How the Amazonians got their Australasian

Nature recently came out with two blockbuster papers establishing a better chronology on the settlement of the New World by humans. More precisely, the papers seem to push the likely date back by over 15,000 years. The figure above is from one of the papers. It shows human-derived artifacts from sites that date to 25,000 years BP and even 32,000 years BP.

I have recorded a podcast with the first author of one of the papers (she is second on the other). The podcast should post later today. Nevertheless, talking to the author I am more than 50% convinced that humans were present in the New World 32,000 years ago, and 90% convinced they were here 25,000 years ago. This is well before what is needed and expected from the standard “Beringian standstill” model.

The Beringian standstill alludes to the fact that the proto-Amerindians, a mix of Paleo-Siberian (ANE) and diverged East Asian, may have occupied Beringia for thousands of years before finally pushing southward ~15,000 years ago. The sites in the database of these papers show that a huge explosion of human occupation characterized North America during this period. But these were not the first humans.

I believe these new results likely open the possibility for a resolution of the mystery of why some groups in the Amazon seem to have “Australasian” genetic affinities. The result is robust. But it was hard to resolve with the Beringian standstill. The new chronology offers up an opportunity. Clearly the earlier populations before 20,000 years ago may have been the ancestors of the “Australasians” that are still hinted at in the Amazonians. I believe that these early people were members of what I have termed Clade-2 East Eurasians. This clade was dominant in South, Southeast Asia, Tibet, and present in coastal East Asia (Japan), during the Pleistocene. It has closer affinities to Oceanians than East Asians to the north.

If the first humans in the New World arrived as coastal fringe dwellers, it is clearly plausible that populations from Japan and points south could simply have done a circum-Pacific arc. We’ve seen lots of mass replacements in the ancient DNA, and the WST-Clovis groups seem to have been very numerous. Weak to no genetic signature of Clade-2 New World peoples is not surprising. There is no evidence of Oase Aurignacians in modern Europeans.


19 thoughts on “How the Amazonians got their Australasian

  1. The two main problems I have always had with the idea of early settlement are: 1) how would it be possible for modern humans to occupy the Americas for 10,000 years or more without producing populations substantial enough to leave widespread evidence (as Clovis and later populations rather quickly did); and 2) how could newcomers replace entrenched original inhabitants so completely without a substantially higher level of technology.

    Learning about population replacements in Europe has made 2) a little less problematic, but even there replacements seem to have been driven by technology; in particular, first farming, then (maybe) pastoralism. But all of the migrants to the Americas were hunter-gatherers. Could one group have been that far advanced over the other?

    A possible solution to both problems might be if the original settlers were just extremely backward and static. The Australian Aborigines made little technological or social progress over 40,000 years. Maybe the original Americans were like that, and just stuck to the coasts and never penetrated the interior, and as a result their populations were always small and easily overwhelmed? That seems a little hard to credit though. The New Guinea highlands were settled. And Polynesians must have landed in Australia occasionally, yet the Aborigines didn’t get replaced.

    Anyway, Razib, what are your thoughts on those two questions?

  2. I found the tools unlike anything else. Made from limestone. No edge retouching. No bones with butcher marks. No hearths. Just trying to understand thousands of “tools” without associated butchering and cooking and eating. Plus there is no apparent tool type change over 10,000 years or more. I’m skeptical.

  3. @JB

    One other possibility is that the first wave were genetically inferior, not only culturally, due to being extensively inbred.

    We know that some early populations which existed at the fringes of human habitation, like Neandertals, were extremely inbred. This makes logical sense, because when there are high levels of mortality and limited new migration the number of genetic lineages will tend to be reduced over time, resulting in more and more of a genetic monoculture. We see a recent version of this in some small villages in Europe where most people end up with a handful of surnames.

    We know that inbreeding causes lots of issues, from shorter stature, to lower intelligence, to increased risk of genetic disease, to lower levels of fertility.

    A highly inbred lineage may be fit enough to survive, but not thrive. But if it meets up with another, less inbred population occupying the same niche it will tend to lose out, because the other population can do all the same things much better. Add to this potential differences in human culture due to a bottleneck and the problems are magnified.

    The bulk of the modern Amerind gene pool is of course descended from a relatively small group of people who had a massive population explosion. I believe I have heard estimates the original population size was around 100 people, but this may be out of date. What if the original “Native Americans” descended from a handful of close relatives? Or even a pregnant mother? Obviously purifying selection should, over time, result in the really nasty genetic diseases from dropping out of the gene pool. But a lot of beneficial variants would also not be in the founding population. In order to develop new beneficial variants they’d have to do it the hard way through mutation – and with a small population size, novel beneficial mutations will happen rather infrequently.

