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Thread: Pleistocene Siberian Genomes / Ancient North Siberians (Sikora et al)

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    Pleistocene Siberian Genomes / Ancient North Siberians (Sikora et al)

    Far northeastern Siberia has been occupied by humans for more than 40 thousand years. Yet, owing to a scarcity of early archaeological sites and human remains, its population history and relationship to ancient and modern populations across Eurasia and the Americas are poorly understood. Here, we report 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-year-old (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found. These genomes reveal complex patterns of past population admixture and replacement events throughout northeastern Siberia, with evidence for at least three large-scale human migrations into the region. The first inhabitants, a previously unknown population of "Ancient North Siberians" (ANS), represented by Yana RHS, diverged ~38 kya from Western Eurasians, soon after the latter split from East Asians. Between 20 and 11 kya, the ANS population was largely replaced by peoples with ancestry from East Asia, giving rise to ancestral Native Americans and "Ancient Paleosiberians" (AP), represented by a 9.8 kya skeleton from Kolyma River. AP are closely related to the Siberian ancestors of Native Americans, and ancestral to contemporary communities such as Koryaks and Itelmen. Paleoclimatic modelling shows evidence for a refuge during the last glacial maximum (LGM) in southeastern Beringia, suggesting Beringia as a possible location for the admixture forming both ancestral Native Americans and AP. Between 11 and 4 kya, AP were in turn largely replaced by another group of peoples with ancestry from East Asia, the "Neosiberians" from which many contemporary Siberians derive. We detect additional gene flow events in both directions across the Bering Strait during this time, influencing the genetic composition of Inuit, as well as Na Dene-speaking Northern Native Americans, whose Siberian-related ancestry components is closely related to AP. Our analyses reveal that the population history of northeastern Siberia was highly dynamic, starting in the Late Pleistocene and continuing well into the Late Holocene. The pattern observed in northeastern Siberia, with earlier, once widespread populations being replaced by distinct peoples, seems to have taken place across northern Eurasia, as far west as Scandinavia.

    https://www.biorxiv.org/content/early/2018/10/22/448829

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    A basal U2'3'4'7'8'9 (since earlier K14 is basal U2), and a basal or even ancestral P1.

    Some old stuff:

    Quote Originally Posted by parasar View Post
    ...

    On another point I slightly disagree with Dr. Hammer when he says: "SE Asian Origin of Hg P"
    This to me is not proven and also looks unlikely. The P node could have been born in SE Asia, but South Asia, Siberia, or Eastern Europe are better possibilities. But we are nowhere close to pinpointing, we could draw a triangle from Kostenki to Yana to Balangoda, a vast region for the origin of P.
    Quote Originally Posted by parasar View Post
    If you notice for ANE there is not only an eastern cline but also a northern one.
    Samara EHG is further east of Karelia EHG but lower in ANE than the latter. Therefore, my thinking has been that ANE looks to be not only Siberian but also Arctic. We know that ANE got to the Americas across a bridge bordering the Arctic. And we have some of the oldest settlements at Yana - http://science.sciencemag.org/content/303/5654/52 -likely an ANE population.
    ...
    Quote Originally Posted by parasar View Post
    How about Yana? Was its tool-kit related to Mal'ta?
    http://news.nationalgeographic.com/n...nhumans_2.html
    "Russian researchers have found a wealth of hunting tools, which date back 31,000 years, along central Siberia's Yana River. The artifacts include hundreds of stone tools and flakes, as well as spear foreshafts made of rhinoceros horn and mammoth tusk... most of the Yana tools were based on flake production from pebbles available in the riverbed. Using radiocarbon dating, Pitulko established them to be more than 30,000 years old ... To add to the intrigue, the foreshaft first found in Yana bears a striking resemblance to others used by the Clovis people, believed by many archeologists to be the first humans in North America.

