Saturday, May 7, 2022

Population genomics of Stone Age Eurasia (Allentoft et al. 2022 preprint)


Over at bioRxiv at this LINK. It'll take me a few days to read this manuscript properly. Here's the abstract:

The transitions from foraging to farming and later to pastoralism in Stone Age Eurasia (c. 11-3 thousand years before present, BP) represent some of the most dramatic lifestyle changes in human evolution. We sequenced 317 genomes of primarily Mesolithic and Neolithic individuals from across Eurasia combined with radiocarbon dates, stable isotope data, and pollen records. Genome imputation and co-analysis with previously published shotgun sequencing data resulted in >1600 complete ancient genome sequences offering fine-grained resolution into the Stone Age populations. We observe that: 1) Hunter-gatherer groups were more genetically diverse than previously known, and deeply divergent between western and eastern Eurasia. 2) We identify hitherto genetically undescribed hunter-gatherers from the Middle Don region that contributed ancestry to the later Yamnaya steppe pastoralists; 3) The genetic impact of the Neolithic transition was highly distinct, east and west of a boundary zone extending from the Black Sea to the Baltic. Large-scale shifts in genetic ancestry occurred to the west of this "Great Divide", including an almost complete replacement of hunter-gatherers in Denmark, while no substantial ancestry shifts took place during the same period to the east. This difference is also reflected in genetic relatedness within the populations, decreasing substantially in the west but not in the east where it remained high until c. 4,000 BP; 4) The second major genetic transformation around 5,000 BP happened at a much faster pace with Steppe-related ancestry reaching most parts of Europe within 1,000-years. Local Neolithic farmers admixed with incoming pastoralists in eastern, western, and southern Europe whereas Scandinavia experienced another near-complete population replacement. Similar dramatic turnover-patterns are evident in western Siberia; 5) Extensive regional differences in the ancestry components involved in these early events remain visible to this day, even within countries. Neolithic farmer ancestry is highest in southern and eastern England while Steppe-related ancestry is highest in the Celtic populations of Scotland, Wales, and Cornwall (this research has been conducted using the UK Biobank resource); 6) Shifts in diet, lifestyle and environment introduced new selection pressures involving at least 21 genomic regions. Most such variants were not universally selected across populations but were only advantageous in particular ancestral backgrounds. Contrary to previous claims, we find that selection on the FADS regions, associated with fatty acid metabolism, began before the Neolithisation of Europe. Similarly, the lactase persistence allele started increasing in frequency before the expansion of Steppe-related groups into Europe and has continued to increase up to the present. Along the genetic cline separating Mesolithic hunter-gatherers from Neolithic farmers, we find significant correlations with trait associations related to skin disorders, diet and lifestyle and mental health status, suggesting marked phenotypic differences between these groups with very different lifestyles. This work provides new insights into major transformations in recent human evolution, elucidating the complex interplay between selection and admixture that shaped patterns of genetic variation in modern populations.

Allentoft et al., Population Genomics of Stone Age Eurasia, bioRxiv, posted May 06, 2022, doi: https://doi.org/10.1101/2022.05.04.490594

See also...

Understanding the Eneolithic steppe

247 comments:

  1. When will the samples be added to the G25 datasheet? I look forward to using these samples to model my ancestry using the models the researchers used in the paper. Thank you in advance.

    ReplyDelete
  2. I don't think the samples have been released yet because this is a preprint.

    ReplyDelete
  3. That's a massive paper, hopefully the samples will be available soon.

    I have a couple of questions.

    Why does EHG ancestry peak in Mongolia, and Anatolian in Africa? I can understand the latter part is due the authors not utilizing Natufian, but I cannot comprehend EHG maximizing in Mongolia, or Central Asia for that matter.

    The new CHG-rich Don samples have been hyped for a while now. Correct me if I'm wrong but don't they seem almost identical to the CHG-rich outlier found in Khvalynsk, or do the Don samples carry more WHG ancestry? And on a related note, why is there a seemingly complete absence of CHG-related mtDNA in the aforementioned samples?

    ReplyDelete
  4. I see. That's a shame to be honest but I guess we will get it when the researchers release the actual paper.

    ReplyDelete
  5. @KikuyuBulalba

    Why does EHG ancestry peak in Mongolia, and Anatolian in Africa?

    I haven't looked closely at this yet, but yes it's probably due to the methodology, because obviously these results don't make much sense.

    Correct me if I'm wrong but don't they seem almost identical to the CHG-rich outlier found in Khvalynsk, or do the Don samples carry more WHG ancestry?

    They're older, possibly almost 1,000 years older. And yep, they're more western shifted.

    And on a related note, why is there a seemingly complete absence of CHG-related mtDNA in the aforementioned samples?

    U4 is common in parts of the Caucasus.

    There's also U4 in some of the Khvalynsk samples which are heavy in CHG but belong to the non-CHG R1b.

    ReplyDelete
  6. There's some very cool stuff in this paper in regards to Germanic origins.

    Lots of I1 going back to the Corded Ware period. One R1a among them as well.

    There's also R1b-L51 in Borreby remains. Borreby people had brachy skulls like the Bell Beakers.

    ReplyDelete
  7. @Davidski

    The results are indeed very nonsensical. I'm surprised they even made it to the pre-print.

    The Western shift makes sense, given that the majority seem to have U5 mtDNA, with one sample having U2e and another two U4.
    But is U4 being common in the Caucasus has anything to do with the local forager ancestry? Parts of the Caucasus are very steppe-rich, which might explain the presence of U4 and other Steppe-related mtDNA in the region.
    Granted, the appearance of U4'9 in the new Dzudzuana-like sample is indeed fascinating, but it is a very isolated clade and there has been a disrupted continuity in LGM Caucasus.
    Far as modern Caucasus is concerned, there doesn't seem to a presence of very deep rooted U4 clades, which coincides with our currently available CHG samples harboring mtDNA that share a closer clade with Anatolians rather than European foragers.

