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ncomms4163-f1

Citation: Nature Communications 5, Article number: 3163 doi:10.1038/ncomms4163

Mbuti

Mbuti

Etienne Patin has another paper out on the genomics of Central Africa, and the relationship of the Pygmies to their agriculturalist neighbors, The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists. It is to a great extent expanding upon earlier work with denser marker sets, larger sample sizes, and of course ~2014 statistical genomic techniques (e.g., ALDER). As background you have to remember what Patin established before: the western and eastern Pygmy populations of the Congo rainforest seem to have diverged tens of thousands of years ago, tens of thousands of years after their divergence from the ancestors of their agriculturalist neighbors. By and large these neighbors speak Bantu languages, which have swept out of the eastern fringe of what is today Nigeria only within the last 3,000 years. The numbers alluded to the paper are separations on the order of ~20,000 years before the present for the Pygmy groups (west vs east), and then ~50,000 years for the ancestors of the agriculturalists vs. the proto-Pygmies. Think about this: diversification within Africa occurred at about the same time that the most distant of the non-African groups were starting to become isolated from each other. The Pygmies are not just interesting from an ethnological perspective, along with the Khoisan they preserve to a high degree an ancient and diverged group of populations which have largely been marginalized due to the demographic expansions of peoples speaking Niger-Congo and Nilo-Saharan languages (the Pygmy speak the languages of their agricultural neighbors, but this seems a recent development).

An interesting twist revealed in this paper is that admixtures seem to be relatively recent (on the order of 1,000 years), and, those levels are quite high indeed in many Pygmy populations. This is not the case with agriculturalists. In other words, the genes of agriculturalists seeped into the Pygmies, but far less moved in the reverse direction. As analogy, consider that the average Native American is far more European than the average European American is Native. But, as with the case of the Pygmies and their neighbors it may be that there is more Pygmy ancestry in the aggregate in their numerous neighbors, than among the relatively rare Pygmies!

Finally, I think we need to now broach the topic of genomic value for posterity. It is well known that in the Congo region today Pygmies have been the target of conscious genocide, as well as suffering from the consequences of the great wars of the past few decades (I recommend Dancing in the Glory of Monsters: The Collapse of the Congo and the Great War of Africa to anyone with a modicum of interest in this topic). But the results in this paper indicate that the Pygmies are under clear threat of being demographically absorbed by their neighbors before the passing of this century. In particular this paper reinforces what has been clear in other results: the Mbuti of the eastern regions of Congo in particular harbor unadmixed genetic variation. While the Khoisan of southern Africa reside in a quiescent zone of the continent, the Mbuti are not so fortunate. I hope that we get at least hundreds of whole-genome sequences from this population within the next decade, for the sake of all of humanity. Ancient DNA seems unlikely from most of Africa, so massive surveys of the contemporary genomic landscape of this continent is going to be essential to understanding our species’ collective past.

 
• Category: Science • Tags: Pygmies 
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  1. Pygmies possess no identifiable language substrate and are weird in other ways, notably uniqueness in their absence of lithics which also goes against descent from the Sangoan toolmakers. Blench reasonably questioned whether they are an ‘ethnographic fiction’.

    http://www.academia.edu/2390225/Are_the_African_pygmies_an_ethnographic_fiction

  2. this paper, an other stuff i’ve read, questions the idea of no linguistic substrate. also, if they are an ethnographic fiction it is strange that they have deep, but real, relationships genetically to east and south africa HG populations, and NOT their neighbors (except via admixture).

  3. Maybe but there remains something strange to explain about their culture. I can’t help but wonder where the archaic admixture detected in the Mbuti fits in. The archaic admixture mitigates against Blench, but still unanswered questions and a lack of bioarchaeological data.

    Of other interest notice the non-pygmies have a red and a purple component, where the purple is concentrated in the Sahel zone. Likely Caucasian admixture as reflected in hair texture and dental trait frequencies displaced towards Mediterraneans?

  4. From what I understand the Bantu originated on the Nigerian-Cameroonian border. Why aren’t they a basal group? Also, do they have ancient non-African admixture like the khoisan and east Africans? Basically, what is it about the Bantu genome that would make a geneticist prefer to focus more on pygmies and Khoisan?