    However, Pitulko says the connection remains tenuous. The Clovis foreshafts are around 16,000 years younger than those found at Yana River and were found 6,000 kilometers (3,700 miles) away."
    Quote Originally Posted by parasar View Post
    http://arctic.ru/analitic/20160704/386534.html
    "When did people arrive in the Arctic? What is the oldest evidence of human activity in this region? ...

    The wolf's wounded shoulder was dated to 45-47,000 years ago, and this figure can be accepted because the animal continued to live after the injury. It was not a postmortem but a perimortem injury, and its mechanics excludes any bites, stripping or other actions that would not be typical of a human. The creature that wounded the wolf from Bunge-Toll/1885 had stabbed it with a spear, and it happened 45,000 years ago ...

    The same approximate age has been estimated for the remains of a mammoth killed by a man (likely a man) from Sopochnaya Karga ...

    recent article in Science (Pitulko V.V., Tikhonov A.N., Pavlova E.Y., Nikolskiy P.A., Kuper K.E., Polozov R.N. Early human presence in the Arctic: evidence from 45,000-year-old mammoth remains // Science. 2016. Vol. 351. P. 260-263). In my opinion, these findings clearly indicate that people had colonized this Arctic area about 45,000 years ago. They had probably moved there even earlier because by that time they had already settled extensively around the Yenisei's mouth (72 degrees of north latitude) and on the Yana (69 degrees) and even more to the east and the north, on today's New Siberian Islands ...

    people also moved towards the north of west Siberia at least, a 42,000-year-old Ust-Ishim human hip bone was found 2,000 km south of the killed Sopochnaya Karga mammoth, near Tobolsk ...

    The short answer to the question would be: for the moment, the oldest known human traces in the Arctic date back to 45,000 years ago, or perhaps, even a little bit more...

    What was the status of the climate in the Arctic when humans first arrived, according to the excavation results?

    plus 2 Celsius in July is a good day on Zhokhov Island and plus 4 is almost hot, unlike the Yana RHS (a Paleolithic site on the Yana River) 800 kilometers south of Zhokhov Island, where such a temperature means very cold and a normal summer day is plus 20. Everything is relative.
    Some 8,500 to 9,000 years ago, the climate in the east Siberian part of the Arctic (the New Siberian Islands and the northern part of the Yana-Indigirka Lowland) was much milder than it is now ...

    We can clearly distinguish between cold and warm phases, but there were shorter cold and warm periods during the long and relatively warm phases, like the interglacial period that lasted between 55,000 and 24,000 years ago.
    The oldest human sites we have identified in the Arctic (B-T/1885 and the Sopkarga mammoth that was killed by humans) date to about 45,000 years ago, the end of the first warm MIS3 interstadial (Marine Isotope Stage 3, Kargin Interstadial, Siberian climatostratigraphic scale), which is known in east Siberia as the Khomus-Yuryakh interstadial. In the central Siberian part of the Arctic Taimyr Peninsula and the adjacent territories), this period marked the beginning of a long Malokhet warming (the climatic optimum of the Kargin interstadial) after a relatively long unnamed cold phase. Even the enumeration of these names and events is evidence of a very complex picture of paleoclimatic changes ...

    Climate in the Arctic regions, where we found the earliest evidence of humans dated to about 45,000 years ago, can be only described provisionally ...

    about 45,000 years ago the region west of the Taimyr Peninsula, where the Yenissei estuary is now, was a grassy steppe-tundra, with a dry continental climate and few wet periods. Summers were quite warm, with an average temperature of 2 or 3 degrees Celsius above the current temperature, and with severe winters ...