    Which then makes me wonder if these "Steppe CHGs" were heavily admixed with ANE or EHG populations, more so than the current CHG samples from South Caucasus. You also have this new NEO163 sample with J1 Y-DNA and U5 mtDNA which might reinforce this theory and explain why U5 was also common in the other Don samples.

    ReplyDelete
  8. I don’t know about elsewhere, but in the UK, the consensus amongst archaeologists is that brachycephaly among Beakers is not generally congenital but acquired, most likely by cradleboarding or some sort of swaddling. A “saddle”, sometimes subtle and sometimes marked, is observed across the top of the skull. Often there is also a degree of asymmetry. (Both are marked in the “Ava” skeleton which was a very early generation.)
    Swaddling and cradleboarding , in various places to the historic period, has been done not only to make the baby a convenient “package” for people working outdoors, or to soothe and warm it, but with a conscious objective of making the child tall and straight. (It actually may add an inch or two.)
    There are early (for Britain) Beaker sites such as one at Cassington (and in the larger Thames area / south east of England) where most Beaker burials are dolichocephalic people. There are one or two grave sites in Scotland where people with pre-Beaker genetics or people who seem to be a first-generation mix have Beaker type graves — with and without brachycephaly. It seems to disappear in the UK, or rather, fade to a more modern frequency, a little before other elements of the Beaker “package”.

    ReplyDelete
  9. Among the IE groups, what caused the Brachy/Dolicho divide in your opinion?

    ReplyDelete
  10. And another thing, J2b is now found in a CHG sample that is contemporary to the J2a Kotias Klde. Not sure what this implies for L283 and its origin. But it does suggest that the relation between Iran_N and CHG is indeed very close, since the TMRCA of J2b is about 16k years(?), this date likely highlights the point of Iran_N-CHG divergence.

    ReplyDelete
  11. @Arvind Pandit

    Among the IE groups, what caused the Brachy/Dolicho divide in your opinion?

    Bell Beakers were often very brachy, and I think this was due to them mostly originating from a brachy population in the Lower Rhine region.

    There are still many Bell Beaker-like brachy individuals in Northwestern Europe, especially in northern Germany and nearby, but they're much less common there than during the Bell Beaker period or even the 19th century.

    The average head shape in populations can change within a few generations, but the causes of this haven't yet been investigated properly.

    ReplyDelete
  12. I see! It's interesting how the Indo Iranian branch is extremely dolichocephalic. What do you think is the cause for the extreme dolichocephalic nature of groups like Sintashta or Andronovo?

    ReplyDelete
  13. @KikuyuBulalba

    Granted, the appearance of U4'9 in the new Dzudzuana-like sample is indeed fascinating, but it is a very isolated clade and there has been a disrupted continuity in LGM Caucasus.

    I think we'll see more U4 in really old Caucasus samples.

    But it does suggest that the relation between Iran_N and CHG is indeed very close, since the TMRCA of J2b is about 16k years(?), this date likely highlights the point of Iran_N-CHG divergence.

    Or those Haji Firuz samples with J2b have recent ancestry from the Caucasus.

    ReplyDelete
  14. @Arvind Pandit

    I see! It's interesting how the Indo Iranian branch is extremely dolichocephalic. What do you think is the cause for the extreme dolichocephalic nature of groups like Sintashta or Andronovo?

    Their ancestors from the Corded Ware/Fatyanovo culture were extremely dolicho.

    ReplyDelete
  15. Interesting! I've been told I am dolichocephalic too and my family have a similar head shape to me. It's nice to see the continuity up to the present day.

    ReplyDelete
  16. @Davidski

    It is certainly a possibility, but as I've mentioned previously there's a lack of deep-rooted U4 clades in contemporary Caucasus, but you still see K3 and H13c.
    I wasn't talking about Iran_C, but about Iran_N. Tepe Abdul Hosein has J2b.

    ReplyDelete
  17. This paper is interesting and all but one must wonder where the hell was R2 gang hiding when all these interesting things happened? R2 is almost like the forgotten brother of the R lineage imo but I may be biased since my haplogroup is R2-M124.

    ReplyDelete
  18. So steppe recieved CHG like ancestry upto 35% twice. Once around 7300bce and later around 3000bce.

    Good luck convincing wise people this group had no impact on language.

    ReplyDelete
  19. @KikuyuBulalba

    I forgot about Abdul Hosein.

    It looks like there may have been continuous gene flow between CHG and Iran_N.

    ReplyDelete
    Replies
    1. Could that be said about Iran_N related of harappans?

      Delete
  20. @Assuwatama

    So steppe recieved CHG like ancestry upto 35% twice. Once around 7300bce and later around 3000bce.

    No, just once, and way too early to be relevant to any dispersals of Indo-European languages.

    The problem is that the relevant CHG-heavy steppe population hasn't yet been sampled.

    The authors are just working with what they have.

    ReplyDelete
    Replies
    1. Source: archaeogenetics

      From pre-print
      https://www.biorxiv.org/content/10.1101/2022.05.04.490594v2
      "Interestingly, two herein reported ~7,300-year-old imputed genomes from the Middle Don River region in the Pontic-Caspian steppe (Golubaya Krinitsa, NEO113 & NEO212) derive ~20-30% of their ancestry from a source cluster of hunter-gatherers from the Caucasus (Caucasus_13000BP_10000BP) (Fig. 3). Additional lower coverage (non imputed) genomes from the same site project in the same PCA space (Fig. 1D), shifted away from the European hunter-gatherer cline towards Iran and the Caucasus. Our results thus document genetic contact between populations from the Caucasus and the Steppe region as early as 7,300 years ago, providing documentation of continuous admixture prior to the advent of later nomadic Steppe cultures, in contrast to recent hypotheses, and also further to the west than previously reported.