  4. Rich, perhaps it was a restless but stupid population. Restless enough to leave Asia and migrate down the western American coast but stupid enough not to be able to advance the tool kit they came with (and maybe to gradually lose it).

  5. That’s another “oh really, now you see it too”, moment for parts of the American scientific community. There was never any doubt that modern humans lived in America about 25.000 years ago. The whole “Clovis first” debate was ridiculous. I sometimes asked myself why it was even kept alive so long? Probably to tell modern American natives that they were the first? Or the prestige and standing of some of its proponents? What else?
    Of course its good if its finally being settled down by irrefutable evidence and the crazy ideas die off, like they should. Unfortunately its not always possible to come up with with evidence clear and acceptable enough to disprove common misconceptions of the current scientific consensus, even though they are as wrong.

    There were always the old records from South America and the physical anthropological results pointing to different layers of American inhabitation. The most likely scenario is that they first moved along the coast, with little traces, until they reached a climatic zone and tropical river habitats. In the latter they left more descendents and got caught by the new wave of East Asians the latest.

  6. Generally, like jb and Rich, and for the same reasons, I’m skeptical. Also, even if there is early, low level modern human habitation, there is no good reason for these Paleo-Americans to have significantly different genomes from the primary first wave founding population of the Americas. In the paradigm of Beringian standstill, the people who are at the launching off point for a Pacific route expansion at the right time for these tools are still the same source population as for the later primary first wave founding population.

    This evidence pushes me in the direction of an early pilot wave of hominins in the New Word, but I’m still not at a 50% probability that their narrative is correct.

    It is an even more huge leap to conclude, and there is really no good affirmative evidence to support, the inference that a pre-LGM wave of Paleo-Americans would have “Australasian” genetic affinities (and the papers in Nature don’t try to connect those dots).

  7. We know that long RoH have their problems and are correlated with depression in traits, but I don’t know that there is much evidence that short RoH do, in humans. Like, do the Kalash, with a huge bottleneck, have problems/differences with traits relative to their close relatives, once accounting for long RoH?

  8. * @Karl “I believe I have heard estimates the original population size was around 100 people, but this may be out of date.”

    The body text of the 2018 article below states that the current best estimate, based upon genetic data, places the size of the founding population of the Americas in the range of 229 to 300 with a best fit of about 284 people.

    “In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals.”

    Nelson J.R. Fagundes, et al., “How strong was the bottleneck associated to the peopling of the Americas? New insights from multilocus sequence data”, 41(1) Genetics and Molecular Biology (2018).

    * Relevant to Paleo-American genetics:

    “Our results demonstrate that humans occupied the site as early as 24,000 cal BP (19,650 ± 130 14C BP). In addition to proving that Bluefish Caves is the oldest known archaeological site in North America, the results offer archaeological support for the “Beringian standstill hypothesis”, which proposes that a genetically isolated human population persisted in Beringia during the LGM and dispersed from there to North and South America during the post-LGM period. . . . the Yana River sites indicate a human presence in Western Beringia ca. 32,000 cal BP, the Bluefish Caves site proves that people were in Eastern Beringia during the LGM, by at least 24,000 cal BP, thus providing long-awaited archaeological support for the “Beringian standstill hypothesis”. According to this hypothesis, a human population genetically isolated existed in Beringia from about 15,000 to 23,000 cal BP, or possibly earlier, before dispersing into North and eventually South America after the LGM.”

    Lauriane Bourgeon, Ariane Burke, Thomas Higham “Earliest Human Presence in North America Dated to the Last Glacial Maximum: New Radiocarbon Dates from Bluefish Caves, Canada” PLOS (January 6, 2017).

  9. Rich, maybe people only came there to make tools?

    jb, maybe these Australasian people were more fishers, while Clovis people were more big game hunters? The first would only hug the West coast until they reached Central America, while the second would be all over the place in North America. Plus, with the worst of the glacial maximum, maybe many of these Australasians tribe were wiped out and only the South American ones survived, isolated from the rest of the world?

  10. If they were a coastal people avoiding the Smilodons, American lions and Arctodus of the interior, I suppose most of the evidence is now under the sea.

    There is no evidence of Oase Aurignacians in modern Europeans
    Pardon my ignorance because I don’t really know, but is that true for all Aurignacians, or just the Oase ones? I know Oase 2 is closest to Tianyuan, but I wasn’t sure about the others.