    Life wasn't bad in the Arctic 8,000 years ago. Their tools and household technology were rather close to what we know from ethnographic studies today. They bred sled dogs and made sophisticated sleds. Alexei Kasparov and I have studied the dogs' osseal remains, which lead us to assume that these were actually draught dogs close to present-day Siberian Huskies in looks and weight, which is the principal factor in determining thermoregulation, hardiness and working ability. Their weight stays in the 23-27 kg bracket and doesn't usually exceed 27 kg. The Zhokhov people possessed just such dogs along with large hounds probably for bear hunting (Pitulko V.V., Kasparov A.K. Osseal Remains of Early Holocene Domestic Dogs from the Zhokhov Site (Eastern Siberian Arctic) and the Authenticity of Identifying the Ancient Canis familiaris in Archeological Excavations // Stratum plus. 2016. N 1. P.171-207.).

    What did the ancient people do according to the excavation findings? Hunting mostly?

    Of course, they were mostly involved in hunting if we talk about life ...

    Hunters often targeted non-food resources like, for example, fur. At the Yana RHS site, people hunted for hares but not because they wanted meat. They skinned the bodies and threw them away ...

    Mammoths were hunted for their tusks. We can convincingly demonstrate this in a series of works discussing the findings from the Yana RHS site. The hunters preferred females over males as the females' tusks were relatively straight, which means time-consuming straightening was not required ...

    At the Yana RHS site, humans spent a significant amount of time making jewelry. They loved decorating themselves and knew how to do it by making pendants of animal teeth, beads from mammoth tusks and small hare bones, tiaras and headbands from mammoth tusks, pendants, bracelets and other items...

    Humans on Zhokhov Island were largely involved in manufacturing wooden goods, including dog sleds and exceptionally well made woven goods. Obviously, during any period in history humans also spent time making clothes and shoes, and roofs for their shelters ...

    So far, we can look at human existence in the Arctic as far back as 50,000 years ago. Since then, there have been major changes in the environment and climate, including the Last Glacial Maximum ..."

    See also Ref:
    Early human presence in the Arctic: evidence from 45 000-year-old mammoth remains
    http://science.sciencemag.org/content/351/6270/260

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    I find table S6.1 particularly interesting.
    The population sharing most affinity to the Yana individuals is MA1, as would be expected... but it is by a very slight margin.
    1)
    AG3 is pretty far down the list for Yana1, not so much of a discrepancy for Yana2 however.
    Still, something like D: Outgroup Yana_merge MA1 AG3 looks like it would be significantly negative, begging an explanation.
    2)
    Given the similar East-West mix, and y-hg P1, it's most parsimonious to say Yana and MA1 form a clade, but if so it is pretty shallow.
    Either Yana is an early split from the 'proto-ANE' group, and were a mostly dead end, or the East-West mix was relatively recent at 31kbp, and ANE as a population wasn't really drifted enough to strongly cluster together.

    If hypothetically we posit ANE as a mixture between something in the Kostenki/Sunghir/Vestonice/Goyet neighborhood of things, and something East-Eurasian, at ~75-25 proportions...
    West portion: Would be a trifurcation, with Kostenki/Sunghir/Vestonice being one branch, Goyet being a second, and ANE-west being the third.
    East portion: Also a trifurcation, with Tianyuan being one branch, Oceanians being a second, and ANE-east being the third.
    Any alteration of these proportions would make things a lot more complicated, though in reality it may be (regarding Goyet's East-Eurasian affinity).

    At this point though, the simplest solution regarding Goyet may be something like Goyet > proto-East-Eurasians.
    Whether or not that's accurate or even realistic would probably benefit from the perspective of someone knowledged in archaeology.
    Last edited by Kale; 11-03-2018 at 05:45 AM.
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    So much going on in this paper that I hardly know where to start...

    Quote Originally Posted by Kale View Post
    East portion: Also a trifurcation, with Tianyuan being one branch, Oceanians being a second, and ANE-east being the third.
    Would you put AASI and ancient Southeast Eurasians (the Onge and Hoabinhian clade) under the Oceanian umbrella? What about East Asians proper? Do you see merit in the McColl paper's model, which posited that East Asians are ~75% Proto-Southeast Eurasian + ~25% Tianyuan-like?

