of hair texture, but it’s pretty clear that it must be a pretty significantly polygenic trait involving lots of variants which still affect hair texture when heterozygous. It’s interesting to note that biracial people who have half SSA ancestry still usually have functionally kinky hair. To a large extent this is because there’s not that much difference between curly hair with a 1/2 cm diameter and hair with a 1 cm curl – it’s still going to look kinky unless it’s pretty long. Still, that humans can and do have hair so much curlier than any other species suggests it was very heavily selected for in Africa.

  26. @Jm8
    I doubt that there is substantial non-Australiasian ancestry in Australians or even if there is enough of it to have introduced a new trait. Over at global25 they somehow get a good fit with papauan(about 2/3) + onge (about 1/3)-> both kinky haired populations. Though idk if it has much meaning since Onge is kind of a hammer that happens to hit a lot of nails. Using hoabinhan instead gives similar results, but then they were negrito-australasian as well.

    Maybe early on, the polyenic trait encompassed both wavy and kinky hair (higher frequency of the latter), with the heavier straight hair being the more recent variant.

  27. @DaThang

    I didn’t mean so much that there was substantial non-Australasian ancestry in Australians, but rather that they were perhaps affected by later waves of settlement (by peoples also within the broad Australasian family, but who may have lost the trait/had developed a modified/less basal genetic profile regarding hair type).

  28. >by peoples also within the broad Australasian family, but who may have lost the trait/had developed a modified/less basal genetic profile regarding hair type

    Could be this.

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