  11. RE thoughts others expresed of why a population might have stayed small.
    One big misgiving I have overall with my return to hobbyist level reading of these issues is preoccupation with human and apes; I almost perceive a deliberate blinders on in fields of human study not to seek comparisons to ecological niche and populations of say instinct driven beavers with quite elaborate instincts to change the physical environment (is damn building including float channels and lodges so different from flaking) and social mammals like meerkats and wolves and the limit on their population density in relation to competition with other species as well as their own.

    In this light, I think that human populations must be seen as having limits of various types and not necessarily malthusian in regard to what land could support.

    A greater willingness to look at say, habitat restoration and other species return that wolves and beavers reintroduction allowed by resultant changes in vegetation with greater water retention from beavers or fewer ungalates of certain types eating young tree shoots changing forest composition..

    What held human populations in check places might not have been simple calories but might have been other types of bottlenecks (pumas or birds of prey preying on children?)or disease vectors causing infection during first childbith

    Or…so many others. Humans are uniquely flexible but were we always so? Certainly many cultures had taboos about what might be logically obvious things to try (i.e. Diamonds postulations about Greenlanders reluctance to tap sea calories?)

  12. So they came from coastal SE Asia?

    Also if this type of ancestry was widespread in South Asia is y H AASI associated after all?

  13. I hate that we are calling this ancient genetic trace “Australasian”… Actual Australasians are a very divergent group that separated very early from the people that originated this signal, they acquired unique and considerable denisovan admixture and their phenotypes were probably greatly affected by this… I don’t get it when people try to make genetic and/or anthropometric connections between modern Australasians and Jomon and
    “population y”, they just aren’t there and never will be. Australasians just retain some of that very basal affinity more because they weren’t affected by all the demographic turnovers in east asia. The genetic distance between Australasians and any of these other ancient northeast asian and siberian groups is IMMENSE. What we are talking about here is an ancient coastal east asian group.

  14. “But all of the migrants to the Americas were hunter-gatherers. Could one group have been that far advanced over the other?”

    Sure, why not? The Dorset and Thule peoples were both hunter-gatherers and the latter replaced the former.

  15. @MarianneRichard

    But the genetic descendants of these people are not coastal. They are exclusively on the inland side of a continent divide that is on one side a Caribbean coastal watershed and on the other side, the furthest inland extent of the Amazon River’s watershed.

    The most plausible way for someone to get there is to start on the South American Caribbean coast, follow a river up to its source, and then travel the short distance to a tributary of the Amazon which has its source nearby and to follow it down into inland South America.

    This seems out of synch with coast hugging people who avoided the inland and also begs the question of how they got to the Caribbean watershed. Presumably they went overland rather than the long way around the South American coast.

    The rejoinder would be that other New World Americans killed them off. But the reason that there are no Oase Aurignacian genetic traces in modern Europeans is that Europe was completely, 100% depopulated by the time of the LGM when most of Europe was under Antarctic grade thick glaciers.

    Even the most extreme genocides of history and prehistory almost always managed to involve the introgression of a few members of the exterminated group into the replacing population. Modern English people have traces of Mesolithic Western European hunter-gatherer DNA despite two successive rounds of quite extreme population replacements: first the Neolithic replacement of the hunter-gatherers, and then the metal age Bell Beaker people’s replacement of the first Neolithic people there.

    Indeed, Europeans even have Neanderthal ancestry (just like all non-Africans do), modern humans in Papua New Guinea, Australia and the Philippines have archaic Denisovan ancestry, and there are similar traces of archaic hominin ancestry in some Africans from “ghost” populations who were presumably replaced by modern humans.

    But there was no comparable population obliterating event the the impact of the LGM in Europe, in inland northern South America, which would have been quite habitable even at the peak of the LGM and the most severe arid periods of the region.

    If one stone age hunter-gatherer population of modern humans replaced another continent-wide, we’d expect to see the very dilute presence of the Paleo-Asian genetic component (@Alex, I like the term “Paleo-Asian” better than “Australasian”), in multiple communities across the Americas and especially in Meso-America and South America (which harbors only Pacific route ancestry for the most part, unlike North America)

    Also, while the Clovis culture is notable because its archaeological traces are so distinctive and widespread in North America, it was a 300 year blip a thousand years or more after the first wave of the Founding population of the Americas which ended abruptly when the Younger Dryas climate event hit. “The human remains and Clovis artifacts can now be confidently shown to be the same age and date between 12,725 to 12,900 years ago,” from here in relation to Lorena Becerra-Valdivia, et al., “Reassessing the chronology of the archaeological site of Anzick.” Proceedings of the National Academy of Sciences 201803624 (2018) DOI: 10.1073/pnas.1803624115


    “The Dorset and Thule peoples were both hunter-gatherers and the latter replaced the former.”

