Son of Yamnaya.

In this 700+-comment thread, which seems to have become a dumping-ground for all DNA-related commentary, Dmitry Pruss said mildly but convincingly:

An ob gripe, I don’t think that it’s the best idea to discuss “everything DNA” in this, already oversize, thread…

So I’m hereby opening this as a continuation. If you have thoughts about genomic components and Denisovan signatures, this is the place for them!

Comments

  1. Trond Engen says

    I did recently link to a paper on Mongolia and the, eh, genetogenesis of the Xiongnu and the Mongolians in They Perished like Avars, where we have discussed much Post-Indo-European Steppe stuff. It didn’t attract any follow-up comments, so feel free to move it here.

  2. David Eddyshaw says

    Will we be seeing “Bride of Yamnaya” in due course?

  3. And possibly eventually Second Cousin Twice Removed of Yamnaya.

  4. Canonically, “Bride of Yamnaya” should have come first. Then “Son of Yamnaya”, then “Ghost of Yamnaya”, then “Yamnaya meets Dravidian”, then “House of Yamnaya”. The final(?) one should probably be a duo of comedians meet Yamnaya — I’d suggest “Nyland and Goropius”, but there is a surfeit of them to choose from.

    /Hammertime

  5. David Eddyshaw says

    Yamnaya in the KONGO. (Perhaps too controversial for these politically correct times …)

  6. Oh, the wind that blew through the whiskers on the flea in the hair on the tail of
    the dog of the daughter of the wife of the Dayak has just come to town….

  7. A new paper by Ioannidis et al., Native American gene flow into Polynesia predating Easter Island settlement is the most careful approach I have seen toward demonstrating early Polynesian-American contact using genetics. The paper finds an American genetic signature in Eastern Polynesian populations. What’s distinguishes this paper from earlier such studies is that it clearly separates the purported American signal from a European one; that it dates both plausibly; and that it clearly distinguishes different coastal American populations, and ties the source of the Polynesian signal specifically to a population in Colombia.

  8. Interesting!

  9. Trond Engen says

    Y: Ioannidis et al 2020

    We briefly discussed it here back in July. I still haven’t read the full text.

    Dmitry (in Mother of Yamnaya): (Huang et al 2020).

    I love it. This seems to take historical genetics to a whole new level, using the sheer power of numbers to shake out genetic commonalities that can be traced back to a common ancestor. The multi-ethno-linguistic matrixes are essentially the comparative method on genomes, but used to identify the oldest common elements rather than to reconstruct a complete ancestral genome.

  10. Trond Engen says

    A few seconds late to edit I meant to add a few random observations:

    They identify a “Northeast Asian Cluster”, which must be more or less identical with what Jeong et al dub ‘Ancient North Asians’ in the paper on the genetic history of Mongolia..

    They identify a gene flow from “European” into “Inland South Asian” (likely including the group speaking Proto-Sino-Tibetan) at ~5800 kA. I wonder where that came from.

    Note the predictive force. They posit a yet unsampled group in a specific location and with a specific genetic signature as the linguistic ancestors of Kra-Dai.

  11. Thanks, Trond. I somehow missed that discussion (and what followed it, which was very interesting, too.)

  12. Trond Engen says

    (This connects to several discussions. Most immediately me (July 29, 2020 at 7:25 am) in They perished like Avars:

    I got the Yu paper (thanks!) and just finishen reading it. Not much time to digest, but my takeout is that it’s a complementation to what we already knew about Eastern Siberia. On the ancient and basal level, it fills out the picture of the North Asian population that is ancestral to Non-Arctic Native Americans. Additionally it starts to untangle the movements and admixtures of the Late Neolithic and Early Bronze Age that eventually would lead to the formation of the ethnic and linguistic groups we know today. The plague is part of that. Intriguingly it’s found in two individuals without Steppe ancestry. They were from the same site, but one of them had migrated in his early childhood. The date and the strain of Yersinia pestis are practically identical to those of a Corded Ware individual from the Baltic. This fits well with the population crisis in Scandinavia before the arrival of the Bell Beakers.)

    A new Siberian archaeo-genetics paper from Dmitry on Facebook:

    Kılınç et al “Human population dynamics and Yersinia pestis in ancient northeast Asia” Sci. Adv. 2021; 7 : eabc4587.

