The phylogenetic trees falling on the tundra

A massive new ancient DNA preprint just dropped, The population history of northeastern Siberia since the Pleistocene:

…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.

The preprint is very interesting and thorough, and the supplements are well over 100 pages. I read the genetics and linguistics portions. They make for some deep reading, and I really regret making fun of Iosif Lazaridis’ fondness for acronyms now.

I will make some cursory and general observations. First, the authors got really high coverage (so high quality) genomes from the Yana RS site. Notice that they’re doing more data-intense analytic methods. Second, they did not find any population with the affinities to Australo-Melanesian that several research groups have found among some Amazonians. Likely they are hiding somewhere…but the ancient DNA sampling is getting pretty good. We’re missing something. Third, I am not sure what to think about the very rapid bifurcation of lineages we’re seeing around ~40,000 years ago.

The ANS population, ancestral by and large to ANE, seems to be about ~75% West Eurasian (without much Basal Eurasian) and ~25% East Eurasian. Or at least that’s one model. Did they then absorb other peoples? Or, was there an ancient population structure in the primal ur-human horde pushing out of the Near East? That is, are the “West Eurasians” and “East Eurasians” simply the descendants of original human tribes venturing out of Africa ~50,000 years ago? Also, rather than discrete West Eurasian and East Eurasian components, perhaps there was a genetic cline where the proto-ANS occupied a position closer to the former, as opposed to some later pulse admixture?

Without more ancient DNA we probably won’t be able to resolve the various alternative models.

10 thoughts on “The phylogenetic trees falling on the tundra

  1. Razib,

    You may recall my previous warning that the Onge-related Population Y did not represent a pre-Clovis migration wave. The “Australasian” affinity didn’t show up in a pre-Columbian Taino genome, either, which makes its pre-Contact existence even in Amazonia very doubtful.


  2. stuart,

    it shows up in 10kya brazilian higher fraction. soon to be published. might be artifactual, but it’s robust

  3. Hmm…I think I may have read the same recently submitted ms reporting MANY ancient South American genomes, but that one actually has a section entitled,”Failure to Detect Population Y Ancestry in Ancient South Americans” (although they still see it in modern Surui).

    On a related topic, do you know anyone who saw this poster at the ASHG meeting?:

    D.I. Cruz Dávalos 1,2; M. Allentoft 3; S. Reis 4; M. Bastos 4; J. Stenderup 3; C.S. Reyna Blanco 5; S. Neuenschwander 1,2; V. Moreno-Mayar 3; C. Rodrigues-Carvalho 4; E. Willerslev 3; M.C. Ávila Arcos 6; A.S. Malaspinas 1,2

    1) Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; 2) Swiss Institute of Bioinformatics, Lausanne, Switzerland; 3) Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark; 4) Setor de Antropologia Biológica, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.; 5) Department of Biology, University of Fribourg, Fribourg, Switzerland; 6) International Laboratory for Human Genome Research, National Autonomous University of Mexico, Juriquilla, Mexico

    When the Portuguese settlers arrived in Brazil, they named “Botocudos” the Central-Eastern inhabitants who wore wooden lip and ear plates. The Botocudos actually comprised several cultural groups speaking distinct languages. Most of the Botocudo groups became extinct by the end of the 19thcentury, when the Portuguese Crown declared war to all indigenous tribes that refused to accept the regime. The National Museum of Rio de Janeiro owns a collection of 35 Botocudo skulls. While analyzing the mitochondrial DNA of 14 of these samples, Gonçalves et al. identified two individuals with Polynesian haplogroups. The ancestry of those individuals was further explored at the nuclear level by Malaspinas et al., who determined that both samples had a Polynesian ancestry without signs of admixture from Native American or African populations. Several scenarios were put forward to explain those results including that these individuals arrived in the Americas as part of the Polynesian expansion, or as crew or passenger members in European ships. Here, we report preliminary genomic data from 21 individuals from the Botocudo collection. We perform population genetic analyses to characterize and identify the population structure of those samples. Finally, we specifically look into whether any of our samples had a genetic affinity to non-Native American populations.

