We don’t know much about deep East Asian paleogenetics

A comment below that captures my thoughts well:

The deeper I dig into the Tianyuan discussions posted online, the less I seem to understand… seriously, we NEED more samples from east Asia, specifically China to piece together the east Eurasian developments and to understand where Tianyuan fits in all of this. Is it even more divergent than Papuans and Onge? Is it somewhere between them and east Asians in a very broad term (this includes east, southeast Asians and native Americans) or is it in the broad east Asian ‘protomongoloid’ nest…. I have no clue at this point.

The reality is it is only in Europe do we have a really robust and well-supported graph of human population history over the last 40,000 years. Even in West Asia, there is some fuzziness (at least until the Reich group comes out with their West Asia paper, which has new samples according to Iosif Lazaridis), and what we know about South Asia is ancillary to what we know about West Asia and Europe (ergo, non-West Eurasian ancestry in South Asians gets thrown into a big bucket).

If you read papers about the Jomon one thing that seems clear is that there are lots of “basal” lineages in the past. It’s hard to place them robustly on a modern graph.  What this really reflects is that rapid demographic expansion in the Holocene of farming groups seems to have obscured a lot of the deep structure that had existed in the Pleistocene. The erratic results on the Jomon, the “Australo-Melanesian” ancestry in Amazonians, and the distribution of Y haplogroup D is all part of this bigger puzzle.

D is found at high frequency among Japanese, some Siberians, Tibetans, and Andamanese natives. To me, this isn’t due to close relationships, but the fact that these groups relate somehow to the near polytomic diversification of “East Eurasian” lineages ~45,000 years ago. Oceanian people are clearly part of this, and some ancient Southeast Asian people seem to be closer to Oceanian people than Northeast Asians. This is not surprising seeing as Oceanians almost certainly derive from ancient Southeast Asians (or, that that was the last bifurcation).

Finally, there’s the issue with “Denisovans.” The most likely hypothesis to me is that this was a highly divergent group of human populations, which occupied a much more ecologically diverse territory than Neanderthals. And, unlike Neanderthals, they were not genetically homogeneous, as southern “Denisovans” had larger population sizes and did not suffer periodic extinctions in the meta-population.


29 thoughts on “We don’t know much about deep East Asian paleogenetics

  1. Razib, I saw on your other blog that you started using qpAdm, have you developed any mastery of qpGraph yet as well? A user on Anthrogenica, Kale, came up with some very interesting graphs earlier this year trying to tease out the nuances of deep Eurasian phylogeny, and one of his more interesting insights that I recall was that the entire Easter Non-African clade has a small but non-negligible (I think maybe 5%?) amount of West Eurasian ancestry. Obviously it’s just a model, but he seemed pretty convinced there was something to it, and I believe he was also sceptical Basal Eurasian existed as a real population as well, it was just an artifact of some ancient asymmetrical West-East Eurasian cross-breeding or something. Would be curious to see any of your models if you ever work on any graphs as well.

    On the subject of Admixtools, I think I literally only know of three amateurs spread across this whole online genetics community who seem to have some proficiency with it – David at Eurogenes, Chad Rohlfsen, and Kale. Since I know you need Linux to run it, does anyone know if it’s possible to get it to run on a virtual machine, and if it actually works well on one?

  2. Mick, I was thinking about how the settlement of Asia could have happened in two waves: an initial southern wave carrying Y haplogroup C and a slightly later wave carrying K2 and D, which mixed with the southern group before heading north through India. Could this second wave be regarded as West Eurasian?

  3. The good thing about East Asia is the preservation status, especially in comparison to tropical regions.
    As much as I want to know more about Europe, just a few carefully chosen samples (physical type and cultural context considered) might clarify so much which is nothing but more or less plausible conjecture right now.
    But one thing is quite clear to me, when the details come out, the results will prove one of the strongest long term, complex selection pressures in recent human evolution and the massive replacement of whole macro-populations in East and South East Asia.
    Like with depigmentation and lactase persistence in Western Eurasia, some people still seem to downplay the implications.
    We deal with very drastic selection models necessary, the traits were important and I assume for some clear cultural : genetic relations, for almost conscious co-evolution. Which means people got new genetic variants, but they spread because of cultural trends in aesthetic and behavioural norms. The cultural ideal of how for example people have to look or smell had biological consequences, were part of who reproduced more successfully than others.
    This is different from simple, small groups of foragers for which, the worse the situation they lived in, the more, sexual partner choice and social selection were still less important than environmental adaptation in comparison (!), not necessarily overall. Especially elaborated social norms.
    To make it clear for a concrete example: I think the probability of extensive and genetically significant admixture with Neandertals and Denisovans was lower during and after the Ice Age than before.
    Because partner investment and therefore sexual selection, but also social selection and exclusion, became much more important in the colder regions during the LGM.