      We demonstrate that this “steppe” ancestry (Steppe_5000BP_4300BP) can be modelled as a mixture of ~65% ancestry related to herein reported hunter-gatherer genomes from the Middle Don River region (MiddleDon_7500BP) and ~35% ancestry related to hunter-gatherers from Caucasus (Caucasus_13000BP_10000BP) (Extended Data Fig. 4). Thus, Middle Don hunter-gatherers, who already carry ancestry related to Caucasus hunter-gatherers (Fig. 2), serve as a hitherto unknown proximal source for the majority ancestry contribution into Yamnaya genomes."


      One correction , i said 7300bce but its 7300BP aka 5300bce.

      Delete
  21. @Davidski

    "It looks like there may have been continuous gene flow between CHG and Iran_N."

    I am a bit confused about this, because I remember in other blogposts you had highlighted the distinction between CHG and Iran_N.

    And is it not the case that CHG and Iran_N have (by and large) different uniparentals?

    Unless the direction was mostly CHG-> Iran_N

    ReplyDelete
  22. @Assuwatama

    People with much more CHG ancestry than Yamnaya were already living on the steppe at least ~4,300 BCE.

    You know, like those from Progress and Vonyuchka.

    So the CHG admixture came early and then there was mixing within the steppe.

    ReplyDelete
  23. @gamerz_J

    Populations can be in continuous contact with each other but still relatively distinct.

    It's also possible that CHG and Iran_N were part of a massive cline that existed since the Mesolithic all the way from the steppe to southern Iran.

    ReplyDelete
  24. I've left some comments on GNXP.com on this paper (https://www.gnxp.com/WordPress/2022/05/05/eurasia-the-stone-age-and-revenge-of-the-danes/#comments). If anyone has any thoughts based on what I've said there, will be happy to respond there or here.

    There are some particular parts of how the paper does PCA that I think are relevant to how people may have to think about using PCA for ancestry modelling in the future.

    ReplyDelete
  25. The CHG-related ancestry that is found in Sarazm and later Jeitun samples might indicate a flow, or it could also indicate an archaic yet undiverged proto-Iran_N/CHG type. It might also explain the Sarazm and Progress, Vonyuchka affinity.

    ReplyDelete
  26. @gamerz_J

    Iosif Lazaridis recently mentioned that CHG differs from Iran_N in having more European HG-related ancestry and thus both did not derive from the same population in what he called as the WHG-ANE continuum.

    This paper posits CHG as mostly derived from an Iran_N-related + Caucasus_UP and ANE ancestry (extended Figure 5).

    The amount of shared ancestry this paper suggests between them doesn't to me to speak of continuous contact between 2 distinct populations but more of shared ancestry.

    ReplyDelete
  27. I predicted Don hunter gatherers would have significant CHG ancestry two years ago.

    This was based on the fact already published Dnieper hunter gatherers had some CHG. Hunter gatherers further east inevitably would have more.

    ReplyDelete
  28. CHG in Don hunter gatherers, by itself, proves Proto Indo European originated in the European Steppe.

    The debate is over.

    ReplyDelete
  29. The Extended Figure 3 is a good reference for exactly which samples sit where: https://imgur.com/a/kiAgX7w

    ReplyDelete
  30. This study got lots of DNA from West Siberian hunter gatherers.

    Now that we have more samples from them, we can confidently say their Y DNA and mtDNA makes them distinct from East European hunter gatherers.

    They both mostly derived from ANE, but based on their mtDNA/YDNA we can say they didn't have significant common ancestry for 1,000s and 1,000 of years.

    ReplyDelete
  31. @Davidski,

    Btw, the I1 rich cemetery in Sweden, dating circa 1800 BC, shares specific mtDNA types with modern Finland. They look like the pre-Germanic Scandinavian ancestors of Finland.

    Maybe the Battle Axe culture in Finland was I1.

    ReplyDelete
  32. @Matt

    Could you expand a bit more on the PCA stuff? Their PCA does seem compressed plotting Europe too close to West Asia unlike previous academic ones (sort of WHG appearing to define variation a lot more) and on top of that you have their "weird" inferences about peaks of EHG/ANF/CHG ancestries using PCA.

    I wonder how much imputation affects PCA accuracy, or their results at large.

    ReplyDelete
  33. @Genos

    There's very old Germanic influence in Finland.

    ReplyDelete
  34. @gamerz_j, only the projected samples really should be compressed by the PCA inference... unless there is something vastly wrong with the imputation procedure that exaggerates differentiation for the ancient samples, but their tests would argue against that. Therefore the present-day West Eurasian samples shouldn't be compressed from their 'true' position but rather the ancients are decompressed and more reflect their 'true' position than in typical academic PCA. Though Davidski is more the PCA guru here... in any case it probably needs a look at and consideration of the impacts in a longer term.

    What inferences do you think are weird and driven by PCA?

    ReplyDelete
  35. 2 weeks ago DNA was taken from 2 skeletons from Rakhigarhi ( x_x again women). They are claiming it to be 3000bce old. Any idea how long it takes to get data from it?

    https://www.google.com/amp/s/www.tribuneindia.com/news/haryana/dna-samples-from-2-human-skeletons-found-in-burial-pits-at-harappan-era-rakhigarhi-sent-for-analysis-392985

    ReplyDelete
  36. @Matt

    So how does this reflect on the accuracy of G25? I am not really good with the technicalities here so trying to understand...

    "What inferences do you think are weird and driven by PCA?"

    Take a look at figure 5 for example, the inferred peaks of a variety of ancestries are quite nonsensical to me (for example EHG peaking in Mongolia and CHG peaking in Pakistan) or for that manner ANF being so high in East Africa.