  4. IMO, this confirms the ANE genetic signature originated in Siberia. It’s safe to say most modern non-African pops have Paleolithic Siberian ancestry. Before ancient DNA, Siberia was ignored as an important source.

    The Devil’s gate samples 7ky and Kolmya1 (AP-“Ancient Paleosiberians”) 9.6ky samples are interesting.

    Kolyma1-like people forms the basis of the ancestry of northeast Siberians & Native northern north Americans?????

  5. Beneath the scholarly exterior the paper is comically race-conscious. They were trying to determine whether 32000 years old teeth were Asian or European… as if the result one way or another would affect the “racial” assignment of the specimen.

    They were also comically obsessed with East-West Eurasian division as if it is something concretely set in stone. Lazaridis et. al. were pretty cautious, even apologetic when they coined the terminology as it was just a matter of convenience. They seriously considered to make only the Basal Eurasians true West Eurasians.

    Even according to the paper, the separation of “Europeans”(I suppose they meant the main branch of “West Eurasians”) and “East Asians”(I suppose they meant “East Eurasians”) occurred 43000 years ago. And then 39000 years ago, the Ancient North Siberians branched off from the “European” main branch.

    With just 4000 years of separation of these two branching off points, when the ANS later mixed with East Asians they probably did not think “Wow these East Asians look so different from us compared to our European “brothers””. For them the Basal Eurasians or BE-rich populations somewhere far west would have looked and felt far more alien.

    And if they somehow knew that their distant descent population (that they contributed only a tiny fraction to and who were heavily mixed with the aforementioned Basal Eurasians- ie Europeans) would be so butt-hurt – Europeans were not involved in peopling of the vast prime real estate of Siberia and Americas – that Europeans would claim them as their own, they would feel quite funny. Why? All this because ANS branched off from the West Eurasian side merely 4000 years later than from ENA.

  6. I have a question for Razib. This paper mentions the ~37% ANE mixture into Native Americans, but then says that a “ghost population related to [old] Yana (ANE)” contributed 18% of the ancestry to Ancient Beringians. What’s up with these numbers? Enlighten a rank amateur.

  7. I don’t think interpreting the split times literally makes a lot of sense. There wasn’t literally a separate Sardinian population that evolved in isolation, nor a East Asia (Han) population either. Probably inflates split time?

    I’m surprised by this paper, though there’s some basally East Eurasian ancestry edge into ANS quite early (that isn’t closely related to the streams ancestral to East Asians in particular over Onge and Papuan, which all branch quite deeply), the earliest Native American like sample is at 9.8 kya (7800 BCE). Although of course the in-situ data from North America suggests must have been in that region somewhat earlier than that (hence they estimate replacement at 20 and 11 kya / 18000 BCE to 9000 BCE; similar kind of time frames to the post-LGM turnover in Europe).

    Suggests that the movement into North America and North East Siberia may have been more part of a single impulse of expansion from northern East Asia and that the Beringian Standstill idea – where a proto-Native American population was forced to hang out in the tundra in Beringia for 15 ky – is perhaps not quite right.

    (Replacement looks perhaps a bit more thorough in those proto-NA than some previous estimates; 37% ASE in Clovis+Anzick, 25% in Kolyma_M.)

    Then the Neosiberians represent a whole other later Holocene wave between 11 – 4 kya (9000 BCE to 2000 BCE; Gobekli Tepe times up to the Iron Age).

    To me that raises some questions about how we think about long term adaptations (cultural and physiological). My impression is the usual story has been to think of “Neosiberians” as long term inhabitants of East Siberia, heavily physiologically adapted to the environment there over tens of thousands of years and with technology adapted for the environment from tens of thousands of years of experimentation. But this all may be more the result of relatively more recent adaptation than we thought (still over hundreds of generations), and introgression of adaptations from older groups there (analogous to the hypoxia response in Tibet; an introgression into a population base of Northern Han like farmers from an older AMH group who got it from a Denisovan population). It may even be that the specialized technology they have is much more an overflow from changes in societies going on to the south that *allowed* them to replace earlier peoples who were more physiologically adapted to the environment.