    Another very realistic example:
    I found it very interesting that in various encounters of East Asians with other people they noted their body odor and were disgusted. Now if, even by chance, ABCC11 was able to become dominant in one group, how did the selection look like?

    In the end, if you have to endure days after days in a cave or tent, people living side by side, including adult males, anything which bothers you might end in disputes with harsh consequences. Its almost like a prison situation.
    So I imagine a lot of the selective pressure coming from ostracism and the prevention of becoming the target and rather building larger networks by using societal rules.
    In a different situation being kicked out of the group for a time, or even permanently, was not a death sentence. But in the Ice Age it was. Similarly a woman with a small child could survive on her own and without too much of direct support in a lot of situations, but not in the Ice Age.

    What they should look at too is when exactly traits like ABCC11 and OXTR were positively selected and whether it increased in ANE too or just East Asians. That’s really interesting and important, when and why new traits spread and which consequences this had inside of a population and for their interaction with other populations.

    But this relates directly to the main topic of this post from Razib, because considering the immense, even brutal selection leading to the high frequency of some important traits, this was no chance and it couldnt happen in every possible context.
    Because like explained, it makes a huge difference for sexual and social selection whether you live in an extremely cold environment or not.
    Some trait combinations are so specific that they can be traced back to one setting. And if you find them elsewhere, they expanded from this source.
    Now looking at East and South East Asia from this perspective, it is absolutely clear that most of the variation we see today can only partly if at all explained by how “the first modern humans colonised Asia”. Because thats like a trace in the snow after 100 people walked over it, coming from all directions. You might be lucky enough to find a shoe imprint of the first who walked that way, a survivor in one place, but more likely the later ones will make more of an impression most of the time. So judging the clearly visible footprints just means to count survivors, not who came in when or the like.

    In the case of East and South East Asia its all about a truly massive colonisation from the middle North (Mongolian steppe and Hwangho river) hacking a wedge from one end of the continent to the other. There will be many layers and many extinct lineages, a lot of competition and different selective trends to explore for Eastern Eurasia.

    Actually I even doubt that haplogroup D was that most ancient layer considering its distribution. Rather like in Europe we will find even older layers which went extinct on the fringes. That Denisovan admixture does exist, but is so low, is just a first hint.

  4. Correct me if I’m wrong, but I seem to recall that China is sitting on a trove of potential ancient DNA samples right? That is to say, China intends to build their own in-house version of Reichlab, and isn’t really willing to have outside scientists come in and grind up petrous bones willy nilly because it’s saving the lion’s share of those samples until that time.

  5. On the topic of ABCC11, I’m agnostic of the ultimate reasons for selection, but here’s a selective story for ABCC11 derived variant I haven’t read before:

    If ABCC11 has effects in production of earwax and apocrine secretions and breastmilk (which we know of), I’d guess it may have effects of ill understood proportion on mucosal and respiratory surfaces, which could matter for breathing, congestion under different disease conditions and infections, and that may present a plausible selective factor. Ear, nose and throat are all connected. Most of the changes in human facial morphology relating to climate tend to be side consequences of shifts in nasal cavity to facilitate most efficient response to temperature, so this is a considerable selective force. Maybe this has been investigated, or is biologically implausible (respiration and ABCC11 just have nothing to do with one another!) though!

    ABCC11 derived variant apparently old; Ust-Ishim had a copy (https://febs.onlinelibrary.wiley.com/doi/full/10.1002/[email protected]/(ISSN)1873-3468.reviews).