    The Thule were an iron age people who also had comparatively technologically advanced maritime and hunting tool technologies. Replacement generally only happens when the newcomers have very significant technological advances: farming and herding in the case of the Neolithic replacement of hunter-gathers, and horses and metal, in the case of the Bronze Age replacement of Neolithic farmers.

    But the archaeological record as revealed in the two new Nature articles, and in other finds of purported pre-LGM human occupations that were previously discounted, weren’t dramatically different technologically than the early Founding population of the Americas that gave rise to the post-LGM population surge. Both were using comparable stone tools, and the comparability of the stone tools is the main reason that the authors of the Nature articles can confidently argue for what the found having a modern human source.

    Now, there are other examples of modern human populations remaining marginal in virgin territory, although not many.

    One of those in in Madagascar where African foragers arrived ca. 2000 BCE without causing a mega-fauna extinction or other discernible impact in contrast to hunter-gatherer migrations into Australia and Papua New Guinea, into the Americas (ca. 14000 years BP), in Europe, and into Siberia did. Mega-fauna extinctions in Madagascar only began when the Austronesian people from Borneo arrived together with East African people ca. 500 CE. Robert E. Deward et al., “Stone tools and foraging in northern Madagascar challenge Holocene extinction models.”, PNAS (2013).

    Another example of a population that survived but didn’t thrive is Tasmania which regressed technologically and culturally to a barely sustainable marginal threshold when rising sea levels isolated the Tasmanians, ca. 8000 years BP, from other aboriginal Australians, who settled Tasmania ca. 40,000 years BP, after having been the most thriving part of Australia from 35,000 years BP to 11,000 years BP according to Harry Lourandos, “Hunter-Gatherer Cultural Dynamics: Long- and Short-Term Trends in Australian Prehistory”. 1(1) Journal of Archaeological Research 67–88 (March 1993).

    The basic hypothesis in both of those cases is that there is a liminal population size in the hundreds of people or so, that is just barely large enough to be sustainable, but is too small to thrive.

    But both of those cases involve geographically isolated islands making up a single, small population, not a population spread thinly across two continents. You really have to go back to the Neanderthal genetic evidence to see really prolonged stagnant and very low hunter-gatherer populations, leaving few archaeological remains and showing highly stagnant technology over tens of thousands of years, in situations where they have no competition from other hominins over continent scale geographic regions.

    I think it is fair to guess that the Neanderthal, who were not all that “stupid” relative to our modern human ancestors as measured by brain size and behavioral complexity, had very less brain plasticity; like beavers or orb spiders or bees, they had elaborate more or less innate and instinctual abilities that allowed them to make and use tools and engage in complex behaviors, but it doesn’t seem that they couldn’t learn culturally and adapt to change as well as modern humans. This was probably a major contributing factor to their stagnation, and to them being off base and less able to adapt to volcanic activity driven climate shifts close in time to the appearance of modern humans in Europe in large numbers in the Upper Paleolithic era.

    In contrast, while we have no direct evidence of the capabilities of the Paleo-Asian ancestors of the handful of Amazonian hunter-gatherer tribes where their genetic legacies can still be seen, we have lots of archaeological, anthropological, and genetic evidence to tell us about Clade-2 East Eurasians, and what we know puts these people well within the realm of ordinary modern humans behaviorally. So, it is indeed hard to see how the founding population of the Americas that gave rise to the post-LGM wave could have obliterated pre-LGM modern humans in the Americas so completely, without leaving any trace outside of these handful of isolated deep inland Amazonian tribes, of a genetic legacy.

    So even if there was a pre-LGM first wave of modern humans in the Americas, I think it is far more likely that they were just early migrants from the same population as the post-LGM founding population of the Americans (so as to be genetically invisible). in this narrative the Paleo-Asian genetic traces in the Amazon were do to a one off event such as the incorporation of one or a few individual explores from Southern East Asia or Southeast Asia who arrived just as the founding population set out post-LGM on a Pacific route. They (with their descendants) could have been part of a single tribe at the vanguard of the Pacific route expansion, crossed over central America to the Caribbean coast of what is now Columbia, continued exploring inland up a river to its source there, crossed the mountains into the upper reaches of a tributary to the Amazon, and finally gave up their wanderlust. Then, they settled into an isolated and marginal environment where they remained as a people more or less undisturbed for the next 13,000 years or so after less than 1,000 years getting there in the first place. At the vanguard of expansion and always moving on as a tribe, they wouldn’t have left a genetic legacy elsewhere in the Americas, and if they were late arrivals, they wouldn’t have had a genetic impact on the rest of the founding population.

