The modern human back-sweep from Southeast Asia


The Insight is back with a 2-hour episode. If you unsubscribed due to a lack of new content, please resubscribe. Spencer and I devoted this episode to a “decade wrap-up,” so we had a lot to talk about (OK, ten general things to talk about, as we did a countdown), but there are already episodes in the queue on demographic transition, Levantine and Papuan genomics, and natural selection in the Americas, that will be dropping in early 2020.

Due to the constraint of time, we couldn’t really explore in full depth something that has been on our minds for a while: the likely seminal role of Southeast Asia, and Sundaland in particular, in the (re)settlement of Eurasia. Spencer has been telling me for years that Y chromosome researchers (e.g., Michael Hammer) have been noting that Southeast Asia, in particular, seems to be harbor the ancestral lineages for venerable branches such as R. These seem to derive from mutations in this area. For example, one can argue for a scenario where the ancestry of R & Q percolates up to Siberia, and shifts west, where R1 emerges among the “Ancient North Eurasians”, and eventually R1b and R1a diffuse across western and southern Eurasia. Today, R1a in Southeast Asia is an indication of migration from South Asia, closing the circle.

About ten years ago maps like the one to the right were all the rage. They are focused on uniparental haplogroups. The phylogenies are easily simply overlaid upon a map to trace out migrations. Implicit is the ‘serial bottleneck’ out of Africa framework.

But what if we have something seriously wrong? We now know there was lots of reticulation. Gene flow across populations. And it wasn’t unidirectional. Additionally, there is the weird fact that across the Middle East there seems to have a population now termed “Basal Eurasian” which split off from other non-Africans earlier, and probably had no Neanderthal ancestry at all. In contrast, Pleistocene Europeans, East Eurasians, the people of the New World and Oceanians, form a lineage.

So here is a hypothesis that I have minimal confidence in, but is not crazy as such

– “Basal Eurasians” are the primal population of the Near East

– “Eastern non-Africans” mix with Neanderthals on the way into southern and southeast Asia.

– One group of “Eastern non-Africans” moves into Oceania. Another group continues northward and eventually percolates back into the center of Eurasia, and gives rise to “West Eurasians.”

– This backflow population eventually mix with “Basal Eurasians” in the Near East.

The extremely ancient genomes from Europe, Siberia, and China are very strange in the results they present. Though the west vs. east bifurcation is evident, it looks have to occurred not much earlier than 40,000 years ago. The Goyet sample’s strange affinity to East Eurasians, as well as the fact that the first modern Europeans and Siberians seem to be not particularly more closely related to modern West and East Eurasians, also makes more sense.

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13 thoughts on “The modern human back-sweep from Southeast Asia

  1. Really interesting. There are some bits that seem possible after digesting this. I’d comment:

    1) Tianyuan is as you note really basal to the present day Eastern Non-African group and is at about 40.5 kya. In some models extant ENA are an exclusive clade to him, in others he has a migration edge to East Asians (and it appears the extent of that is really hard to figure out as he such little phylogenetic divergence from the base, and East Asians can vary from 25:75 to 75:25 Tianyuan:Onge-ancestor in different models, depending on the tree structure and populations).

    So if we did have an early inhabitation of SE Asia well pre-Tianyuan, almost none of this survives in any structured way in any of the present day populations like Onge, Papuans, etc. (And that leads to the question of it being possibly unintuitive that y-dna + mtdna diversity would survive if autosomal diversity did not?)

    Same applies for any migration back to West Eurasia via NE Asia and Central Asia (rather than via South Asia?). To my knowledge nothing of this would really survive in terms of being visible in D(Mbuti,Upper Paleolithic European/Ust Ishim:Tianyuan;ENA_today) or …DevilsGate;Onge/Papuan) stats. Net of what we expect from the Denisovan effect on these stats. There’s something in the GoyetQ-116 stat, but this is not consistent across ancient UP Europeans, less UP Europeans+Ust Ishim (and including Yana in NE Asia), and doesn’t really suggest a branching clade.