  6. Correct me if I’m wrong, but I seem to recall that China is sitting on a trove of potential ancient DNA samples right? That is to say, China intends to build their own in-house version of Reichlab, and isn’t really willing to have outside scientists come in and grind up petrous bones willy nilly because it’s saving the lion’s share of those samples until that time.

    fu out of the reich lab went back to china to work on this. she has had a child so that has an impact, but hard to explain that that’s the only reason…

  7. Nice link Erik. Should be full of interesting data for those who want to dig for it, particularly in India and Insular SE Asia / Oceania.

    The sampling in Mainland SEA is a fairly weak addition unfortunately, only 2 each new genomes from Myanmar and Thailand and 28 from Vietnam. Likewise for Central Asia, not much.

    Downside of that is that looking at their ADMIXTURE results can be pretty misleading to the eye/intuition – for’ex they have Uyghur labelled alongside a large bloc of homogenous Northeast Asian samples, but only when you look very close do you actually see the very few Uyghur samples who pop out with approximately 50% West Eurasian components. Likewise looking at the set they label “Burmese, Thai, Dai, CDX and KHV” it looks very homogenous, but this is because this is dominated by very large numbers of CDX (Chinese Dai) and KHV (Kinh Vietnamese) from the 1000 Genomes, and only on close inspection do the Thai and Burmese samples with different proportions of ancestries including South Asian ancestry actually become apparent to the eye.

  8. @ Donovan

    Honestly without Upper Paleolithic DNA from across South, East, Southeast, and Australasia I really don’t know if it’s worth speculating much about which haplogroup entered which area first or what. And I’m not really sold on the proposition that modern distribution of any given uniparental, even if it appears to be quite deeply rooted in a particular locale, is entirely informative of the deep population history or structure of a place.

    I will say the oldest southeast Asian DNA we have, from the Hoabhinians, had both C and D (samples were to poor to have higher downstream resolution I believe), and I think D was likely in at least parts of the Malay archipelago nearest to the mainland. But if you look at contemporary native populations in Papua and Australia (Sahul), they’re all C1, C2, K2 derived, and these haplogroups have likely been there 40,000+ years. Maybe they all entered Sahul together at one time, maybe they each reached it at different points between 40,000-50,000 years ago, and maybe they had some other fellow travelers with them that died out over time.

    D in general is super interesting haplogroup and needs to be better studied IMO. The Andamanese and Japanese Ds form a clade with each other to the exclusion of the Sino-Tibertan branch. I believe there was also a paper that came out within the past year on the Jomon which confirmed that they did seem to have Southeast Asian shift relative to other East Asian groups.

  9. Its a shame they don’t produce results. Or is there even something like in India going on? If some of the earlist Shang had significant West Eurasian or even just Mongolian influences, this might not be received too well? I mean some people in China still love the “Sinanthropus” as their direct ancestor – or at least did so until recently. This was an actual debate in China, at least before the modern DNA analysis developed and was finally accepted.
    What else should hold them back? Plenty of potential samples which could be all really, really important for East Asian and even human anthropological history. The technical issues shouldn’t be too big any more as well.

    @Matt: Its old and widespread indeed, but near fixation only in populations related to what I described as the core type.
    But while searching for South Asia, I detected this older post by Razib:

    While Japan’s North-South gradient is easy to explain (Ainus vs. Yayoi!), the indigenous people of India (ASI) are not. But I think the final judgement is right. I think it was negative under some conditions, neutral to moderately positive in most more developed cultures, but highly advantageous in some.

    Interesting to note:
    “In addition, we show that absolute latitude is significantly associated with the allele frequency of rs17822931-A in Asian, Native American, and European populations, implying that the selective advantage of rs17822931-A is related to an adaptation to a cold climate.”


    Now this is not always true, but it is so for Eurasians in colder habitats and for most of the Mongoloid expansion zones. ASI/Southern Indians might really stick out.

    However, there is a lot more to learn for sure and all this is just the tip of the iceberg and I expect a whole avalanche to come in once we have aDNA and a better genotype-phenotype assessment. Because many physical and already known genetic traits have costs which are quite significant, which is why they didn’t spread before and in other people, or just much slower, even if the mutation as such is fairly old and widespread.
    So the conditions which produced the already known results must have been related to extreme cold and high selective pressures in the given population.