    Additionally, in figure 1 I believe Southern Europe (unless they included Cypriots and Ashkenazi Jews in it) are inferred as being closer to the Levant than they really are, and if one was to interpret their PCA literally, one would be led to believe that Europeans are on a Steppe-> EEF cline without additional HG ancestry which does not seem to be the case.

    Furthermore, on the same figure, the sample labelled as "Europe post-Neolithic" (unless I am reading it wrong, which I might be) would give the impression that Europe as a whole has been shifted towards West Asia since then.

    ReplyDelete
    Replies
    1. CHG peaking in Pakistan
      More reasons for them to deride AASI rich Indians ;)

      BTW its IranN like ancestry that peaked in ancient samples from Pakistan ~75%.

      Modern samples have more AASI & steppe.

      Are they mixing IranN/CHG again? As far as i know Iranian HG ancestry is claimed to be related to IranN not CHG.

      Delete
  37. @Matt

    Forgot, to type this earlier, Haobinhians also seem shifted west on their PCA which to my knowledge should not be the case, which probably means that high drift in East Asians (and Native Americans) is impacting their PCA.

    ReplyDelete
  38. @gamerzj, I think the G25 may be generally still a little compressed ancients->moderns generally (even though Davidski improved massively on the academic state of the art in published papers) and also maybe ther a little more for some ancients->moderns compared to the ground truth (those ancients that are more distant to modern people)? I'm not totally sure though. It depends on the particularities of the imputation procedure vs smartpca's projection though. Maybe when they release their dataset others can have a look.

    Re; pecularities, well, first point would mention is that Fig 5 isn't actually driven by the PCA and they use a separate model to infer proportions there. But re; Mongolia and Pakistan, I think that's a limitation of the model; e.g. they have no free ANE component and they have no Iran_N component, so we get some EHG and CHG top up which actually represent ANE and Iran_N. The model is probably not well specified for populations far outside of Europe.

    Barrie, who did this analysis, explains how they did it - https://twitter.com/WilliamBarrie/status/1522903206568685570?cxt=HHwWhMCj7bmZuKIqAAAA. Basically PCA is only involved inasmuch as the used PCA on the huge UKBiobank dataset to get representative samples for countries across the world (rather than using academic references with differences in coverage etc); they went to UKBiobank, identified individuals born abroad, removed those that overlapped with British on PCA reference (e.g. representing British born overseas), and then removed outliers, then they used a Chromopainter based method I believe.

    Re; "Europeans are on a Steppe-> EEF cline without additional HG ancestry", where EEF is population like Globular Amphora, we do generally find that steppe_Emba->GAC works pretty well in qpAdm? I don't think there's a lot of shift in Fig 1D as well - it seems like most populations are overlaid by the 3000-1000 BCE samples, with some exception for the Balkan cline and Italy (where it is actually plausible there's been geneflow from West Asia since 1000 BEC?).

    ReplyDelete
  39. @gamerz_j, although don't get me wrong; having had a bit of a chance to understand the methodology for Fig5, I do think there is at least one potential problem with it (or with interpreting it):

    For Europeans, for the model under Fig 5, they lump a bunch of donors from Early Neolithic farmers (with little WHG ancestry) to Late Neolithic Farmers (with lots more WHG ancestry) under the donor label of "Farmer". This is probably partly responsible for a greater West->East European difference than shown by Anatolian vs WHG. Because Western Europeans seem to me more likely to get their WHG via sampled farmers as an intermediary (while this is less the case for Eastern European groups today, because of whatever happened with the HG rich population that is ancestral to Balto-Slavic groups).

    I also generally wonder about some of the more advanced Chromopainter methods they use to model ancestry for ancients.
    E.g. one thing I noticed was that when modelling lots of Bronze Age France samples in Supplementary Table 10, they end up with about 10% contribution to Bronze Age France of "LevantEuropeS_4700BP_1700BP" which represents largely a lot of later samples from Roman Italy. (Quite consistently over 12 samples). This cluster also shows up as contributing to a sample in Bronze Age Beaker Germany (RISE559). This rises to 18% in Iron Age France and 15% in Iron Age-Roman Britain (excluding 3DT26), before dropping to 5% in Saxon England. This seems a bit dubious in that the relationship is more likely the other way around, or reflects some shared ancestor (e.g. the donors didn't even exist in the Bronze Age?).
    So there are these issues with some of their admixture analysis where Chromopainter and IBD based methods are good at identifying clusters (albeit often throwing lots of hard to classify samples into a wastebin), but I still wonder if many of Davidski's longer standing criticism don't stand and there are some problems for reconstructing ancestry with them, that need to be sense checked against qpAdm and PCA. It seems like a big improvement in them, but yeah.

    ReplyDelete
  40. Interestingly, two herein reported ~7,300-year-old imputed genomes from the Middle Don River region in the Pontic-Caspian steppe (Golubaya Krinitsa, NEO113 & NEO212) derive ~20-30% of their ancestry from a source cluster of hunter-gatherers from the Caucasus (Caucasus_13000BP_10000BP) (Fig. 3). Additional lower coverage (non-imputed) genomes from the same site project in the same PCA space (Fig. 1D), shifted away from the European hunter-gatherer cline towards Iran and the Caucasus. Our results thus document genetic contact between populations from the Caucasus and the Steppe region as early as 7,300 years ago, providing documentation of continuous admixture prior to the advent of later nomadic Steppe cultures, in contrast to recent hypotheses, and also further to the west than previously reported.

    Was that the final nail in the coffin to delusions about PIE from Iran?