    Their conclusions corroborate and expands on earlier studies:

    Conclusions
    Northeast Asia, particularly the Baikal adjacent area and the entire Russian Far East, presents a complex demographic picture with hitherto unknown genetic shifts since the post-LGM. The Trans-Baikal area displays few genetic turnovers with an extended period of genetic continuity over a period of c.6000 years. This unique demographical pattern throughout the Holocene stands in sharp contrast to the recurrent gene flow events of Cis-Baikal and Yakutia. We document that the human group that was represented by Khaiyrgas-1 must have dispersed to Yakutia after the LGM. This group was genetically distinct from the first inhabitants of the Siberia who settled the area before the LGM. The genetic legacy of this group is visible among human groups in the area ~6000 years later. Our data fit well with Belkachi groups as having key position in the ancestry of Paleo-Inuits who launched the second wave of gene flow into the Americas c.5000 years ago. We also document the presence of the most northeastern occurrence of ancient Y. pestis in the less populated Yakutia region and in the highly connected Cis-Baikal area. The bacterium may well have had consequences in shaping human population dynamics in both regions, visible in the reduction in the effective population size and the genetic diversity levels ~4400 years ago. Consistent with the finding of the same bacterium in the Lake Baikal region during the Bronze Age ([Yu et al 2020]), this finding suggests that a plague pandemic in this part of northeast Asia could be a hypothesis worth exploring with more data. Our results demonstrate a complex demography in northeast Asia from the Late Upper Paleolithic up until the Medieval era in which Siberian populations expanded interacting with each other and with populations from distant geographical areas.

    Apart from that, the paper is unusually hard to digest, but the supplementary text is more readable. I guess they had to edit it down to the available number of pages. Anyway…

    Expanding on Yu et al this study makes it very likely that there was a regional plague pandemic at around the year 2500 BCE. In my view the region could well turn out to be the entire continent, but there’s not enough data to tell yet. A few centuries later the bacterium is found at the Kolyma river in the farthest end of Yakutia. I’d think that to spread in a sparsely populated region like that, this early incarnation of the plague must have been both a slow killer and independent of rats.

    Something close to the source population of Paleo-Eskimos (and hence also of Na-Dene?) is found with the sampling of two 7th millennium BP individuals from the region of Yakutsk in Yakutia, associated with the Belkachi culture and its immediate predecessor, the Syalakh culture. This is in line with earlier hypotheses based on material culture. The two seem to be close to a mid-9th millennium BP individual from east of Lake Baikal, also in line with hypotheses from material culture. All three are said to show genetic affinity with modern Chukotko-Kamchatkans — as is Saqqaq.

    Two 5th millenium BP individuals from the Lena Basin and three 4th millenium BP individuals from the Kolyma River further northeast form a distinct group, apparently descended from Syalakh/Belkachi with additional admixture from southeast. An interesting outlier was left unmentioned in the main text but shown on the maps and diagrams, where it’s intriguingly grouped with the Yakutian individuals. This is a mid-5th millenium BP individual from south of Krasnoyarsk who seems to fit perfectly within the contemporary population in the Lena Basin. Is this the first Yeniseian? This individual also shows evidence of a recent genetic bottleneck, in line with the plague hypothesis.

    The Syalakh/Belkachi cultures are also thought to be ancestral to the Bronze Age Ymyyakhtakh culture that spread almost explosively along the Arctic coast in the late 2nd millennium BCE. The Kolyma individuals are late enough that they could be part of this movement, but I can’t find anything on their cultural affinity.

  13. Trond Engen says

    I’m on record suggesting a Dene-Yeniseian homeland (providing there is such a thing as Dene-Yeniseian) on the Arctic Coast. I’ll note that a mobile riverine culture on the Lena could easily spill over into the Yenisei Basin via the Angara or Tunguska rivers (or vice versa). It’s the distance from there to Alaska that disturbs me. The ancestors of the Paleo-Eskimos (and/or Na-Dene) would have migrated from the Lena Basin long before those of the Syalakh-Belkachi descendants found on the Kolyma River. For the Yeniseian branch to have been brought from the Lena to the Yenisei in the 5th millennium BP, we’d have to suppose that the stay-behind groups on the Lena were Pre-Proto-Yeniseian for a long time, even as new East Asian groups moved into the area and were integrated in its genetic profile. If so, also the movers north should be (Para-)Pre-Proto-Yeniseians. Maybe these coastal Leniseians were yukagrified from the west.

  14. It is a mainstream view in Russia that Yukaghir languages came into region with the Bronze Age Ymyyakhtakh culture in late 2nd millennium BC.

    From Baikal region, but their original homeland was further west, closer to Urals.

  15. Trond Engen says

    Since this is the Great Eurasian Plague thread, I’ll link to

    Julian Susat et al: A 5,000-year-old hunter-gatherer already plagued by Yersinia pestis Cell Reports, 2021

    Summary
    A 5,000-year-old Yersinia pestis genome (RV 2039) is reconstructed from a hunter-fisher-gatherer (5300–5050 cal BP) buried at Riņņukalns, Latvia. RV 2039 is the first in a series of ancient strains that evolved shortly after the split of Y. pestis from its antecessor Y. pseudotuberculosis ∼7,000 years ago. The genomic and phylogenetic characteristics of RV 2039 are consistent with the hypothesis that this very early Y. pestis form was most likely less transmissible and maybe even less virulent than later strains. Our data do not support the scenario of a prehistoric pneumonic plague pandemic, as suggested previously for the Neolithic decline. The geographical and temporal distribution of the few prehistoric Y. pestis cases reported so far is more in agreement with single zoonotic events.