    I’m also quite interested in how the Hwangho river people expanded. My interpretation is that we don’t seem to see such radical expansions by now is, because the forager population in the area was fairly large even before the Neolithic time and was the result of a regional fusion of different hunter gatherer groups. From then on, this population was fairly stable with different branches and additional Northern steppe (Mongolian steppe primarily) influences. When the Neolithic package, or at least parts of it, were introduced from outside, even if this was demic diffusion initially, what it might have been, it was just swallowed. Because unlike in Europe the population density in the Hwangho area was high already, but the incoming people not that numerous. And when they had adopted farming and began to expand even faster, they did so on the shoulders of highly developed forager networks.
    The expansion itself might have been different too, more community than clan based than in Europe. Some of the biggest expansions South were already highly organised enterprises it seems and not just some clans and families, not even medium sized social units. It was not small groups expanding with innovations over wide territories, like in Europe, but already large and more complex communities. Nevertheless, the waves from the North really overwhelmed the Yangtse people, the river valleys, the jungles in the South and the islands to the South East. The Hwangho was just prime quality soil for foragers already and even more so for farmers. The Chinese as the last and most successful wave had the great advantage of combining classic crop farming with pastoralism and the ethics of the herder warrior. This is again something which in Europe developed largely independently and in stages, with one group of quite different character replacing the next.
    In Northern China the successful forager population, which adopted farming and diversified in different cultures, even ethnolinguistic units most likely, was largely the same ever since pre-Neolithic times. Long term stable development and whole diversified groups moving South, mixing with locals, but overall just overwhelming the more distant people which were not part of this original Hwangho-source culture for the most part.
    So I expect a large part of the variation we see in East and South East Asia to come from the Mongolian steppe and the Hwangho itself, just being transplanted South. The real, regional continuity further South, especially beyond the Yangtse, is supposedly rather weak to non-existent.
    So it might seem like no big expansions took place, because of the specific structure which developed in the North already and which was further increased due to limited, but still significant admixture with locals. Significant because the locals were, like in South Asia, more different than in Europe, not part of the Mongoloid metapopulation. But the vast majority of people in EA and SEA are most likely descendents from the core group at the Hwangho river. Just different branches moving South at different times, being pushed always further South by the next wave coming down the river systems and along the coast respectively.

  10. ABCC11 in case of Europe looks like steppe-related looking at the distribution. Higher in Eastern (20 %) and Western (17 %) and lower in South (10%). Does not look like it was “selected” for in Europe.

  11. @Obs, hopefully adna will allow us to test this stuff!

    Agree steppe mediated influences important for why China’s later expansive influence within East Asia. Less so because of a herder mentality, which Han civilization tended to think it did not possess, more because of serving as a mediator of technology and domesticates from West Eurasian diffusion areas (with some flow back).

    Bronze, the wheel (and chariots), probably notions of writing (if not any actual adaptation of the Near Eastern systems), wheat, cows, horses, sheep, and probably more, including some notions of sophistication through Central Asian trade from the early centres like BMAC and on the military side, probably new tried and tested notions of how to fight tested from diffusion between the West Eurasia centres of the steppe and Near East.

    If that exchange of technology and crops had somehow been prevented (though it’s difficult to see how!) without that I expect you would probably have seen North China more on a parity with the southern frontier, and possibly an eventual “Reversal of Fortune” as the influences spreading out from South Asia (and ultimately from the Near East) to SE Asia via a maritime route.

    (That, is I don’t think the continued prominence of Henan cultures after the initial neolithic was alone due to advantages of North China in population, though important, but also due to its continued advantages in effectively trade through Central Asia and the steppe and access advances from West Eurasia faster than South China, and then the snowball is rolling too fast to stop by the late first millennium BCE).

    China’s often thought of as a “primary civilization” in the sense of arising independently uninfluenced by other civilization “hubs”, but I really tend to think only the Near East and Native American civilization stand as truly independent, uninfluenced by anything that came before (which actually makes the accomplishments of the NAs even more impressive).