    Finally, we investigated the fine-scale genetic structure in southern Scandinavia after the introduction of Steppe-related ancestry using a temporal transect of 38 Late Neolithic and Early Bronze Age Danish and southern Swedish individuals. Although the overall population genomic signatures suggest genetic stability, patterns of pairwise IBD-sharing and Y-chromosome haplogroup distributions indicate at least three distinct ancestry phases during a ~1,000-year time span: i) An early stage between ~4,600 BP and 4,300 BP, where Scandinavians cluster with early CWC individuals from Eastern Europe, rich in Steppe-related ancestry and males with an R1a Y674 chromosomal haplotype (Extended Data Fig. 8A, ; ii) an intermediate stage until c. 3,800 BP, where they cluster with central and western Europeans dominated by males with distinct sub676 lineages of R1b-L51 (Extended Data Fig. 8C, D; Supplementary Note 3b) and includes Danish individuals from Borreby (NEO735, 737) and Madesø (NEO752) with distinct cranial features(Supplementary Note 6); and iii) a final stage from c. 3,800 BP onwards, where a distinct cluster of Scandinavian individuals dominated by males with I1 Y-haplogroups appears (Extended Data Fig. 680 8E). Using individuals associated with this cluster (Scandinavia_4000BP_3000BP) as sources in supervised ancestry modelling (see “postBA”, Extended Data Fig. 4), we find that it forms the predominant source for later Iron- and Viking Age Scandinavians, as well as ancient European 683 groups outside Scandinavia who have a documented Scandinavian or Germanic association (e.g., 684 Anglo-Saxons, Goths; Extended Data Fig. 4). Y-chromosome haplogroup I1 is one of the dominant haplogroups in present-day Scandinavians,s, and we document its earliest occurrence in a ~4,000- 686 year-old individual from Falköping in southern Sweden (NEO220). The rapid expansion of this haplogroup and associated genome-wide ancestry in the early Nordic Bronze Age indicates a considerable reproductive advantage of individuals associated with this cluster over the preceding groups across large parts of Scandinavia.

    A proto-Germanic cluster was identified. Now we know where the I1 haplogroup came from and why it spread so quickly.

    ReplyDelete
  41. I got an update from one of the author on Twitter that the samples should be publicly available in "a month or so".

    ReplyDelete
  42. You know who else was highly brachy? The ANE rich Tarim Basin Mummies. Hard to still deny ANE was the vector for brachy headshapes in Europe. All modern populations rich in ANE ancestry are brachy.

    ReplyDelete
  43. They are using new methods (757) in this study, very interesting.

    ReplyDelete
  44. @gamerz_J

    They used new method and tool called ChromoPainter. It seems to be picking up old and excess affinity.

    "To investigate the distribution of Stone Age and Early Bronze Age ancestry components in modern populations, we used ChromoPainter 100 758 to “paint” the chromosomes of individuals in the UK Biobank (https://www.ukbiobank.ac.uk) using a panel of 10 ancient donor populations (Supplementary Note 3h). Painting was done following the pipeline of Margaryan et al. 101 760 based on GLOBETROTTER 102 761 , and admixture proportions were estimated using Non-Negative Least squares."

    "Haplotypes in the modern genomes are assigned to the genetically closest ancient
    763 population as measured by meiosis events, which favours more recent matches in time. Therefore, ancestry proportions assigned to the oldest groups (e.g. WHG) should be interpreted as an excess of this ancestry, which cannot be explained by simply travelling through more recent ancient populations [RK: e.g. small % WHG in Yamnaya] up to present times...."

    ReplyDelete
  45. How genetically similar are European hunter gatherers and Neolithic farmers? Are they as distinguishable as two separate races?

    ReplyDelete
  46. Interesting paper, which clarifies some doubts. Regarding uniparental markers;

    1-NO R1b-L754>P297>M269>L51 in mesolithic Ukraine-EHGs and neolithic-chalcolithic Ukraine- Igren, Mamaj Gora, Volniensky, Vovnigi1, Vovnigi2, Dereivka-HapY-Q1b, I2a1b, I2a2a/1b1, IJ, I2a2, I2, I2a2a, I2a1b/1a2, R1b-V88, R1b-V2219, R1b-Z2105- In addition, the samples that we are aware of at Sredni Stog are Z2103

    2-NO R1b-L754>P297>M269>L51 in Siberia -Mergen6, Koshinskaya, Vengerovo2, Fofonovo, Itkul, Omskaya Stoyanka2, Ust'-Isha, Dolgoe Ozero, Protoka, Kostenkova, Isbushka-HapY-Q1b2, Q1b1, Q1a2, C2b, C2, K2b

    3-NO R1b-L754>P297>M269>L51 in middle DON- Golubaya Krinitsa- HapY-I2a1b/1a2, R1a-M417-

    4-NO R1b-L754>P297>M269>L51 in SGC Denmark until 2.300 BC- Before that only HapY-I2a1b1a1b, I2a1a2, R1a-It does not seem easy to continue to defend the origin of R1b-L51 in the SGC and the transformation of this culture in the BBC. The Dutch model has been buried for many years. The genetic variability of CWC has been demonstrated once again.

    5-Samples from Lyalovo, Volosovo have been published-7 men are R1b1a1-Given the influence of the Baltic cultures and the proximity of the sites, they will probably have the same subclades as the Baltic ones. Their autosomal composition is typical of mesolithic Russian HGs, according to Allentoft and colleagues, nothing to do with Ukrainian or Siberian HGs. Moreover, they did not contribute at all to the formation of the autosomal steppe profile in the Middle Don (which is basically Ukraine+ CHG+ a little Siberia). Neither Yamnaya nor CWC inherited R1b-P297>M269>L51 from Russian hunter-gatherers.

    6-Another 10 Russian Hgs are R1b and R1b1a/1, probably with the same subclades as those of Lalovo and Volosovo, also did not contribute at all to the genesis of Yamnaya-CWC (Allentoft et al).

    7-One sample from the Danish Neolithic (3,500 BC) belongs to the same subclade (R1b1a1) as the Russians, of course with no trace of steppe ancestry.