    The Narasimhan paper on South and Central Asia doesn't assume a very close connection between East Asians and Onge, though. The model in that paper assumes the major Eastern Crown Eurasian branches are nearly equally divergent, though the East Asians are separated from the rest:
    "In our fitted admixture graph, AASI, Onge, and AncientPapuan (a hypothesized ancestral population to modern Papuans, prior to Denisovan admixture) are a clade with respect to Nicobarese, representing the East Eurasian ancestry that plausibly dispersed with the Austroasiatic language expansion, and indigenous Chinese groups. The split between AASI, Onge, AncientPapuan is modeled as nearly a trifurcation. It seems probable that the split between AASI and AncientPapuan occurred prior to modern humans reaching Sahul (the ancient continent uniting Australia and New Guinea). Radiocarbon dating shows this is unlikely to be much more recently than 47,000 years before present."

    It's noteworthy that Yana is modelled as ~22% Proto-East Asian by Sikora. I guess that means its eastern ancestry is indeed close to East Asians, as opposed to being the result of gene flow from a generalized ENA lineage undifferentiated from Australo-Melanesians and the like. Sikora estimates the Western-Eastern Crown Eurasian divergence to be ~43,000 years ago, but given the deep splits in ENA that Narasimhan assumes, wouldn't something closer to 50,000 be more realistic? Ust-Ishim is 45,000 years old, and I've noticed he vacillates between being considered closer to Western or Eastern Eurasians depending on the paper. I guess we'll need more Paleolithic DNA from East Asia and Oceania to work it all out.
    Last edited by Michalis Moriopoulos; 11-03-2018 at 06:54 AM.
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    Quote Originally Posted by Kale View Post
    I find table S6.1 particularly interesting.
    The population sharing most affinity to the Yana individuals is MA1, as would be expected... but it is by a very slight margin.
    1)
    AG3 is pretty far down the list for Yana1, not so much of a discrepancy for Yana2 however.
    Still, something like D: Outgroup Yana_merge MA1 AG3 looks like it would be significantly negative, begging an explanation.
    2)
    Given the similar East-West mix, and y-hg P1, it's most parsimonious to say Yana and MA1 form a clade, but if so it is pretty shallow.
    Either Yana is an early split from the 'proto-ANE' group, and were a mostly dead end, or the East-West mix was relatively recent at 31kbp, and ANE as a population wasn't really drifted enough to strongly cluster together.

    If hypothetically we posit ANE as a mixture between something in the Kostenki/Sunghir/Vestonice/Goyet neighborhood of things, and something East-Eurasian, at ~75-25 proportions...
    West portion: Would be a trifurcation, with Kostenki/Sunghir/Vestonice being one branch, Goyet being a second, and ANE-west being the third.
    East portion: Also a trifurcation, with Tianyuan being one branch, Oceanians being a second, and ANE-east being the third.
    Any alteration of these proportions would make things a lot more complicated, though in reality it may be (regarding Goyet's East-Eurasian affinity).

    At this point though, the simplest solution regarding Goyet may be something like Goyet > proto-East-Eurasians.
    Whether or not that's accurate or even realistic would probably benefit from the perspective of someone knowledged in archaeology.
    If ANS or Yana is closely related and ancestral to ANE with both being around 75% West Eurasian and 25% East Eurasian or more, does this means that Native Americans have around 28-30% ancient West Eurasian ancestry and might have very low levels of CHG-related admixture being that they are around 40% ANE?

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    Quote Originally Posted by Michalis Moriopoulos View Post
    So much going on in this paper that I hardly know where to start...



    Would you put AASI and ancient Southeast Eurasians (the Onge and Hoabinhian clade) under the Oceanian umbrella? What about East Asians proper? Do you see merit in the McColl paper's model, which posited that East Asians are ~75% Proto-Southeast Eurasian + ~25% Tianyuan-like?