  8. Samuel Isaac Andrews wrote,

    “The Devil’s gate samples 7ky and Kolmya1 (AP-“Ancient Paleosiberians”) 9.6ky samples are interesting.

    Kolyma1-like people forms the basis of the ancestry of northeast Siberians & Native northern north Americans?????”

    The Mesolithic Kolyma1 specimen’s haplogroups are reported as mtDNA G1b and Y-DNA Q1a1a.

    In the present day, G1b is common among indigenous peoples of northeastern Siberia, but no member of any subclade of mtDNA haplogroup G has been found among native people of the Americas as far as I know. MtDNA haplogroup G appears to have very deep roots in East Asia.

    If the nomenclature that the authors of the present study have used is the same as that of ISOGG 2018, then Y-DNA haplogroup Q1a1a should refer to Q-M120. It appears that most extant members of Q-M120 should be Chinese, but a few members of this haplogroup have been found in various other places (Azerbaijan, Kalmykia, Mongolia, southern Vietnam, Korea, eastern Japan, Brunei, Peru, etc.). It is a subclade of Q1a1-F746/NWT01, which also includes the Y-DNA of a prehistoric specimen from Saqqaq, Greenland, many modern Inuit (at least among those in Alaska and western Canada), at least one modern Athabaskan in northwest Canada, and several modern Koryaks.

    All “Neolithic” (in a Jōmon- or Baikal Neolithic-like sense) specimens from Devil’s Gate Cave have been assigned to mtDNA haplogroup D4m (n=3) or mtDNA haplogroup D4 (n=3). MtDNA haplogroup D4m2, one subclade of D4m, may be found most commonly among Nivkhs. However, mtDNA haplogroups Y1a and G1b also appear to be common among present-day Nivkhs. The one male specimen from Devil’s Gate Cave has been assigned to Y-DNA haplogroup C2b (which would be C-L1373 according to ISOGG 2018), a clade that is very common not only among present-day Nivkh males, but also Tungus, Mongols, Kazakhs, Koryaks, etc.

    Curiously, the indigenous population that is now geographically the nearest to Devil’s Gate Cave, the Udegeys, exhibits an almost entirely different mtDNA pool that appears to be mostly descended from females from the Japanese Archipelago of the Jōmon period. However, it seems that most Udegey males do belong to the C-L1373 clade of Y-DNA. Most present-day Udegey males who do not belong to C-L1373 probably belong to Y-DNA clades that are typically found among Chinese, Koreans, or Russians.

  9. Kolyma1 (Table 4.2) has only 2/68 ISOGG 2018 mutations derived for Q-M120 level, and YF puts 1 of those at the Q-F746 level. So he is a very early split off pre-Q-M120, or maybe just Q-NWT01*.

    He had no archaeological context but his location (far northeast Sakha) and date (~10-9.5 ky old) would associate him with either the latest period of Dkyuktai or the earliest of Uolba or Sumnagin. The former might mean a direct cultural relationship to USR1 (Denali complex). I wonder if they could be modelled as the same source with different mixture (Amerindian in USR1).

  10. According to the paper, “East Asian” admixture into ANE occurred between 39000BP and 32000BP. So the maximum divergence has a ceiling of 11000 years, probably much less. One should say at the time they were rather closely related populations.

    They were clearly less divergent from each other than a pair of divergent WHG groups or divergent European populations of mere 5000 years ago. They may be less divergent than even a Tianyuan-like population and a southern ENA component which together are thought to have formed the ancestors of modern East Asians.

    Similarly, ANE and East Asian component of Native Americans would have been less divergent from each other due to the timing of their admixture than EEF and WHG though WHG component in EEF complicates the matter.

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