    The picture is devastating for the dogmatic Kurganists who continue to defend an origin of M269>L51 in Eastern Europe and for all those who believed Haak, Allentoft and their colleagues when in 2015 they linked the spread of IE to massive migrations of R1a and R1b lineages originating in the Yamnaya culture. They should start looking at the Balkans, Northern Russia or the Baltics.

    They still do not know the origin of the CWC, but miraculously R1b-L51 and R1a-M417 are no longer the only ones responsible for the spread of the Yamnaya signal in mainland Europe, now it seems that the GAC was essential in this process-Many years ago we said that the spread of an autosomal genetic component cannot be understood without mixing with other cultures through exogamy.

    ReplyDelete
  47. Greatings

    Data from the Tunisian IA paper is out

    https://www.ebi.ac.uk/ena/browser/view/PRJEB49419

    Is it suitable for G25?

    ReplyDelete
  48. I was hoping that this paper was big enough for you to break your self imposed boycott.

    ReplyDelete
  49. @Gaska

    Good analysis. I tried saying here awhile ago that U106 in Northern Europe is not from SGC and I got met with some delusional arguments but can't deny it now. U106 were metalworkers from Mid/Southern? Germany/Bohemia? with ties to Unetice. Italo-Celto-Germanic share a common ancestor there and the U106 who brought metal working technology to Scandinavia to start the Nordic Bronze age were probably the Æsir.

    ReplyDelete
  50. Everyone not biased by their own commitment to an unrealistic theory could see that CWC did not acquire EEF ancestry locally and it was there prior to the migration. There was no EEF in the Fatyanovo area or the Baltic to acquire, but nice to see researchers do analysis to thoroughly confirm it. The R1a rich CWC pops probably came from Usatovo and the R1b-L51 rich pops must have come from somewhere southwest of that which will explain their relatively higher EEF ancestry/Unetice like autosomal profile. L51 took a Danubian route into Europe at the same time as CWC proper but the general absence of any CWC material culture casts doubt on the connection to, as does the apperance of L51 in Neolithic contexts like Aesch25. In the past I elaborated here extensively on how the singular L51 man buried with a Neolithic axe has more in common with the CT material culture than CWC.

    ReplyDelete
  51. Except that the Borreby/proto-Bell Beaker population was native to Northern Europe.

    So Borreby/Bell Beaker L51, including P312 and U106, spread from Northern Europe.

    These people also had a lot of steppe ancestry, and there was no L51 in Northern Europe prior to the appearance of steppe ancestry there. So it went like this...

    L51 Steppe > Corded Ware/SGC > Bell Beakers

    ReplyDelete
  52. Hi! Could you remove this sample from the ancient spreadsheet? It has abnormal distances, there is definitely something wrong.

    Iberia_Southwest_CA:I11600,0.126344,0.165531,0.059208,-0.027455,0.089247,-0.022032,-0.0094,-0.002077,0.082014,0.12228,0.002436,0.023079,-0.048463,-0.032479,-0.020629,0.000398,0.02047,0.014442,0.003645,0.005127,0.02558,0.009274,-0.025882,-0.11098,0.027423

    Distance to: Iberia_Southwest_CA:I11600
    0.07915427 Iberia_North_CA:I1846
    0.08563321 Iberia_Northeast_CA:I4565
    0.08736311 Bell_Beaker_Iberia:I1970
    0.08740857 Iberia_North_MLN:I7602
    0.08777136 Bell_Beaker_Iberia:I0460
    0.08792154 FRA_N:I15032
    0.08822952 FRA_N:I15031

    Even when modeling it with other averages the distance is too high.

    Target: Iberia_Southwest_CA:I11600
    Distance: 8.1160% / 0.08116039 | R3P
    70.0 Iberia_Northeast_CA
    20.2 FRA_Alsace_EN_o
    9.8 ITA_Grotta_Continenza_Meso

    ReplyDelete
  53. @Romulus

    You have an annoying habit of making egregiously false comments on this article.

    Almost all of the early Tarim mummies have dolicoceohalic skulls.

    Source:

    https://www.google.com/books/edition/The_Cygnus_Key/cN0zDwAAQBAJ?hl=en&gbpv=1&dq=tarim+mummies.dolichocephalic&pg=PT305&printsec=frontcover


    Most populations with high ANE ancestry are dolicocephalic. The ones that aren't are brachycephalic because they have East Asian admixture. Remember that all high-ANE non-Europeans are predominantly East Asian.

    There is no doubt that ANE were extremely dolicocephalic, as we would expect predominantly West Eurasian steppe populations to be.

    ReplyDelete
    Replies
    1. This comment has been removed by the author.

      Delete
  54. @Genos Historia

    Three Scandinavian clusters were found.

    Scandinavia 4600-3800 BP (R1a cluster)
    This cluster has the most steppe and the least amount of WHG ancestry

    Scandinavia 4200-3200 BP (R1b cluster)
    This cluster has the most EEF ancestry and the second most WHG ancestry

    Scandinavia 4000-3000 BP (I1 cluster)
    This cluster has the most WHG ancestry and the second highest steppe ancestry

    The last two expanded at the expense of the first and pushed them north. The first cluster (R1a) is associated with Battle Axe and the Finnish Battle Axe culture was probably also predominantly R1a. Finnish I1 is mainly L258 which probably represents an early Iron Age expansion from Scandinavia. They likely brought the ancestry associated with the last cluster which was also found to have contributed to the Goths and Anglo-Saxons, into Finland, hence the Germanic ancestry in the Finnish population and the very old Germanic loanwords in the Finnish language.

    ReplyDelete
  55. Some Initial remarks re: paper

    - cool New Satsurblia genome (26,000 bp). J2b2 & mtDNA U4-9. Might have something do do with post-glacial Euro HGs (although would need phylogenetic resolution, e.g. relation to U4; could be shared ancestry rather than direct migration ?)

