Razib Khan One-stop-shopping for all of my content

June 6, 2017

Origin of modern humanity pushed back 260,000 years BP (?)

Filed under: Ancient DNA,Genetics,Khosian,South Africa — Razib Khan @ 12:45 am

The above figure is from a preprint, Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago. The title and abstract are pretty clear:

Southern Africa is consistently placed as one of the potential regions for the evolution of Homo sapiens. To examine the region’s human prehistory prior to the arrival of migrants from East and West Africa or Eurasia in the last 1,700 years, we generated and analyzed genome sequence data from seven ancient individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherers date to ~2,000 years ago, and we show that they were related to current-day southern San groups such as the Karretjie People. Four Iron Age farmers (300-500 years old) have genetic signatures similar to present day Bantu-speakers. The genome sequence (13x coverage) of a juvenile boy from Ballito Bay, who lived ~2,000 years ago, demonstrates that southern African Stone Age hunter-gatherers were not impacted by recent admixture; however, we estimate that all modern-day Khoekhoe and San groups have been influenced by 9-22% genetic admixture from East African/Eurasian pastoralist groups arriving >1,000 years ago, including the Ju|’hoansi San, previously thought to have very low levels of admixture. Using traditional and new approaches, we estimate the population divergence time between the Ballito Bay boy and other groups to beyond 260,000 years ago. These estimates dramatically increases the deepest divergence amongst modern humans, coincide with the onset of the Middle Stone Age in sub-Saharan Africa, and coincide with anatomical developments of archaic humans into modern humans as represented in the local fossil record. Cumulatively, cross-disciplinary records increasingly point to southern Africa as a potential (not necessarily exclusive) ‘hot spot’ for the evolution of our species.

These results in the outlines were actually presented at a conference. I saw it on Twitter and don’t remember which conference anymore. But this is not entirely surprising.

First, much respect to Mattias Jakobsson’s group for breaking through the Reich-Willerslev duopoly. Hopefully this presages some democratization of the ancient DNA field as expenses are going down.

Second, notice how in most cases ancient DNA shows that modern reference populations turn out to be admixed. This was the problem with much of Eurasia, and why using modern genetic variation to make inferences about the past totally failed.

I am entirely convinced that the genome from Ballito Bay dating to ~2,000 years does not carry the Eurasian inflected East African admixture. The Mota genome implies that Eurasian admixture did not come to eastern Africa much before 4,500 years ago. There needs to be a much deeper big picture analysis of the archaeology of Africa and the genetic information we have to get a sense of what happened back then…but, it seems likely that the Bantu migration has over-written much of the earlier genetic variation.

The fact that ancient genomes always show that our current populations are admixed makes me wonder if the Ballito Bay sample itself is admixed from more ancient populations. That is, if we found a genome from 20,000 years ago, would it be very different from the Ballito Bay samples? The relatively thick time transect from Europe indicates that turnover happens every 10,000 years or so. Australian Aborigines seem to have been resident in their current locations for ~50,000 years, but this seems the exception, not the rule. Do we really think that the ancestors of the Bushmen were living in southern Africa for five times as long as Australian Aborigines?

Another curious aspect of this paper is that it suggests the effective population size of Bushmen is smaller than we might have thought, and they’re somewhat less diverse than we’d thought. That’s because East African (with Eurasian ancestry) gene flow increased heterozygosity, as well as inferred effective population sizes. I’ve mentioned this effect on statistics before. Unless you have a true model of population history (or close to it) your assumptions might distort the numbers you get.

There is another aspect to this preprint mentioned glancingly in the text, and a bit more in the supplements: they seem to only be able to model Yoruba well if you assume that they themselves are a mix of “Basal Humans” (BH) and other African population which gave rise to East Africans and “Out of Africa” populations. Note that the BH seem to diverge from other human populations before the ancestors of Southern Africans like the Ballito Bay sample. That is, BH could push the diversification of the ancestors of modern humans considerably before 260,000 years before the present.

The possibility of deep structure in the Yoruba is pretty notable because they’ve been the gold standard in many human population genetic data sets as a reference population. But this is not result of deep structure is not entirely surprising. For years researchers have been hinting at confusing results in relation to the possibility of Eurasian back-migration. Perhaps the deep structure was confounding inferences?

The authors themselves are quite cautious about their dating of the divergence. It’s sensitive to many assumptions, and in particular the mutation rate being known and constant over time. But I think it’s hard to deny that this is pushing back the emergence of modern humans beyond what we know today. The earliest anatomically modern humans are found in Ethiopia 195,000 years ago from what I know. As I said, I’m convinced that the ancient genome has shown that modern “pristine” populations have some serious admixture. But I’m not as convinced about any specific point estimate, because that’s sensitive to a lot of assumptions which might not hold.

Finally, first a quick shout out to the blogger Dienekes. As early as ten years ago he anticipated the basic outlines of these sorts of results in the generality, if not the details. We really have come a long way from popular science declaring that all humans descend from a small group of East Africans who lived 50,000 to 100,000 years ago. The real picture was much more complex.

Also, I have to admit I considered titling this blogspot “Wolpoff’s revenge.” As in Milford Wolpoff. The reason being that we’re getting quite close to territory familiar to the much maligned multi-regionalist model of modern human origins.

Note: These findings should make us less surprised perhaps by a “modern” human migration before the primary one out of Africa.

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