  5. more evidence of gene flow into those pops from non-africans. some whole genome analyses have shown west african/bantus maybe closer to non-africans than groups like mbuti, but might be due to archaic admixture.

    Of other interest notice the non-pygmies have a red and a purple component, where the purple is concentrated in the Sahel zone. Likely Caucasian admixture as reflected in hair texture and dental trait frequencies displaced towards Mediterraneans?

    looks like a relatedness cline from senegal to kenya (purple to red). also, don’t use the word caucasian unless you are talking about ppl from the caucasus on this blog.

  6. What race is pygmie considered? What race are they closest to?

  7. What race is pygmie considered? What race are they closest to?

    probably not useful to pigeonhole the pygmies into a platonic idea of a set of informative races. they’re closest to to other african HG populations, hadza and khoisan. but that’s a very distant relationships too (on the order of more than 20,000 years).

  8. “Basically, what is it about the Bantu genome that would make a geneticist prefer to focus more on pygmies and Khoisan?”

    Apart from anything else Bantu-descended populations aren’t likely to disappear.

  9. You know, I had a realization about this this afternoon. Isn’t it a bit odd that there are Pygmy populations live in Cameroon, only a short distance from the presumed Bantu homeland? And that Pygmies and West Africans split 50KYA, and didn’t admix until very recently? Particularly considering there’s no major mountain range or desert splitting the two apart?

    It’s well established that prior to the Bantu expansion, Southern Africa was inhabited by a range of hunter-gatherer populations totally unlike modern demography, including Pygmies, Khoisan, and probably other extinct groups. But their is still this weird unspoken assumption that West African agriculturalists basically lived where they do now since time immemorial. Clearly this can’t be true, since Niger-Congo is a well-defined language family and must have expanded within near prehistory. And, judging by what happened elsewhere, this couldn’t have merely been a cultural/technological expansion, but also had to be a genetic one to some degree.

    It seems the most parsimonious thing to presume is that Niger-Congo came out of the same expansion as Nilo-Saharan somewhere in the East African Sahel. It fits the YDNA, as E is found all around Africa, but seems to have origins in East Africa, and is related to non-African lineages. Although it’s a bit controversial, it seems Sahel agriculture came about somewhat before West African tuber-based farming.

    Of course, West Africans today seem genetically distinct from East Africans, even when you discount East Africa’s West Eurasian admixture. But there were certainly hunter-gatherers living in the West African forest zone before agriculturalists displaced them. Some level of ancient stabilized admixture (similar to South Asians) would explain a lot here.

  10. Anonymous • Disclaimer says:

    Dear Mr Khan, I was updating my understanding of y chromosome lineages last night and I got off on a tangent with the pygmies as a people, wonderning if they are an en vivo model of generic hominid extinction, a dynamic which we must presume to have happened countless times in the past. For instance, assume that the pessimism of current trnds holds, what signatures would be left of the pygmies in other populations vs the polymorphisms we could archive now? Would it be comparable to the scale of the signature from Neanderthal, denisovan, and hominid X of the africans? Reversing the lens of the pygmy extinction model, and applying to the neanderthal genome family, how much further diversity could we expect from a random neanderthal bone discovery?

    Finally, as a bit of a compliment, I would say that your writing has hit a new level recently. Would you share that perspective, and if so to what could you attribute it?

  11. Razib, it does look like a relatedness Cline but Europeoid physical traits of some SSA populations really are striking and peak in the Sahel. Dienekes also claimed western Eurasian admixture in the West African agriculturalists (Yoruba,) which also fits my proposed identification of the purple/Mandenka component with Europeoids, and given the ‘Mechtoid’ and Mediterranean phenotypes at Gobero, Niger a ‘super-Saharan’ presence is indeed ancient thanks to the Green Sahara acting as a pump.

    I wish I knew enough to ‘play with’ the samples in Treemix for myself, to see if the frequency of the component in question truly demonstrates an admixture event or not.

  12. “Finally, as a bit of a compliment, I would say that your writing has hit a new level recently. Would you share that perspective, and if so to what could you attribute it?”

    my agreement with ron unz does not tie compensation to any particular frequency of posting. so i think it’s the fact that i take long breaks and only write when it reaches a particular threshold of motivation.