    The Narasimhan paper on South and Central Asia doesn't assume a very close connection between East Asians and Onge, though. The model in that paper assumes the major Eastern Crown Eurasian branches are nearly equally divergent, though the East Asians are separated from the rest:
    "In our fitted admixture graph, AASI, Onge, and AncientPapuan (a hypothesized ancestral population to modern Papuans, prior to Denisovan admixture) are a clade with respect to Nicobarese, representing the East Eurasian ancestry that plausibly dispersed with the Austroasiatic language expansion, and indigenous Chinese groups. The split between AASI, Onge, AncientPapuan is modeled as nearly a trifurcation. It seems probable that the split between AASI and AncientPapuan occurred prior to modern humans reaching Sahul (the ancient continent uniting Australia and New Guinea). Radiocarbon dating shows this is unlikely to be much more recently than 47,000 years before present."

    It's noteworthy that Yana is modelled as ~22% Proto-East Asian by Sikora. I guess that means its eastern ancestry is indeed close to East Asians, as opposed to being the result of gene flow from a generalized ENA lineage undifferentiated from Australo-Melanesians and the like. Sikora estimates the Western-Eastern Crown Eurasian divergence to be ~43,000 years ago, but given the deep splits in ENA that Narasimhan assumes, wouldn't something closer to 50,000 be more realistic? Ust-Ishim is 45,000 years old, and I've noticed he vacillates between being considered closer to Western or Eastern Eurasians depending on the paper. I guess we'll need more Paleolithic DNA from East Asia and Oceania to work it all out.
    Since Broushaki 2016 there's been solid evidence for Onge-EastAsian being an ancient split, same for Oceanians and AASI. In that paper there was an attempt to model modern populations with ancient (+Han/SSA) haplotypes with no ANE or ancient American haplotype donor, and Oceanians, South Indians, Onge and Native Americans all preferred Ust-Ishim, suggeting that both ANE and old splits within the ENA branch were modelled with it. Now we have the top donors from a new haplotype model with both ANE and Native American samples included:

     


    Native Americans and Neo-Eskimos prefer Clovis instead of Ust-Ishim and Clovis also accounts for their ANE, Kolyma should do the same for Uralic and Yeniseian West Siberians. No modern population prefers Yana as a top donor, and South Asia, the Andamans and Oceania are still primarily Ust-Ishim as in the Broushaki paper which means it is proxying for Oceanian, Onge etc. This to me is a clear indicator that the EA/rest split within ENA must be close to Ust-Ishim/ENA split, closer than to Devil's Gate at least.

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    Re; the questions of different models for ENA and Tianyuan, note, the splits are really deep between the three structured present day ENA members, and East Asians in absolute terms share very little extra shared drift with Tianyuan relative to the Onge or AncientPapuan.

    Even in McColl's model, the shared drift with Onge is a very low number of units (3 units) after split of Onge Papuan.

    Fu's model came out with Tianyuan weakly on the East Asian branch (https://www.cell.com/current-biology...22(17)31195-8) and a separate Papuan branch.... *but* did so only via avoiding fitting Onge in the model, and stated Onge was hard for them to fit. They also state, "The best-fitting graphs for the Onge (Z = −3.4) always include them as a mixture of populations related to the Ami and Papuan". McColl seems to have come from another tree based on the relatedness of Tianyuan to Onge and "AncientPapuan", where East Asian is a mixture of a weakly Tianyuan related and weakly Onge related lineage. At the moment, McColl's graph is I think the only graph that's out there that fits Tianyuan, Onge, East Asians, Papuans and ancient Hoabinhian SE Asians.

    Re: Narasimhan's paper, I'm not sure that they would be able to tell between a trifurcation and connections between Onge and East Asian without Tianyuan as a reference, because the connection of Tianyuan to East Asian exclusive of Onge and Papuan and Onge to Papuan exclusive of Papuan are all pretty shallow. (Narasimhan's model is also seems possibly a bit deficient because McColl strongly suggests Onge related Hoabinhian ancestry in Nicobarese, which the model lacks).