  12. @Daniel, that’s an interesting idea. Potential problem – if we take best guess estimates of Steppe ancestry in Europeans (say http://eurogenes.blogspot.com/2017/01/qpadm-tour-of-europe-bronze-age-invasion.html, which is better than the published ones by Haak), assume ABCC11 frequency is explained by this and that Northern Europeans are in the range 42% (English) – 48% (Latvian), then scaling up from around 18.5%, you have about 40% in Steppe EBA.

    But I don’t know that any of the adna samples we have actually show anything like a frequency where most Steppe EBA (e.g. Yamnaya, if not the true admixing population then close to it), actually have that sort of frequency, where effectively most samples should be heterozygotes for the derived variant. I’m not sure adna has at all shown this is the case in quite large samples of Steppe_EBA now.

    (You also have the question of where Steppe EBA got a high frequency from, as they are a complex mix of EHG, CHG, Anatolian and WHG in about 45:45:7:3. Did ABCC11 evolve to high frequency through selection in Steppe EBA, or to an even higher frequency in one of the ancestral cultures which then admixed?).

  13. @Daniel: Agreed, but which population element of significance was adapted to the Ice Age steppe tundra? ANE. All the other populations repopulating Europe came from refugia, if they had the allel at all.
    The selection happened primarily during the Ice Age, thats what I was saying.

    @Matt: The Han definitely had the spiritual and ethical steppe warrior influences. Just read the descriptions, way of thought and deities.
    Its even possible that Sino-Tibetans might have been a (“Mongolian”) steppe herder group as a whole imho. We have many different language groups in the developed, already expanding Hwangho-Yangtse sphere. Let’s wait for aDNA.

  14. @Matt
    Ancestral cultures of Steppe EBA likely had higher frequency of it. Mediated by ANE to EHG & CHG I’m guessing.

    snpedia rs17822931 gives CEU Americans 23% CT [that is mix of TT dry and CC wet], 0.9% TT (dry) and rest is CC (wet). Presence of CT allele suggests considerable mixing, and dilution of TT.

  15. @Matt: Well the near east would be independent if we only look as far as back the neolithic. They might have had influence from the north African epiplaeolithic in the form of the Mushabian culture.

    I have a hunch that the Levant E1b came from the north African Mushabians while the pre-Natufian Kebarans would have been primarily G and H in terms of yDNA and autosomally very much like Anatolian/Pinarbasi hunter gatherer.

    Though you could argue that Kebaran alone would have gotten to Natufian-like sophistication even without the Mushabian influence.

  16. @Daniel, OK, but seems at some point this has to show up in ancient dna, and there has to be a really good explanation for why it hasn’t shown up already in ancient dna, or we can’t really argue for it.

    @DaThang, the interplay of those cultures is pretty worth thinking about (can’t say much more about the topic other than I’ve heard of the names of them), but would say I am thinking more in terms of “Primary civilization = civilization that passes the threshold of civilization without receiving cultural influence and diffusion directly or indirectly from any culture that already has passed that threshold” – though this may not be a distinction that really holds up…. Anyway, in that sense, mutual influence between the Near East and North African cultures in the epipaleolithic, wouldn’t have much bearing on that question.

  17. On the subject of the Neolithic in the Near East, does anyone know of any good papers or other references regarding the bona fide first signs of true farming in the Near East, and where exactly? I know the Natufians in Israel/Jordan are considered to be a transitional culture from the Epipaleolithic to true Neolithic, but I swear I’ve also read that first actual traces domesticated grains come from southeast Turkey/north Syria? Then I know there was also an apparent independent Neolithic emergenece in the Zagros, but I have a hard time believing that the Levantine, Anatolian, and Zagrosian Neolithics all emerged sui generis at roughly the same time 10-12,000 years ago without any interchange amongst each other.

  18. From what I gathered, if someone knows better, please correct me, Natufians were crucial for the development of actual agriculture.
    But it was in some subgroups, rather at the end of their culture, we see real innovations taking place.
    I think also that ideas, plant and animal breeds can be culturally diffused fairly easily without too much of a trace left.
    We see successful groups expanding with the help of cultural innovations, but the genetic and cultural expansions can come together or alone, there is no general rule.

    But I guess that some techniques for agricultural practises, even if quite rudimentary, were quite widespread especially in the Near East.

    The main change was about larger, sedentary communities, with fixed dwellings and a larger cult and social organisation.
    The beginning of individual specialisation.