  13. “their is still this weird unspoken assumption that West African agriculturalists basically lived where they do now since time immemorial. Clearly this can’t be true, since Niger-Congo is a well-defined language family and must have expanded within near prehistory. And, judging by what happened elsewhere, this couldn’t have merely been a cultural/technological expansion, but also had to be a genetic one to some degree.

    It seems the most parsimonious thing to presume is that Niger-Congo came out of the same expansion as Nilo-Saharan somewhere in the East African Sahel. It fits the YDNA, as E is found all around Africa, but seems to have origins in East Africa, and is related to non-African lineages. Although it’s a bit controversial, it seems Sahel agriculture came about somewhat before West African tuber-based farming.”

    First, it is worth recalling that the urheimat of the Bantu languages at the coastal Niger-Cameroon border, and the urheimat of the Benue-Congo language sub-family of the Niger-Congo languages that includes Bantu at the confluence of the Benue and Congo Rivers in Central Nigeria (well to the North and a bit to the West of the Bantu urheimat). Both of these locations are wide consensus views and they are not the same as each other. Neither of these, in turn, are the same as the urheimat of the Niger-Congo macrofamily of languages.

    The most plausible theory is that Niger-Congo languages have their origins in the expansion of West African Sahel agriculture, and that the subsequent expansion of Bantu languages is associated with the development of tropical agriculture in West-Central Africa. I would not regard Sahel agriculture predating tropical West African farming as at all controversial, although there is controversy regarding how old West African Sahel agriculture is. Importantly, until the Bantu break through with regard to tropical farming, tropical West Africa could have only supported much lower population densities than it did around the time of Bantu expansion and those would have been hunter-gatherer populations (although possibly quite prosperous compared to modern hunter-gatherers due to fishing in rivers and lots of plants and animals that thrive there, compared to the marginal ecological niches of modern hunter-gathers).

    The Nilo-Saharans were never farmers. They were herders and arrived in East Africa only a few centuries before the Bantus did, probably from origins near Lake Chad or Southern Sudan. Chadic populations which arrived at Lake Chad ca. 5200 BCE were also herders rather than farmers.

    Modern Sahel farming domesticates represent a mix of crops with wild progenitors native to the East African Sahel and to the West African Sahel that were exchanged at some point, but with very little demic admixture of the peoples involved. Probably each developed independently and then an ah-ha moment when the first crop exchanges occurred and completed each group’s package of domesticates. The closest modern proxy for East African Sahel farmers are probably Ethiopian Cushitic populations. Farming probably arises quite a bit later in the East African Sahel than in the West African Sahel, however.

    The Niger-Congo v. non-Bantu genetics differentiation issues are complex (and one must look at mtDNA, Y-DNA and autosomal DNA plus archaeology and language and food production histories to piece together a meaningful narrative) but suffice it to say that the divisions are not terribly recent – probably at least dating back to the Mesolithic era (ca. 12,000-6,000 BCE), if not earlier. Genetic evidence strongly disfavors the presence of people genetically similar to Niger-Congo people prior to Bantu expansion in East Africa about 3000 years ago or less.

  14. ohwilleke,

    My main point was just that it seems clear that West Africans are not only not indigenous to the modern Bantu region, they also are probably not indigenous to most of West Africa proper. Indeed, presumably with such an ancient divergence from Pygmy populations, they developed somewhere at rather great remove from Pygmies, and stayed isolated from them for tens of thousands of years. This area lacked impassible mountain ranges, great deserts, intervening oceans, or glaciers – things which kept different “races” apart elsewhere.

    Clearly there were originally Pygmy peoples in most of Cameroon, not just Southeast Cameroon as today, given all of the agriculturalists from Cameroon show some Western Pygmy ancestry. If it was only a few of the populations a back-migration could be posited, but since they all share it, Pygmies must have originally been throughout the region. Only the Mandenka, and possibly the Yoruba, show no evidence of pygmy ancestry in this study.