    I expect East Asians probably are a combination of deeply splitting lineages related to Tianyuan and Onge, one or more of which probably split quite basal with ENA and contributed to populations back west, but I think we'll need more proximate samples to actually generate strong stats to drive the models.

    In terms of where East Asians formed, it seems like the deeper and more consistently to the present we Yana related ancestry, the less it's possible that East Asians could have formed in those regions, which is much of Siberia now(?), since it's very unlikely gene flow would only go one way if the populations were living in the same region. This paper fleshes that out more. We also find from McColl that the Hoahbinian ancient SE Asian population, to the exclusion of Onge, has a clear connection with Jomon*, suggesting Hoahbinian related ancestry was common along the whole mainland East Asian rim+mainland SEA, while there's a lack of specific such connection in most East Asians (weakly present in Ami I think?), which seems to limit the degree to which East Asians could form in the easternmost edge of East Asia.

    *Buuut, Jomon actually has no closer connection to Onge than East Asians do, which challenges the specific tree in the paper where Onge & Hoahbinian split off, then Hoahbinian contributes to Jomon along with a lineage that's a clade with East Asian (since in that model, total connection to Onge would go up). Seems like it has to be some ancient population that has no connection to Onge, or at least no more than what East Asians have, but contributed to Hoahbinian? More complexity to the picture of intra-ENA paraphyletic splits and recombinations.

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    Quote Originally Posted by Michalis Moriopoulos View Post
    Would you put AASI and ancient Southeast Eurasians (the Onge and Hoabinhian clade) under the Oceanian umbrella? What about East Asians proper? Do you see merit in the McColl paper's model, which posited that East Asians are ~75% Proto-Southeast Eurasian + ~25% Tianyuan-like?
    I'm not so sure. I don't have Onge, and I've been lazy and haven't looked into the ancient SEA samples yet.
    From D-stats others have run, this is what I'm seeing...
    1) Outgroup Papuan/Australian Onge East-Asian = 0
    2) Outgroup Onge Papuan/Australian(adjusting for excess Denisovan) East-Asian = 0
    3) Outgroup East-Asian Onge Papuan/Australian(adjusting for excess Denisovan) = 0
    4) Outgroup Tianyuan Onge East-Asian = +
    5) Outgroup Onge Tianyuan East-Asian = +
    6) Outgroup East-Asian Tianyuan Onge = 0
    7) Outgroup Papuan/Australian Tianyuan East-Asian = 0
    Assuming Tianyuan is Proto-East-Asian or somehow contributes largely to East-Asians to the exclusion of others...
    If Onge were Oceanian+East-Asian we should see... 1) - 2) could be 0 3) - 4+5) + 6) could be 0 7) 0
    If East-Asians were Tianyuan+Onge we should see... 1) 0 2) + 3) - 4+5) + 6) could be 0 7) 0
    Neither of those sets of conditions are met, so it can't be that simple.
    Last edited by Kale; 11-03-2018 at 04:08 PM.
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    Quote Originally Posted by Tsakhur View Post
    If ANS or Yana is closely related and ancestral to ANE with both being around 75% West Eurasian and 25% East Eurasian or more, does this means that Native Americans have around 28-30% ancient West Eurasian ancestry and might have very low levels of CHG-related admixture being that they are around 40% ANE?
    Yes, that's what it could mean. See mtDNA X2 -- found in Iran_N around 8,000 BC and many subsequent CHG-rich populations, and also a distinct branch in Kennewick Man and many modern Native Americans.

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    The AETA or Agta tribe of the PHILIPPINES are the only group that shows ydna Basal P* (28%), P1* and the very rare P2 found together along with significant levels of K2b1. The Timorese of Indonesia shows 10% of males have Y dna P*.
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