    The domestication and planned agriculture was to a large degree the result of these communities becoming unable to feed themselves from the wild, unguarded and unfinished resources.

    So they started to produce and guard their food to keep up their way of life, size and character of their communities.

    That’s why the Northern and Eastern European foragers, living in naturally plentiful habitats close to the sea and rivers, didnt started to go into agriculture even when their neighbours did.
    I mean it means a lot of work and makes you even more dependent on a given place which you have to defend. It robs you from freedom and flexibility.

    I wouldnt wonder if the first farmers did start with their agriculture because their political or religious leaders commanded them to do so. And if they started without such a command, it was the sheer necessity of the moment, when the wild resources weren’t sufficient any more.

    Only when they started and it worked better and better with more care and technical improvements, they sticken with it.
    But I imagine a lot of “first farmers” to Fall back to foraging as soon as their was the opportunity.
    But Natufians started to create communities which were highly dependent on the plenty to never cease, but for sure at some point it did, so they and those inspired by them had no choice.

    Similarly the Northern and Eastern European foragers got social structure and higher cultural needs before switching to agro-pastoralism.
    They made a choice. The knowledge was there long before.

  19. I always find it interesting how Near East is the cradle of civilization. I know it was more fertile back then but i don’t think it was ever as livable as Western Europe or Eastern China. Those Near Eastern guys who invented the civ must have been really smart.

  20. @Cpluskx: Actually you have to consider that after the Ice Age, the climate was constantly changing until it reached a more stable condition which would more or less be recognisable to us.
    When Natufians came in, it was for sure one of the best places to live in, because there was natural, wild gras to eat, even make bread with, which could be harvested with little effort. There were herds of wild animals, better meat than we eat today, grasing in the open and the climatic conditions too were mild and highly favourable. In comparison to most of the world, it was like a Garden of Eden.

    But when the climate became drier and humans overused the resources, exactly because of this relative large, concentrated settlements like the Natufians introduced them and the climate went on changing to the worse, they had to consider breeding and irrigation, all the planning, work, the lifetime and energy you have to invest to increase the output of the country. It truly relates to the story of the bible.

    The Hwangho river people had a similar situation, they too lived from the plenty, adopted farming and it hopped from one related forager group to the next. This was very much unlike in Europe, Central and Southern Asia, where the Near Easterners which first crossed the borders of their habitats expanded rapidly from one small source group and largely replaced the indigenous people.
    Both in the Near East and the Hwangho, it was about different foragers, adopting the new ideas and lifestyle at roughly a similar time on their own. Before one small group could take full advantage of their increased productivity and higher specialisation.

    In Europe that was simply not the case for farmers, but it was for agro-pastoralists, like first the Northern European, then the Eastern European Southern steppe people. They too introduced something new for their habitat (agro-pastoralism, pastoralism) and it worked so well, they could jump on, cross the ecological niche borders and expand beyond it, until they reached the final ecological borders for their breeds, way of life and own race.

    Here again the same can be observed in China, with one big difference: That the advantage of the Hwangho crop farmers and pastoralists was so huge, they could overtake the still densely wooded rice cultivation area of the Yangtse, adopt that crops for themselves, and this strategy was suitable for much of South East Asia as well. Similar to Indo-Aryans (steppe) and Dravidians (Near Easterners) in South Asia, when the competition in the North resulted in the rapid adoption of rice cultivation which enabled them to move deeper in the more tropical parts of South Asia.

    The Hwangho people were just more exclusive, with massive settlements from their Northern centres which reduced whatever remained from the earlier waves, yet alone the pre-Mongoloid inhabitants of the region, to something almost unrecognisable.

  21. @Mick
    Kebaran people were using grains before Natufians but not on the same scale, which is why I said that they could have gotten to that kind of Natufian large scale sophistication without the Mushabians.
    Kebaran people were also practicing seasonal movement: in the summer they were living in the highlands while in the winter they moved to lowland lakes.

