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Africa’s great demographic transformation

Stonehenge has been a preoccupation for moderns since the Victorian period. It was built over 5,000 years ago, and its usage in some fashion continued down to about 2,500 years ago. For a long while it had been associated with the Celts, but more recently there has been some suspicion that its roots must be pre-Celtic.

And that is almost certainly true. The original site of Stonehenge had a wooden structure. But during the arrival of the Bell Beaker culture it was extensively rebuilt, and eventually stone monoliths were erected in the fashion we are used to seeing today.

Bernard Cornwell’s novel Stonehenge deals with this period. There is no major focus on physical conflict between the native populations, and the Bell Beaker groups. Rather, the plot centers around the cultural tumult and innovation that was triggered by the arrival of the newcomers.

In Stonehenge the Bell Beakers occupied more marginal, out of the way, territory. The novel presumed that ultimately there would be cultural fusion between the two groups, as there was a lot of interaction inter-personally among the characters of the two groups. We now know that the reality was likely one of near total replacement. From the abstract to be presented on shortly on the Bell Beakers:

British individuals associated with Beakers are genetically indistinguishable from continental individuals associated with the same material culture and genetically nearly completely discontinuous with the previously resident population.

This is not entirely surprising. Ancient Ireland seems to have been characterized by discontinuity with the arrival of Bell Beakers genetically.

Ancient DNA is not magic. But it can literally put some flesh on the bones of cultural shifts that archaeologists have seen in the material culture. One key element here is that the predominant ancestry across the British Isles today derives from migrations that date to the early Bronze Age.* I do not know if this has any relevance as to the arrival of the Celtic languages to the Britain and Ireland, but I suspect it does.

This was percolating in my mind because there’s a new paper which attempts to explore in more detail the Bantu expansions which occurred between 1000 BCE and 500 CE. It’s pretty incredible that from Gabon to Capetown Africans speak one language family, with similarities at least as close as that of the Romance language family.

But then is it incredible? Indo-European languages span the North Sea to the Bay of Bengal. The Bantu expansion in some ways serves as a template for the argument in First Farmers, as an agricultural revolution triggered a demographic expansion which did not stop until they reached the their geographic limits.

The paper in Science, which is open access, Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America, focuses on two issues. First, the demographic history and phylogenomics of the Bantu populations. Second, using population genomic methods it explores the dynamics of natural selection in these peoples. They utilize and extensive SNP data set, with more than 500,000 markers in their core analyses.

In general I think there are lots of interesting results in this paper. But the one angle I was unsatisfied by was their purported increase in coverage. As you can see it’s highly localized to a few countries. This is probably common sense since much of Africa is not accessible due to political issues (e.g., sampling in the Democratic Republic of Congo is treacherous right now). But one always has to be careful of the limitations of the data when making inferences. Though they have samples from the southwest (Angola, Namibia), the the African Great Lakes region around Uganda, and in South Africa, huge zones between are missing. And, they are highly over sampled in and around Gabon.

With all that said, I think with a variety of methods they probably have confirmed a major aspect of Bantu migration. I’ll quote:

Two hypotheses have been proposed concerning the dispersal of Bantu-speaking populations across sub-Saharan Africa (2–4). According to the “early-split” hypothesis, the western and eastern branches split early, within the Bantu heartland, into separate migration routes. By contrast, the “late-split” model suggests an initial spread southward from the Bantu homeland into the equatorial rainforest (i.e., Gabon/Angola), followed by expansions toward the rest of the subcontinent. We tested these hypotheses by determining whether eBSPs and seBSPs were genetically closer to wBSPs from the southern part, relative to wBSPs from the northern part, of western central Africa….

…Although additional sampling of African populations may further refine these patterns, our results, together with previous genetic data supporting the late-split model (2, 3), indicate that BSPs [Bantu-speaking peoples] first moved southward through the rainforest before migrating toward eastern and southern Africa, where they admixed with local populations. This model is further supported by linguistics (15) and archaeoclimate data (16), suggesting that a climatic crisis ~2500 years ago fragmented the rainforest into patches and facilitated the early movements of BSPs farther southward from their original homeland.