  16. One quick additional point to the long discussion in my previous comment. There is one technology available to the founding population of the Americas that might not have been available to pre-LGM migrants to the Americas: domesticated dogs.

    We also have one archaeological indicator that strongly suggests that domesticated dogs could provide a decisive advantage to modern human hunter-gatherers that could upset the ecological balance. This is that there are two waves of distinctive mass extinctions in the Australian archaeological record. The first is when modern humans arrive on the continent at the beginning of the Upper Paleolithic era. The other is ca. 8000 years BP in the early Holocene era, when the dingo arrives in Australia.

    Domesticated dogs might also have been a distinction between Clade-1 East Asians and Clade-2 East Asians, although that is a conjectural guess.

  17. I have absolutely no formal understanding of genetics, but in the case where a highly inbred or sickly population, smaller than the later waves, was overwhelmed, is it not possible that negative selection against some aspects of their ancestry would remove a significant portion of the remainder of it by association? I’m thinking of how I had read Dionekes saying that certain mtDNA halpogroups are associated with some traits, presumably (again, given my limited understanding) because having x haplogroup implies slightly greater odds of sharing wider ancestry with its source population. If a gene can be perpetuated by loose association, could it not be purged in the same way?

    I also think of the earliest populations in East and Southeast Asia, who must have been substantially genetically distant, that have left no discernible trace in modern humans. Do the earliest implied Homo Sapiens inhabitants of Eurasia, pre-50kya not have a similar thing going on, Andrew? Not critical, just curious. I’m the rhube here.

  18. @Alkibiades

    “I also think of the earliest populations in East and Southeast Asia, who must have been substantially genetically distant, that have left no discernible trace in modern humans.”

    There are traces of both Denisovan ancestry and of modern human Negrito ancestry in East and Southeast Asian populations on the mainland side of the Wallace line, although the percentages of each are quite small. So, I think your premise here is incorrect.

    It is widely assumed that Homo erectus and modern humans, to the extent that they co-existed at any point, were not capable of producing fertile offspring due to the 1.7 million years or so of genetic divergence between them, and that they co-existed at most briefly if at all, and if they did co-exist, co-existed only in narrow geographical locations. So, it isn’t surprising that the only faint traces of Homo erectus genes in modern humans are proportionate to archaic admixture and probably a result of the archaic hominins with whom modern humans could mate to have fertile offspring having some low level of Homo erectus admixture.

    “Do the earliest implied Homo Sapiens inhabitants of Eurasia, pre-50kya not have a similar thing going on, Andrew?”

    I think that you are asking if there was a selective fitness based selection against Paleo-Asians, although I’m not entirely clear on that point.

    On the whole, it seems that culturally driven selection (i.e. the genes being fitness neutral in and of themselves, but favored because they belonged to a group of people who had a cultural or technological edge) seems much more likely. If anything, you’d expect Paleo-Asians, presumably from tropical or subtropical parts of Asia, to have a selective fitness edge over the founding population of the Americas, which had substantial North Asian sub-Arctic historic origins, in the climate of the upper reached of the Amazon River basin and more generally in tropical and subtropical areas of Meso-America and South America.

    Also, to the extent that there were diseases specific to the Americas to which the post-LGM founding population had not been exposed, you would think that after 10,000 or so years of living in the Americas already, that the first wave of modern humans would have gained adaptations to these local diseases and temperatures that the post-LGM founding population (which had spend thousands of years adapting to life in the sub-Arctic) would lack, given the first to arrive population a decisive edge in terms of the selective fitness of their genes in the local environment.

  19. Ah no, I meant to reference the implied occupation of Southeast Asia by Homo Sapiens itself before the later population expansion post 50kya that Razib also alludes to in his previous post on Paleo-Asians. I was under the impression that there is increasing evidence that our species left Africa earlier than previously thought, but did not succeed in establishing itself very strongly, such that the later groups that came, who define modern Eurasian ancestry, overran them, much like neanderthals and denisovans. Razib has talked about this previously, and how curious it is that these early Sapiens migrants don’t seem to have left a significant genetic trace.

    Sorry for that lack of clarity.

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