    - Mariupol horizon middle Don individuals - Budzhak-related I2a2 & CWC-related R1a (? sublcades). So we can jettison the need for the Lower Don culture, but i expect the some people's obsession with this group will linger

    - the Volosov-related R1b-M269 ? subclades

    - new, improved model for Germanic, glad to see Team took on my suggestions. Initial BAx , R1a-Z645 movement, then R1b-U106 related movement from mainland Europe (earliest find north-central Europe, although continued denials expected), then I1 founder effect (? source)

    ReplyDelete
  56. L51 Romania -> Up the Danube 3000-2900 BCE) -> L51 North of the Alps (Aesch 25 Switzerland, Bohemia, Germany).

    ReplyDelete
  57. @ Davidski


    Lots of I1 going back to the Corded Ware period.”

    More like none

    ReplyDelete
  58. @Romulus

    LOL

    Early Corded Ware was like Yamnaya, with both R1a-M417 and R1b-L51, including U106.

    It then gained more EEF in Central Europe from Globular Amphora.

    Fatyanovo had a lot of EEF, because it's a Corded Ware population that moved east from somewhere near Poland.

    But thanks for the comedy relief.

    ReplyDelete
  59. @Rob

    These are pretty early. So I1 was there even earlier than that.

    NEO220 I1 2036 BC

    NEO223 I1 2018 BC

    ReplyDelete
  60. @EL

    R1a is still there at Falköping in 1748 BC.

    You should learn what founder effects are. Your hypotheses will gain from that.

    ReplyDelete
  61. Some interesting posts from the authors on twitter

    https://twitter.com/EvanIrvingPease/status/1522302847026614272

    https://twitter.com/WilliamBarrie/status/1522903203695579136

    ReplyDelete
  62. @Matt

    Thanks for the elaboration, btw much appreciated!

    "they have no free ANE component and they have no Iran_N component, so we get some EHG and CHG top up which actually represent ANE and Iran_N. The model is probably not well specified for populations far outside of Europe."

    I think if one models East Asians for example using qpAdm, smartPCA or any other method but Chromopainter and utilizing already available genomes from across East Asia, say 10kya as a baseline, one would not find nor excess Anatolian_N nor CHG or any other component they show beyond Mongolia (imo).

    If you look at their IBD analysis in the supplementary Neolithic and BA samples from South East Asia do not show sharing with western pops, and while traces may have trickled in since then I find most of it to be spurious.

    Reason I mention East Asia, is because it's a bit of a more obvious example, with Pakistan and CHG affinity things may be more complicated.

    PS: In regards to G25, on admixture/components (not the PCA mode) mode I've found that it generally does give similar results to qpAdm depending on the model etc, though it sometimes adds extra population than qpAdm does. (But then again you can only run so many with qpAdm).

    @MaxT

    I've seen quite a few results based on GLOBETROTTER it's not that new, been around for at least 8 years or so. But they did publish an updated version of it recently I had linked the paper here I think.

    ReplyDelete
  63. @Davidski

    I was looking at the admixture charts in the paper’s PDF, specifically the ones above “Fig 2. Genetic structure of European hunter-gatherers.” The Russia_Neolithic_MiddleDon EHGs (NEO212 and NEO113) display a blue component related to MA1, but there are four other samples that have it maximized too: NEO72 and NEO73 (Siberia_Neolithic_Koshinskaya); NEO922 (Siberia_Neolithic); NEO75 and NEO78 (Siberia_Neolithic_Sredneirtyshskaya). The Iberia_Mesolithic sample NEO694, also has a very small blue component (a minor ANE signal via Villabruna-like populations?). Do the aforementioned Siberia_Neolithic samples represent pure ANE-like WSHGs, before they received East Asian admixture? On their PCA, one of these Siberian HGs plots west of MA1—and by proxy, Afontova Gora.

    ReplyDelete
  64. I think Kotias klde-NEO283 (23.685 BC) is a female (XX)-mtDNA U4'9 (sample J2b is 7.773 BC)-In any case it is interesting to know the origin of U4, very abundant in all European HGs.

    The subclades of R1b-Volosovo are the same as the Baltic and Scandinavian ones, M269 could not be confirmed, nothing new.

    L51 and U106 for the moment have their origin in Bohemia, not in the steppes. Given the NON-existence of this lineage in Ukraine and the Volga-Don, it would be a miracle if it appeared in that region before 3000 BC.

    Brachycephaly is a matter of the great mountains of mainland Europe (Alps and Pyrenees) where sporadic cases appear even in the Neolithic. Nothing to do with Yamnaya or the steppes. Its appearance in Dinarmarca (Borreby) is a matter of the arrival of P310 from Germany thanks to the influence of BB culture (metallurgy) - therefore nothing to do with CWC which like Yamnaya was overwhelmingly dolichocephalic.

    ReplyDelete
  65. @ Dave

    “ These are pretty early. So I1 was there even earlier than that.
    NEO220 I1 2036 BC
    NEO223 I1 2018 BC”


    I did note those, but they are not ‘within the corded ware period”. Within the context of central, northern & Western Europe , they are even post-Beaker . This is Nordic Bronze Age period
    I get that most people think they’re local TRBs, but I’d point out that Swedish TRB was I2a1b.
    Would be interesting to get TRB Zealand samples, but I’d look to NW Europe (noting the I1 in Neolithic France; but also Stora Forvar. I’d preference the former zone).

    Does seem like quite a bit going on between late TRB and the Bronze Age in Northern Europe; not simply a case of a blanket CWC arrival

    ReplyDelete
  66. @Davidski said @Romulus
    Fatyanovo had a lot of EEF, because it's a Corded Ware population that moved east from somewhere near Poland.

