Models uncovering African population genetic history


In a deep sense, we know a lot more about the population genetic history of England at the fine-grain than we do about the whole continent of Africa. That’s going to change in the near future, as researchers now realize that the history and emergence of modern humans within the continent was a more complex, and perhaps more multi-regional, affair than had been understood.

Because of the relative dearth of ancient DNA, there has been a lot of deeply analytic work that draws from some pretty abstruse mathematical tools operating on extant empirical data. A series of preprints have come out which use different methods, and arrive at different particular details of results, but ultimately seem to be illuminating a reoccurring set of patterns. Dimly perceived, but sensed nonetheless.

Here’s the latest offering, Models of archaic admixture and recent history from two-locus statistics. I can’t pretend to have read the whole preprint (lots of math), but these empirical results jumped out at me:

We inferred an archaic population to have contributed measurably to Eurasian populations. This branch (putatively Eurasian Neanderthal) split from the branch leading to modern humans between ∼ 470 − 650 thousand years ago, and ∼ 1% of lineages in modern CEU and CHB populations were contributed by this archaic population after the out-of-Africa split. This range of divergence dates compares to previous estimates of the time of divergence between Neanderthals and human populations, estimated at ∼650 kya (Pr¨ufer et al., 2014). The “archaic African” branch split from the modern human branch roughly 460 − 540 kya and contributed ∼ 7.5% to modern YRI in the model (Table A2).

We chose a separate population trio to validate our inference and compare levels of archaic admixture with different representative populations. This second trio consisted of the Luhya in Webuye, Kenya (LWK), Kinh in Ho Chi Minh City, Vietnam (KHV), and British in England and Scotland (GBR). We inferred the KHV and GBR populations to have experienced comparable levels of migration from the putatively Neanderthal branch. However, the LWK population exhibited lower levels of archaic admixture (∼ 6%) in comparison to YRI, suggesting population differences in archaic introgression events within the African continent (Table A3).

To be frank I’m not sure as to the utility of the term “archaic” anymore. I sometimes wish that we’d rename “modern human” to “modal human.” That is, the dominant lineage that was around ~200,000 years ago in relation to modern population ancestry.

Skull from Iwo Eleru, Nigeria. Photo credit: Katerina Harvati and colleagues CC-BY

But, these results are aligned with other work from different research groups which indicate that something basal to all other modern humans, but within a clade of modern humans in relation to Neanderthal-Denisovans, admixed with a modern human lineage expanding out of eastern Africa. The LWK sample is Bantu, and has a minority Nilotic component that has West Eurasian ancestry. This probably accounts for the dilution of the basal lineage from 7.5% to 6%.

I wouldn’t be surprised if the final proportions differ. And other research groups have found deep lineages with African hunter-gatherers. My own view is that it does seem likely that one of the African human populations that flourished ~200, 000 years ago expanded and assimilated many of the other lineages. The “Out of Africa” stream is one branch of this ancient population. But it seems possible that the expansion was incomplete, and that other human lineages persisted elsewhere until a relatively late date.

7 thoughts on “Models uncovering African population genetic history

  1. “The LWK sample is Bantu, and has a minority Nilotic component that has West Eurasian ancestry. This probably accounts for the dilution of the basal lineage from 7.5% to 6%.”

    Some Kenyan Nilotic groups (like the Massai, Turkana, etc) have some minor Eurasian admixture (via the Cushitic admixture that many have).
    But I would expect that a Nilotic component even without west Eurasian ancestry (from a non-Eurasian-admixed Nilotic population such as one from South Sudan e.g. the Dinka, Nuer, etc, or other un-admixed Nilo-Saharan populations) would also somewhat dilute this archaic component. Nilotes, being indigenous to East Africa, would seem likely to lack (or almost lack) this archaic component present in West Africans—or many West Africans (and in Africans of Bantu origin—Bantus being related to West Africans/largely derived from a branch of West Africans). Other indigenous East African populations (such as the ones that contributed the subsaharan ancestry of Horn Africans (perhaps represented by the Mota specimen), or an indigenous East African groups such as the Hadza, might have absent-low levels of this archaic component as well.

    It would also be interesting too compare the levels of this archaic component in subsaharan West Africans from the West African forest zone (such as the Yoruba) to those of subsaharan West Africans from the Sahel and Savannah zones (perhaps the latter group may have more ancestry derived from the above mentioned East African wave of modern human migration, and thus have at least marginally less archaic admixture, if the archaic admixture came from an archaic/basal population local to the forest zone).

  2. Edit: “Populations like Nilotes (and other Nilo-Saharans), being indigenous to East Africa (where the population that emerged 200,000 years ago originated), would seem likely to lack (or almost lack) this archaic component…”

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  3. Edit: “…West Africans from the Sahel and Savannah zones…perhaps may have more ancestry derived from the above mentioned East African wave of modern human migration, and may tend to have at least marginally less archaic/basal admixture than those of the W. African forest region, if the archaic (or basal) admixture came (as it seems it may have) from (or mainly from) an archaic/basal population local to the forest zone (such as something ancestral/related to the possibly archaic-admixed Iwo Eleru population which was found in southern Yorubaland)

  4. 460-540 kya seems pretty recent. What archaic humans from the known anthropological record could’ve contributed to the YRI? I am not sure if we have any obvious candidates. I think it’s much more likely that the contribution was smaller but from a more divergent branch of the human family mediated from an already admixed population. I also agree with the other commenter, the Luhya have no to very little Cushitic ancestry but have plenty of Nilotic sans West Eurasian ancestry. This could simply mean that Nilo-Saharan speakers didn’t experience the same admixture event with this putative basal population as Niger-Congo speakers.

  5. @Mwami Rwanda

    We do have an obvious candidate – the 14 000 year old archaic-ish human buried in Iwo Eleru Cave, Nigeria – actually in Yorubaland, even. Though he/she could be an admixed modern/more archaic human, which really seems more plausible than being a straight archaic isolated for hundreds of thousands of years.

    And I agree, Luhya seem to have very little if any West Eurasian, surely not 20% required to bring 7.5% in Yoruba down to 6% in Luhya. I don’t see any reason to think non-Bantu East Africans would have much, if any, of the same basal/archaic ancestry.

  6. @Megalophias

    We are on the same page. I wouldn’t be surprised if the ancient population that Iwo Eleru belonged to is responsible for the archaic signal detected in the Yoruba. But as you indicated, Iwo Eleru was probably admixed if anything.

    I suspect that Africa’s non-hunter-gatherer populations (Niger-Congo and Nilo-Saharan speakers) owe the majority of their ancestry to Ancient North African (ANA)-like populations and a minority to basal African populations that once dominated the landscape of West and Central Africa. Afro-Asiatic speakers having a similar composition but with limited basal African and significant West/Basal Eurasian admixture. I think that this is supported by multiple lines of evidence, but we’ll just have to wait for more aDNA to bear this out or not.

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