    Somewhat against a migration where post-Neanderthal Europe (post 40kya) was population from Central Asia is that there is no strong degree to which Ust Ishim forms a clade with the earliest UP Europeans against ENA/Tianyuan.

    2) In terms of Basal Eurasians as “the primal population of the Near East” would need to look into the archaeology of how continuously inhabited the Near East was during this phase.

    In Europe, things are still Neanderthal territory until post 40kya, and from Oase1 we can guess the early UP Homo Sapiens colonists of Europe encountered still very plentiful Neanderthal populations at this time and interbred with them (about 1 Neanderthal great-grandparent or 1 Neanderthal great-great grandparent).

    We also know that Neanderthals seem to replaced AMH in the Near East until about 55kya https://en.wikipedia.org/wiki/Neanderthals_in_Southwest_Asia“In their turn, starting around 80,000 years ago, Neanderthals seem to have replaced Homo sapiens in Southwest Asia. They inhabited the region until about 55,000 years ago.”.

    So Basal Eurasians may not have inhabited the region continuously since OoA, and may have been later re-entrants from Northeast Africa / Arabia that re-mixed with a wave out of S Asia, after that wave replaced Neanderthal but well before Dzuduana? There must have been some early AMH in the Near East, but these may have been replaced by Neanderthals well before any wave from SE Asia, and may not have been the elusive “Basal Eurasians”.

    The “Ancient North Africans” in NW Africa also seem to have been another population that existed at this time.

    ….

    The back-and-forth on Early Upper Paleolithic AMH occupation of SE Asia is interesting. My chronology of how the idea evolved and was accepted is that at first it was a “Yes”, because of early archaeological evidence and because of uniparental patterns, and then a “No” because autosomally we see nothing of this surviving, or virtually nothing, and greater autosomal diversity in West Eurasia.

    But it may be that it still happened, and massive replacement within East Eurasia and admixture with other basal “OoA”(?) in West Eurasia obscures this in patterns in modern day autosomal dna.

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  2. What I’m wondering about all the time is how safe the assumption of non-Neandertal admixture in Subsaharans is. Aren’t all the estimates based on “Neandertal-free” samples from Africa, of which, in reality, nobody knows whether they are really “Neandertal-free”?
    So what if there was an earlier back-migration to Africa from South West Asia and additional admixture for non-Basal Eurasians? Isn’t the only way to be sure to have older samples, or are the models and calculations applied really sure enough to exclude that possibility?

    Take Mota as an example:
    “The 4,500-year-old Mota man—named for the cave where he was found—shows a distinct lack of Eurasian genes. The sequenced genome therefore appears to support the previously estimated time period for the backflow—and it adds a whole new scale to the event.

    Using Mota man’s genes as the best African baseline to date, the international team showed that modern African populations thought to be basically unmixed actually have a significant amount of Eurasian ancestry. Even in the remote Congo, for example, the Mbuti people now show as much as 6 percent of their genome as West Eurasian, according to the study.

    “What we find is that even West and Southern African populations started showing 6 or 7 percent of their genomes to be West Eurasian,” Gallego Llorente says. “And populations with more Eurasian ancestry like Ethiopians also rise accordingly, so this basically means the backflow migration was larger than we thought.””

    https://www.smithsonianmag.com/science-nature/back-africa-ancient-human-genome-reveals-widespread-eurasian-mix-180956881/

    But Mota is just less than 5.000 years ago, what about the time before? E.g. I doubt that the spread of yDNA haplogroup E happened from within Subsaharan African populations, but rather from outside (East Africa, North Africa, Near East), from a people related to Eurasians mixing in an older sapiens layer, which in turn mixed with local archaic groups in parts of Africa.

    If anything like that took place (which can only be falsified by more ancient DNA?), how can anyone be sure about the level of Neandertal admixture in all of Homo sapiens, including Subsaharans. There might have been more than one admixture event with H. neanderthalensis.