    Still, this shifts the problem only a bit east. If “West Africans” existed in Nigeria even back as hunter gatherers, why did they split off as a separate race from pygmies (who were in Cameroon) so early on, and why did they keep separate?

    At minimum, you could presume the savanna-rainforest boundary (which was probably further north during much of this period) was a natural boundary. West Africans lived in the Sahel and Savanna, pygmies lived in the Central African rainforest, and possibly another now essentially eradicated people lived along the Atlantic coastal rainforest. But I’m still suspicious that this isn’t far enough geographically to act as such a big population break. The idea of a race of humans which just sits at the border between two biomes and doesn’t go any further for tens of thousands of years just cuts against everything we understand about humanity elsewhere in the world. I’d feel more comfortable if their homeland could be pushed even further out – all the way to the Green Sahara or something. And frankly on the basis of West Africans being more closely related to East Africans than Pygmies (or other “Paleo-Africans”) you’d expect that at least a significant component of them springs from the same source.

  15. @Karl Zimmerman
    “But I’m still suspicious that this isn’t far enough geographically to act as such a big population break.”

    Would near the gold fields fit?

    http://www.metmuseum.org/toah/hd/gold/hd_gold.htm

  16. “West Africans lived in the Sahel and Savanna, pygmies lived in the Central African rainforest, and possibly another now essentially eradicated people lived along the Atlantic coastal rainforest. But I’m still suspicious that this isn’t far enough geographically to act as such a big population break. The idea of a race of humans which just sits at the border between two biomes and doesn’t go any further for tens of thousands of years just cuts against everything we understand about humanity elsewhere in the world.”

    Your intuition is wrong. Actually, the evidence that jungles are very powerful geographic boundaries is strongly consistent with human experience pretty much everywhere.

    For example, the population genetic break between SE Asia and eastern India/Bangladesh associated with the jungles of Burma is very well defined. These jungles are basically what kept W. Eurasians and E. Eurasians distinct from each other at the highest K=2 sub-population level for 60,000 years or so. It is plausible to suppose that only an interruption of that jungle ecosystem by the Toba eruption made it possible for modern humans who had not yet developed advanced maritime travel to cross that divide after being bottled up in South Asian until then.

    Bantu expansion into Southern Africa occurred when Bantus went the long way around the Congo jungle, rather than in a much more direct route through it and then only about 3000 years ago after 200,000+ years of continuous human occupation of the Africa on either side of the divide.

    In the Americas, North American and South America are quite distinct in population genetics and jungles are again the dividing factor.

    In Papua New Guinea, which is geographically tiny, pretty much entirely separate populations live in the Highlands and low land jungles.

    In SE Asia and the Philippines, negrito populations endured in jungles despite being wiped out much earlier on elsewhere.

    Empirically, jungles are probably more powerful barriers that either sea channels or mountains.

  17. India prior to the Neolithic was inhabited by populations which were, at the broadest level, East Eurasian. The level to which Ancient South Indians and Southeast Asian Negritos intermixed over time is perhaps unclear, but given the minority genes in populations like Cambodians which is recorded as “South Indian” in modern admixture runs, chances are they were fairly close. The hill country between India and Burma becoming the boundary between West and East Eurasians didn’t seem to happen until the Neolithic, and even here, it was porous initially, as the ancestors of the Munda and the like snuck through.

    Every other population divide you mention is between agriculturalists and hunter gatherers (except for the Americas, where you argument is so general I don’t know what you’re saying). Of course if agriculturalists don’t have an adequate crop package for the forest, they will not penetrate it. Hell, before the advent of ironworking, they couldn’t even cut down old-growth forest quickly enough to make the labor worthwhile. But if you’re dealing with two different populations of hunter-gatherers (as you were everywhere 10,000 years ago), there should be no major barrier to movement from one type of habitable environment with ample food sources and another.

  18. […] Razib takes a look at Pygmies. […]

  19. Are there any other examples of races that have been separate like bantu and pygmy elsewhere?

  20. […] The Fading of the Most Basal of Basal – “[T]he western and eastern Pygmy populations of the Congo rainforest seem to have diverged tens of thousands of years ago, tens of thousands of years after their divergence from the ancestors of their agriculturalist neighbors.” – from razib. […]

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