    (Link from Dmitry, as usual)

    The oldest and most basal strain of Y, pestis yet has been discovered in a 5300-5050 cal. BP hunter-gatherer from northern Latvia. Needless to say, the last line of the summary is controversial. But since every instance of the plague is a zoonosis, the controverse is really about whether the plague is spreading as a pandemic among rodent parasites on human society. It’s when Y. pestis becomes pandemic (or endemic) among rodents, and the bacterium gains the ability to infect humans easily, that the zoonosis in humans becomes pandemic by extension.

    Here’s a thought-provoking paragraph from the discussion:

    Modern Y. pestis can be transmitted from animals (e.g., rodents) to humans (Demeure et al., 2019). It is possible that hunter-gatherers, who frequently killed rodents for food or personal decoration, contracted Y. pestis or its antecessor Y. pseudotuberculosis directly from animals. Interestingly, at the Riņņukalns site, beaver (Castor fiber) was the most frequently recorded species among the archaeozoological finds excavated by Sievers (Rütimeyer, 1877). Beavers are a common carrier of Y. pseudotuberculosis, which directly precedes our early Y. pestis strain (Gaydos et al., 2009). Despite this interesting observation, it remains unknown to what degree hunter-gatherers may have played a role in the zoonotic emergence, early evolution, or spread of Y. pestis.

    The question of how a rodent disease could trigger a human pandemic in a sparsely populated region of Eurasia is important, and I’m trying to get my head around it upthread. So maybe the authors are right and the first instances were isolated infections. Maybe, even, that the plague never was pandemic among hunter-gatherers. Still, I think hunter-gatherers with early Y. pestis are significant. As incrisingly deadly ad/or infectious strains of Yersinia spread among wild rodents, hunter-gatherers (beaver hunters?) could have adapted (by non-fatal exposure or genetic selection) before it infected the rats of the agriculturalists, and they would then be in a position to fill the void after the first plague.

  16. @Trond Engen: It seems to me that the terminology with early plague strains is bit tricky—being based, in part, on what appears to have been an erroneous assumption about how the modern plague strain developed (and thus where to place the dividing line between Yersinia pseudotuberculosis and Y. pestis). As I understand it, it is conventional to call all bacterial lineages with the pMT1 and pPCP1 plasmids Y. pestis. However, it is now known from very early genomes (and according to that Cell Reports paper, the Rinnukalns genetic data confirms this) that pMT1 was actually acquired without the gene for the key virulence factor ymt (Yersinia murine toxin). Only later was the gene for ymt, which makes it much easier for the bacteria to thrive inside the flea vectors, added to the plasmid—meaning that assimilation of the plasmid itself was not one of the primary enablers in the development pestis-level human infectivity. Nomenclature will presumably get even trickier if fossil genomes with only one of the pMT1 or pPCP1 plasmids are found (which has not, to my knowledge, been observed thus far).

  17. Trond Engen says

    @Brett: Thanks. I couldn’t have written that, but I agree.

  18. Dmitry Pruss on Facebook linked to these interesting papers:

    The origins and spread of domestic horses from the Western Eurasian steppes:

    Our results reject the commonly held association between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe ~3,000 BCE driving the spread of Indo-European languages. This contrasts with the situation in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BCE Sintashta culture.

    Dairying enabled Early Bronze Age Yamnaya steppe expansions:

    Our results point to a potential epicentre for horse domestication in the Pontic–Caspian steppe by the third millennium bc, and offer strong support for the notion that the novel exploitation of secondary animal products was a key driver of the expansions of Eurasian steppe pastoralists by the Early Bronze Age.

  19. horse domestication … the novel exploitation of secondary animal products

    Is transport an “animal product” ? Or is primarily horse dung meant ?

  20. Aren’t dairy products the reference there — meat being the only use considered primary?

  21. Yes, if one bothers to click through, one finds (bolding added):

    Here we draw on proteomic analysis of dental calculus from individuals from the western Eurasian steppe to demonstrate a major transition in dairying at the start of the Bronze Age. The rapid onset of ubiquitous dairying at a point in time when steppe populations are known to have begun dispersing offers critical insight into a key catalyst of steppe mobility. The identification of horse milk proteins also indicates horse domestication by the Early Bronze Age, which provides support for its role in steppe dispersals.

    Of course, the reference to “dairying” in the title might have been a clue.

  22. Adding a reference to “Horsing around” in the title would have been yet another welcome clue.

  23. Perhaps “dairying” was misread as “draying”, a nonce synonym for “drayage” . . .

  24. It”s the same paper jack morava linked to in another thread recently. I haven’t had time to read it, but I immediately like it. And I don’t know if it rejects the horse hypothesis as much as nuances and complements it.

  25. @Trond Engen,

    I started trying to take this seriously when I saw

    https://en.wikipedia.org/wiki/Trundholm_sun_chariot

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