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  3. Petr 2019 suggests there may be some Neanderthal ancestry in Africans based on the direct estimate N ancestry that should be better than the indirect estimates* – https://www.pnas.org/content/116/5/1639

    However, Neanderthal ancestry could not really be much more significant than we think in Africans without causing significant divergences in D(Chimp,African;Neanderthal,Denisovan), which are roughly (if not quite) 0.

    It might be possible to get things a little higher if you could reverse the roughly AMH ancestor->Neanderthal ancestor 1% edge that exists in the recent models, after the split of Neanderthals from the main trunk of NeanderSovan ancestry. But you’re not looking at significantly higher percentages, without also explaining why this does not cause deviation in D(Chimp,African;Neanderthal,Denisovan).

    That might still imply significant migration though! There may be some argument about why this edge (AMH->N, postN+D divergence) is non-reversible though.

    *and these are the estimates which Petr argues should indicate Basal Eurasian actually does have the same levels of N ancestry as other Eurasians. Though Lazaridis has argued, and I think fairly plausibly, that BEu may have 0 N ancestry, or at least no more than Africans, if you assume lower levels of Basal Eurasian than Petr’s models do (more in line with recent papers that suggest small but deeply divergent BEu) and look at differences between ancient Near Eastern populations (Natufian vs Barcin vs WHG/UP Europe/Ust Ishim/Tianyuan, etc.). Petr’s argument that the direct estimate refutes the hypothesis of long term selection against Neanderthal ancestry within “Crown Eurasians” (e.g. non-Basal Eurasians) seems very sound, however.

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  4. A crazy theory:

    Groups carrying DE and CF exit Africa separately, the former via Sinai and the latter via Bab-el-Mandeb. Only the DE group encounter Neanderthals.

    The DE group, now with Neanderthal introgression, encounters the vanguard CF group somewhere near the southern Zagros and together they form the ancestral Eurasian population.

    However, other CF groups in Southern Arabia remain isolated. With no Neanderthal ancestry, and only one stream of OoA ancestry, would their genetic contribution (many years later) appear “basal?”

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  5. ‘Sundaland’.

    Indeed.

    Any proud Geordie would second that. Almost as great an achievement as beating Leeds Utd in the 1973 FA Cup.

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  6. I think the Southeast Asia step is possible (wasn’t there a India step proposed some years ago?), but I have some trouble imagining that the bulk of the Eurasian population would come from there given what we now know about Denisovan admixture – which is absent in West Eurasia.

    Regarding Y-chromosome haplotypes, it could also well be that we seeing these old lineages in Southeast Asia is not an effect of its basal state, but rather of the region suffering fewer Y-chromosome turnovers due to being relatively protected from its neighbors. I notice that, even though haplogroup F* is more common in SE Asia, its descendants G, H, I, and J are all mostly found further west, and I’m not aware of basal lineages from these clades found in SE Asia.

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  7. A few questions/thoughts:
    1.Is there any evidence that the mammoth-hunter cultural package originated in the east? The mammoth steppe would be a good vector for East-West demographic spread in the early Holocene – huge latitudinal spread of the same biome, and able to support relatively dense human population because of all the megafauna.

    2. Considering that Neanderthals were found in the Levant, is it really plausible to assume that Basal Eurasians were rooted in the Middle East before the ancestors of non-Basals split off? Or are you thinking that the Basal Eurasian homeland was specifically in the Arabian peninsula/southern Iraq/somewhere else where we don’t think Neanderthals lived?

    3. Related to that, do you think the big Out of Africa event was via the Levant or Arabia? Is there any good evidence for either one? Basal Eurasians as ur-Middle-Easterners would work a lot better if the migration was through Arabia.

    4. Is it still tenable to hold that Basal Eurasians are a later migration out of the same African population that produced all other non-Africans? If Out of Africa was Egypt > Levant, the Nile Valley would remain as a big demographic reservoir right next to the initial migration route.

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  8. Before the Ice Age, like afterwards too, the Eurasian steppe was more like a connection than a border between Western and Eastern Eurasians. The steppe tundra was cut in two only because of the Ice Age, resulting in Caucasoid and Mongoloid proper respectively.

