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

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.

18 thoughts on “Origin of modern humanity pushed back 260,000 years BP (?)

  1. The “Basal Human” ghost population immediately made me think of A00 (Perry’s Y chromosome). IIRC it was dated to 270,000 years ago, which isn’t that much older than the new estimated date for the divergence of the unadmixed proto-Khoisan. However, its presence in roughly the right area for an “archaic” population blending into the ancestors of West Africans suggests it might actually be a Basal Human haplogroup.

  2. “Do we really think that the ancestors of the Bushmen were living in southern Africa for five times as long as Australian Aborigines?”

    Before the horse and the wheel, and iron, Indian Ocean navigation, and crops good for South African soil… Jared Diamond, for one, really thinks that the protoBushmen could have stayed isolated. Likewise the Polynesians and Muslims could easily have visited Australia but didn’t.

    These were remote and inhospitable places, full of violent and uncommunicative inhabitants. The farming was bad too – ancient soil with few nutrients.

  3. The 260000 kya figure, especially once error bars are considered, is not that much of a stretch beyond the oldest archaeological evidence, particularly in light of the Y-DNA evidence noted by Karl Zimmerman in the comment above. Also, while a lot of papers put “behavioral modernity” at ca. 50 kya, lots of the criteria cited for that threshold (e.g. bone tools and harpoon based fishing) are present at least 70 kya in the archaeological record.

  4. “Likewise the Polynesians and Muslims could easily have visited Australia but didn’t.”

    The Polynesians certainly visited Australia. You can’t hit nearly every uninhabited island in the Pacific and Indian Oceans, but miss a whole continent. But they obviously were not welcome, and could not compete with the locals.

  5. Dingoes had to come from somewhere, and they did not arrive in the 1600s. But there were no Muslims anywhere when they did arrive.

  6. Technically my “point” on Polynesians wasn’t falsified (at least not by you two); rick didn’t provide a link demonstrating a Polynesian visit to Australia…

    As for the trepangers, the records come from eighteenth-century Sulawesi. This is a very late visit for a fifty thousand year habitation of Australia! This visit is roughly contemporary with the first European visits.

    But I’ll grant that “no visit” was too strong a claim, even for Diamond’s thesis, since he allows for visits that didn’t take. Like how Leif’s colony in Vinland failed, thus (retroactively) a visit.

  7. There were some suggestions that Australian Aborigines may have had a small introgression possibly related to Dravidians a few thousand years ago, possibly coinciding with the appearance of the Dingo and some technological innovations and new agricultural techniques.


  8. That’s all I meant. They had to have “visited” many times. But they were a people looking for unoccupied lands, very small boats and without strong communication ability.

    They almost certainly landed on North America, South America, and mainland Africa, but besides the sweet potato story, it is probably impossible to prove.

    But, it is extremely unlikely that you could populate Madagascar from the Pacific, without finding either Africa or Australia.

    In some cases, proof is not necessary.

  9. I will gladly go out on a limb here and suggest that the first people to circumnavigate the globe were unidentified

    Their culture of open sea exploration is really amazing, even by today’s standards. They transported families, animals, and crops, multiple times, between very remote islands, in handmade wooden boats.

  10. NotANarc, the India theory is still unsettled (Link on my name.)

    An offshoot of the M42 mtDNA signature is found in Aboriginal populations, but that offshoot is over 50000 years old. Consistent with a M42 population joining the initial settlement, not arriving later.

  11. afterthought, can you post your ‘not-out-of-africa’ theory in detail? (break it up in comments if need be since it might think you are spamming)

  12. There were some suggestions that Australian Aborigines may have had a small introgression possibly related to Dravidians a few thousand years ago, possibly coinciding with the appearance of the Dingo and some technological innovations and new agricultural techniques.

    this has not panned out. researchers were skeptical of the stats in the original paper anyhow.

  13. As if on cue:

    “Scientists Find Oldest Known Specimens of the Human Species: Remains found in Morocco date from about 300,000 years ago, about 100,000 older than any other fossils of Homo sapiens” By Robert Lee Hotz on June 7, 2017

    “The bones of ancient hunters unearthed in Morocco are the oldest known specimens of the human species, potentially pushing back the clock on the origin of modern Homo sapiens, scientists announced Wednesday.