That being said, their sample limitations produce interesting assertions. E.g., “The GLOBETROTTER method estimated that eBSPs resulted from two consecutive admixture events (P < 0.05) occurring 1000 to 1500 years ago and 150 to 400 years ago between a wBSP (~75% contribution) and an Afroasiatic-speaking population from Ethiopia (~10% contribution).” GLOBETROTTER is powerful, but too often people use it in a manner where they assume that the inferences it generates from the data it has are the truth, as opposed to the closest GLOBETROTTER can get to the truth with the tools its given.

In this case I would contend that because there aren’t any Nilotic samples it leaves a major hole in their power to be able to accurately infer what really happened. The presence of pastoralist Nilotic people in close proximity to Bantu agriculturalists has been one of the major dynamics which define the East African landscape. The admixture into eastern Bantu agriculturalists therefore is almost certainly from Nilotic peoples, though there has been Afro-Asiatic (Cushitic) influence as far south as Tanzania, evident in enigmatic peoples such as the Sandawe.

The point here is that just because the GLOBETROTTER method inferred gene flow from a population in the sample set, it does not mean that the gene flow was necessarily from that population. The sampling of the region is sparse, so obviously this is only a first approximation. To some extent I assume the authors assume the readers will connect the dots, but often this sort of thing gets lost in translation, and then it gets into the media….

Though it is difficult to make in the admixture plot above, there are subtle differences in the eastern Bantu groups. The Luyha, who are from Kenya, do not show evidence of the blue component which is clearly Eurasian, while the Bakiga from Rwanda do. But even in the Bakiga the ratio of the violet element that seems to be associated with an indigenous African component which is distinct from that of the Bantu and the blue Eurasian is far higher than in the Afro-Asiatic populations in their data set (this does not mean they don’t have Eurasian ancestry, since admixture plots aren’t perfect proxies).

Because of the nature of the sampling and the utilization of admixture to frame their results I do feel that we don’t get a good sense of the variation among the Bantu across their full range. Granted, the between population genetic distance is actually quite low across this zone, on the order of 0.01, because of the recent shared ancestry. Africans may have much greater total diversity than Eurasians in their genomes, but their between population distance is actually not much different or even lower than Eurasians because of the recent demographic expansions. But did the Bantu expand into empty lands? The Khoisan, Pygmy and Nilotic (I’m sure that’s what it is) contribution to the Bantus across their range is clear, but that’s because we have close enough reference populations to model this contribution. What about areas like Tanzania? Or Mozambique? Were they empty? I suspect the issue here is that we don’t have any non-Bantu indigenous groups as they’ve all been absorbed.

But it is in the selection component that they offer a possible way to ascertain non-Bantu ancestry from ghost populations in the future. They found lots and lots of selection around immune genes. This is not surprising. There were local diseases which they had to adapt to. Therefore, “the HLA region in wBSPs showed a strong excess of ancestry from rainforest hunter-gatherers, at 38%, 6.74 SD higher than the genome-wide average of 16%…..”

In places like Mozambique it would be curious if the regions known to be under selection or enriched for indigenous ancestry in other areas where there are still indigenous populations exhibited a higher Fst against other groups. That is, the Mozambique ghost populations should leave an inordinate impact on regions of the genome associated with immunological function.

Which brings me back to Stonehenge. We do have ancient genomes. But not that many. Especially further back. Apparently the names of rivers and mountains often have very deep histories. For example, the river Humber has a name which may date back to pre-Celtic times (consider the Mississippi river, which has an American Indian origin). These serve as shadows of cultures long gone and replaced. The Bantu expansion is close enough to the margins of history that we don’t have so much time interposed between it and concrete records. We can skein out its outlines with more rigor and surety. And the patterns we see among the Bantus can give us a sense of how past demographic-cultural expansions may have occurred.

* The papers coming out of the PoBI project suggest that a significant minority of the ancestry in eastern England is Anglo-Saxon. But only there.

Addendum: I can’t find the data to download and test some things myself.

9 thoughts on “Africa’s great demographic transformation

  1. While there are no true Nilotic samples, Gumuz is at least a Nilo-Saharan language, and it looks like their inclusion in the PCA resulted in a Nilotic-like component separating out in ADMIXTURE.