    So to find East Asian influences in Europe before the Ice Age is to be expected.

    Also the idea that subtropical and tropical regions are more favourable for modern humans can be questioned.
    Crucial is the adaptation to the colder season with new innovations, but once that was achieved, the temperate climate had a lot to offer. Especially the river habitats were highly interesting.
    The question is, how often did this colonisation of the temperate zone happen, where did it happen? From which transitional habitat. Were there were more, which one was more successful?

    There are, I think, enough arguments for it happening twice already, in the West and East. But these are questions to explore and Eastern one might have been more influential overall, moving further in particular and reaching the West indeed.

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  9. “About ten years ago maps like the one to the right were all the rage.”

    Is it my browser, or is there no map on this page?

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  10. Razib, related to your post – what do you think of this?

    We inferred a pulse of 0.094 (95% CI of 0.049–0.174) from the ghost BasalEurasian population to EEF ancestry (LBK), substantially lessthan the 0.44 inferred by (Lazaridis et al.2014). This admixturewas inferred to occur 33.7 kya (95% CI of 10.8–41.1 kya), shortlyafter the Loschbour-LBK split at 37.7 kya (95% CI of 32.2–42.3 kya). The split time of the ghost Basal Eurasian lineagefrom other Eurasians was inferred at 79.8 kya (95% CI of 67.4–101 kya).

    I cannot judge the math, but maybe you can?

    https://www.tandfonline.com/doi/pdf/10.1080/01621459.2019.1635482?needAccess=true

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  11. @Obs

    You wrote: “Even in the remote Congo, for example, the Mbuti people now show as much as 6 percent of their genome as West Eurasian, according to the study.”

    That study was in error. It authors retracted their conclusions. A more recent re-analysis did not find as much Eurasian admixture in Africa populations as initially proposed (none was found in the Mbuti). See:
    http://anthromadness.blogspot.com/2016/01/the-mota-mistake.html

    “It seems there was indeed good reason to remain cautious about Llorente et al.’s findings that all Africans are part Eurasian or West Eurasian as they’ve now retracted their old results after getting help from David Reich and company. ”

    A quote from the authors:
    “The results presented in the Report “Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent“ were affected by a bioinformatics error. A script necessary to convert the input produced by samtools v0.1.19 to be compatible with PLINK was not run when merging the ancient genome, Mota, with the contemporary populations SNP panel, leading to homozygote positions to the human reference genome being dropped as missing data (the analysis of admixture with Neanderthals and Denisovans was not affected). When those positions were included, 255,922 SNP out of 256,540 from the contemporary reference panel could be called in Mota. The conclusion of a large migration into East Africa from Western Eurasia, and more precisely from a source genetically close to the early Neolithic farmers, is not affected. However, the geographic extent of the genetic impact of this migration was overestimated: the Western Eurasian backflow mostly affected East Africa and only a few Sub-Saharan populations; the Yoruba and Mbuti do not show higher levels of Western Eurasian ancestry compared to Mota.”

    There may indeed be traces of Eurasian genetics in some sub-Saharan populations, but the 2015 Llorente et al. study seems to have greatly/substantially overestimated it/them.

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  12. @Jm8: Thanks for the correction, wasn’t aware of this quite basal mistake they made in the first study. For the general argument I still expect more to come, yet one has to question another aspect: What’s “West Eurasian” admixture. Because the West Eurasian genetic profile might be significantly younger than the first “backflow” events even. Yet how many layers of sapiens related ancestry reached for example even the modern population of Yoruba is nothing which was sufficiently been solved yet from my point of view. Yet we would need (very) ancient DNA from those places which might never come in unfortunately. But who knows, there might be new methods and especially samples like Iwo Eleru should prove to be interesting:
    https://www.bbc.com/news/science-environment-14947363

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  13. Razib, what about Homo Naledi? How did that not make your list? I bet John Hawks thinks it’s one of the biggest discoveries of the 2010s, no?

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