  22. @Donovan, re that paper, a few flags raised to me by their comment:

    “Alternative explanations, where the initial divergences within the Y-chromosomal phylogeny did indeed occur in the west, would require either that C, D and F lineages all migrated east, together with some GHIJK lineages, leaving only GHIJK lineages in the west, or that C, D and F were lost by genetic drift in the west, but not in the east. The first alternative would in turn imply unprecedented levels of male-structured migration, and would be difficult to reconcile with subsequent divergences within GHIJK during the next few thousand years, whereby some of the descendent lineages such as G1, H1 and H3 would also need to have migrated east in a male-structured way. The second alternative seems unlikely because genetic effective population sizes have been lower in East Asia than in Europe, so less genetic drift is expected in the west.

    Firstly, replacement of y-dna has never really tended to have much to do with autosomal population sizes changes in the shifts we are aware of and have evidence happening (e.g. Europe).

    Secondly, West Eurasian population structure is not really necessarily higher *as* a single population rather than a structured population which has re-unified over time. That population could well have gone through periods in which subpopulation size was lower than East Asia.

    Thirdly, we know part of West Eurasian higher effective population size is that West Eurasia pools a more basal set of OoA ancestors, including the Basal Eurasians. Again, the actual population size of each population may have been very low at times. (I also wonder if pooling all the *different* populations in East Eurasia that show basal branches might end up with quite a high autosomal population size?).

    It also seems a bit questionable to think about continuity within a region from 55 kya. Ust Ishim at 45 kya and Oase1 at 39kya show no continuity, until Kostenki14 at 37kya. Tianyuan man also shows only the very earliest indications of continuity in East Eurasia. We could say that bolsters their theory, but to me it seems to make it more questionable that you can learn about a specific 50-55 kya episode from current dna.

    Preprint could also do with some discussion about when AMH are thought to be archaeologically attested in each region. E.g. Fu’s paper in 2016 on Ice Age Europe tends to assume AMH arrived about 45-41 kya (so Oase1 is pretty early), in which case you’re not really talking about replacement of lineages in Europe as such, rather just “colonization of Europe from Southern Eurasia”. Where is the exact range in West Eurasia are they proposed that there were archaeologically attested AMH populations at 60 kya who then were replaced by a subsequent populations (at least in Y) at 55-50 kya?

    So yeah, I think there is some kind of very ancient Upper Paleolithic backflow to West Eurasia at some times from populations that are somehow also ancestral to present day East Eurasian populations, but not sure about how far they are pushing the data here.

  23. Here is the thing about haplogroup diversity- everyone and their mother have been overrunning the Levant since the upper paleolithic (or maybe even earlier), meanwhile SEAsia is probably one of the more shielded places with a long term human habitation, thus making it more conservative in terms of retaining old lineages. So a higher diversity in SEAsia than the Levant doesn’t mean that Levant wasn’t the main source of population (including paternal) dispersal into western Eurasia, although the more recent dispersal of R1 from the east is an exception to this. Am I getting something wrong here?

  24. I would add that South East Asia was, at least for post LGM times, a major sink region with a lot of refuges, islands and habitats. A lot of people just ended there or expanded into it from the major centres and larger metapopulations.
    And unlike in the more central regions of Eurasia there are a lot of places to hide.
    Its not by chance that the Orang Utan, Homo floresiensis, Denisovans and Negritos all ended up in the same macro-region when they were gone everywhere else.
    And its not just true for large primates, but flora and fauna in general.
    The next borderline is that of Wallace.
    I doubt anything did come the other way around big time for most of the worlds biohistory.
    Just look at the massive Eurasian landscape with related, similar habitats over huge stretches of land.

    That was the big minus for America too, that it expands from North to South and not East to West.
    That Mongoloids came up the way they did was because of the isolation during the LGM and the fact that the steppe, how important it was in so many ways, declined in demographic importance after the major farmer societies and states developed.

    I can just repeat that higher diversity in humans usually means admixture events and oftentimes even losing, one group at least being overrun. The winning group is expansive and oftentimes keeps a core region of rather unmixed character unless being overrun itself.
    Most of the Eurasian lineages went through the Eurasian steppe center. Its rather North than East or West. This center was split into two during the LGM, resulting in Caucasoid and Mongoloid proper.
    R is just the major Western group from this split during and after the LGM. Western means West of the barrier isolating Caucasoid from Mongoloid, not West in the sense of Europe necessarily.


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