    “Found among stone tools and the ashes of ancient campfires, the remains date from about 300,000 years ago, a time when the Sahara was green and several early human species roamed the world, the scientists said. That makes them about 100,000 years older than any other fossils of Homo sapiens—the species to which all people today belong.

    “These dates were a big wow,” said anthropologist Jean-Jacques Hublin at the Max Planck Institute for Evolutionary Biology in Leipzig, Germany. He led an international team of scientists who reported the discovery Wednesday in Nature. * * *

    “Until now, most researchers believed that modern humankind emerged gradually from a population centered in East Africa around 200,000 years ago. Previous discoveries of early Homo sapiens fossils have been concentrated at sites in Ethiopia.

    “The fossil discovery at Jebel Irhoud near Marrakesh in North Africa, however, suggests that early humans had already spread across most of Africa by then. * * *

    “As early experiments in the human form, these ancestors had quite modern-looking facial features, but relatively primitive skulls, suggesting that the cognitive capacities of modern brains had yet to take shape, the scientists said. * * *

    “The scientists found bones of three adults, a teenager and a child mixed in with sharpened flint tools and the butchered bones of gazelles and zebra, suggesting that a hunting party had camped there. Fires had scorched the tools and that proved key to determining the age of the find.

    “The researchers tested the tools using a technique called thermoluminescence dating, which reveals how much time has elapsed since an object has been heated. By that measure, they calculated that the tools were 315,000 years old, plus or minus 34,000 years.

    “They also dated tooth enamel from a fossil jaw using electron spin resonance, which can measure the residual radiation that has built up since a material formed. That yielded an age of 286,000 years, plus or minus 32,000 years, the scientists said. * * *”

    Your comment Razib?

  14. “suggesting that the cognitive capacities of modern brains had yet to take shape, the scientists said.”

    This I take issue to. There is no scientific basis for such a suggestion. The skull was within the modern human range of variation, which is the entire basis of how they could even publish this paper.

  15. @ Rick: Not quite, in terms of brain shape, they do seem outside the range of AMH and not closer than Neanderthal.

    Paywall free version of article – http://www.eva.mpg.de/fileadmin/content_files/human_evolution/Homo_Sapiens_presskit/nature22336_Hublin.pdf

    See Figure 3b on page 3. This is a PCA of endocranial shape (shape of brain from internal braincase).

    Irhoud samples are within recent AMH variation on PC1 and PC2 of fig3a, which relates to facial shape, but well outside RMH (Recent Modern Human) variation on PC1 and PC2 of fig3b relating to endocranial shape shape. Really no closer than Neanderthals were. The endocranium for the Irhoud samples is in between the erectus and Neanderthal samples and the dimension that separates them (PC2) and which recent people are diverse on, and no real tilt towards RMH on the dimension that separates RMH from Neanderthal+erectus (PC1).

    You can visualise the differences through the relevant shape morphs in Extended Data Figure 5 (although these leave out the view in the superior for brain shape).

    External braincase PCA is present in the Extended Data Figure 4. More of a mixed picture than endocranium, the Irhoud samples are somewhat shifted in their average towards RMH, but still outside the range of RMH variation. However, some are not too far from Early Modern Humans (Skhul and Qafzeh hominids 80-120 kya) and even some Upper Paleolithic RMH.

    This is the interesting thing about new this paper, that it shows that modern human facial size / shape was present in humans from this period, together with an archaic endocranium and an external braincase which is intermediate. Challenges the model of a Big Bang of co-evolution of modern human face and brain shapes and sizes. The contentious bit of the paper is whether these samples should be labeled within the Homo Sapiens group on the basis of facial shape.

  16. Everything I have read recently about brains suggests that brain structure is just as important as brain size, if not more so. We can’t tell just from external brain shape anything about structure, but the brain shapes of the Irhoud samples are at least suggestive that structure was somewhat different. We can’t know, except for indirect hints from archaeology – material culture. If that shows continuity of tool technology, burial practices, etc. then it doesn’t tell us anything.

    I think John Hawks has nailed it pretty well here: https://medium.com/@johnhawks/the-story-of-modern-human-origins-just-got-more-complicated-9e435bea24f6

    So, the answer is we don’t yet know whether the Irhoud people were on the main stream that led to the modern human genetic range, or whether they were a side branch that made some contribution to it. I have learned not to care too much about labels, but the contentious part of the paper will remain that way until there is more new information. And that could be a long time coming. Or not.

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