    One interesting thing I note on the admixture chart is some of the Southern African Bantu samples (such as the Sotho) don’t seem to have the appreciable Western Pygmy admixture that other Bantu populations have. Maybe this is an artifact of the study, but it seems to indicate that the hunter-gatherer substrate is not something which happened near the founding of the Bantu. Instead, there was an initial period of expansion of a relatively “pure” founder population, followed by localized in situ admixture with local hunter gatherers. On the other hand, the Eastern Bantu seem to have layered Nilotic admixture on top of earlier Western Pygmy admixture, so in that case they likely moved eastward some time after the initial expansion – which makes sense, given they faced much higher population densities rubbing up against pastoralists to the east than hunter-gatherers to the south.

  2. Do you have a compilation of claims about distances between languages, claims like “Bantu languages are at least as close as Romance languages”?

    [yes, i googled it before i said that; you can too. also, it makes sense because it’s similar order of mag of divergence]

  3. According to Oslisly, after the initial Neolithic colonization of this area (Gabon and nearby) about 3500-3000 years ago there was an Iron Age wave beginning ~2800-2500 years ago and replacing the previous (material culture-wise at least).

    This was followed by a population crash about 1600-1000 years ago, with no settlement evidence at all from a considerable area. See e.g. https://journals.uair.arizona.edu/index.php/radiocarbon/article/view/16385/pdf. So not a lot of population continuity in much of this region.

    The CAR and DRC blank spot in sampling is understandable but it does put a large hole in all these arguments about northern or southern migration routes.

    Lots of interesting stuff to digest here aside from that anyway.

  4. The Sandawe are not Cushitic speakers, the language is an isolate, like Hadza. However, the Sandawe live close to Southern Cushitic speakers, the Iraqw, Gorowa and Burunge. Both Hadza and Sandawe use clicks, and both represent indigenous non-absorbed groups.

    [i have looked closely at their genetic data; they clearly have cushitic (not nilotic) gene flow. that’s what i was alluding to. i can use wikipedia as well and know their linguistic status -Razib]

  5. I am skeptical of your particular claim, but I did not ask about it, but rather about the general class. I was surprised that you were making such a comparison at all, particularly implying that the whole class is not controversial. In my experience, linguists study language phylogeny, but are extremely hostile to such comparisons across different branches.

    No, I don’t know how to google it. When I search, eg, “how similar are bantu languages,” I get nothing. What search did you use? Perhaps there is some jargon term for the distances between languages that would open up a whole literature to me?

    [this query. i don’t understand why you think is controversial. if you have any familiar with the romance languages you know that though not intelligible ~2,000 years of colloquial evolution hasn’t made them that difficult to learn across each other. also, i know bengali, and though hindi or punjabi is not intelligible, if spoken slowly i can follow many of the words/concepts in a similar manner to what seems to be the case with romance languages. if the conversation is simple enough the same even happens with farsi!]

  6. I tried that query, probably because google suggested it after my first. All I get from it is that they are not mutually intelligible, that they really are languages. I don’t see any hits on that query that say that the languages are close, as close as romance languages, rather than Latin/Greek, or Latin/Bengali.

    PS—in addition to the https version of this site having css problems, it also doesn’t accept comments.

  7. rather than Latin/Greek, or Latin/Bengali.

    WTF. these analogies are ridiculous. seriously.

    the bantu expansion started ~1000 BCE. the indo-european langauges were already diversified to a reasonable extent by ~1500 BCE because we have written evidence of hittite, greek, and some indo-aryan from the mitanni (as well as the reality that some of the vedic sanskrit we have probably dates to before 1000 BCE). the time divergence difference between the cases you are analogizing is huge.

    unless the bantus have hyper-mutable languages (perhaps because they are oral, but this is not totally generalizable) there’s no way they should be of the distance of greek-latin or latin-bengali (which, depending on who you listen to, have time depths of divergence on the order of 5-10,000 years BP [i lean much closer to the 5,000ish time depth]).

    fwiw, here a swahili speakers talks about being able to understand a little bit of s. african dialects:

    https://books.google.com/books?id=MjzyTQ1BIIEC&lpg=PA117&dq=bantu%20language%20intelligibility&pg=PA117#v=onepage&q&f=false

    (this sounds similar to my ability to comprehend some punjabi or hind, though if written out phonetically i can get a lot more because the similarity of the word fragments is obvious).

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