    Not. Fragment of the admixture graphic, showing the relationship of Fatyanovo with representatives of the CWC of Balts, Poland and Central Europe (no/little EHG)
    http://www.tropie.tarnow.opoka.org.pl/images/fatjanowo-cutlure-baltic-polish-central.cwc.jpg

    ReplyDelete
  67. @Davidski
    Would it be possible to get coordinates for these Japanese genomes:
    https://www.mediafire.com/file/nurxnwqpi31fc1d/Cooke_2021.zip/file

    ReplyDelete
  68. There are apparently new samples from Bolshoy Oleny Ostrov and other Uralic related regions. I wonder what ancestry they will have.
    Would they have picked up some post-Fatyanovo ancestry or is there some other population that replaced them?

    ReplyDelete
  69. The region that R-L51 comes from is still elusive. However there still has not been a single specimen that belongs to R-L51, or a phylogenetic equivalent or a downstream subclade, that does not have Steppe autosomal DNA. SHT001/I6222 (3015 BC) from Afanasievo is R-L52+,P310+,P311+ is still the oldest R-L51 specimen yet found and has Steppe autosomal DNA but it isn't that much older than OBR003 (2893 BC) from Bohemia_CW_Early is R-L151,xU106, xP312 which also has Steppe autosomal DNA.

    The first phylogenetic equivalent to R-L51 is from at least 4100 BC. R-L51 and R-Z2103 descend from R-L23 which is about 300 years older.

    So the specific region that R-L51 comes from can be anywhere between Bohemia and Mongolia but there is still no question that all R-L51 and all R-Z2103 have Steppe autosomal DNA and they descend from the same ancestor in the direct paternal line in a R-L23 male about 6400 years ago.

    This study does show that the samples in IBD cluster RussiaNW_11000BP_8000BP and RussiaNW_7000BP_5000BP that are R1b1a1 are not an autosomal source for Middle Don which in turn is a source of Yamnaya and CWC.

    It will be interesting to see where the population that had R-L23 that contributed to R-L51 Steppe lived since Steppe is calculated to be from about 5000 BP. (Steppe_5000BP_4300BP). Again, all R-L51 and all R-Z2103 have Steppe autosomal DNA they descend from common autosomal ancestors as well as R-L23. It will be interesting to see that happened once there are enough samples.

    ReplyDelete
  70. @StP

    Fatyanovo has a lot of EEF admix, more on average than even German Corded Ware.

    EEF not EHG.

    https://eurogenes.blogspot.com/2021/01/the-great-shift.html

    Romulus seems to think that Corded Ware/Fatyanovo are derived from Volosovo, but he's retarded, so...

    ReplyDelete
  71. IMO the different autosomal ancestries are not conclusive proof of the origin of a uniparental marker, it is simply a clue that we have to take into consideration. In the case of R1b-M269 >L51>L23>Z2103/U106/P312 etc, all ancient samples analyzed in Europe after 3000 BC NOT ONLY have steppe ancestry, all of them also have ancestry from WHG and Anatolian farmers in different percentages. Is that proof of an origin in Anatolia or in any southern European refugia? Of course not, the only definitive test to determine the origin of a uniparental marker is to find the oldest case of that lineage. And obviously in the case of R1b-L754 it is Italy, Rb1-P297-Baltic, R1b-V88-Balkans, R1b-M269-Bulgaria and so on. Regarding the Mongolian sample we have already talked many times, it is not worth repeating my opinion about it.

    ReplyDelete
  72. Welcome back Davidski! this study made me intrigued about the question of the Scandinavian peoples. Denmark practically had western hunter-gatherers while Norway and Sweden had the presence of western and eastern hunters. Could this somehow have influenced the phenotype of the countries? I always thought Sweden was blonder and blue-eyed than Denmark and Norway.

    ReplyDelete
  73. @Xdzyn

    Hunter-gatherer ancestry profiles don't correlate with pigmentation differences in Northern European populations.

    Recent selection and recent migrations pretty much explain all the differences.

    So Swedes are probably lighter than Norwegians due to stronger selection, as well as possibly more Finnish ancestry and/or less Western European ancestry.

    ReplyDelete
  74. @Davidski,Denmark and Norway also have more British Isles DNA than Sweden. I'm curious to know if already in the Iron Age the populations of the 3 countries were different from each other. Today Scandinavian countries have different proportions of Y-DNA and mtDNA.We need Iron Age DNA samples, of course from bodies that weren't cremated!

    ReplyDelete
  75. @All

    I'm having a hard time navigating through the results in this preprint.

    Can anyone point me to a basic autosomal snapshot of the Vasilyevskiy kordon 17 samples?

    ReplyDelete
  76. @Norfern-Ostrobothnian

    https://drive.google.com/file/d/1b2RMwCffW_f3QCv1YVrVMTAa59NI3CxU/view?usp=sharing

    ReplyDelete
  77. @Davidski

    This paper appears to be split into four different parts: the PDF, supplementary information 1 and 2, and the supplementary tables—the last three are all located under “supplementary material.” In the supplementary tables, IBD charts can be located (tables 8-14), and the Vasilyevskiy kordon 17 samples are listed in that file as the following: NEO160, NEO162, NEO163, NEO164, NEO166, NEO167, NEO168, NEO170, and NEO171. In the PDF, page 9 displays some admixture figures; Vasilyevskiy kordon 17 samples are labeled/included under the “Russian_Neolithic” group of targets and admixture bars. Here’s figure 2’s description on page 9:

    “Fig 2. Genetic structure of European hunter-gatherers (A) Ancestry proportions in 113 imputed ancient genomes representing European hunter-gatherer contexts (right) estimated from supervised non-negative least squares analysis using deep Eurasian source groups (left). Individuals from target groups are grouped by genetic clusters. (B)-(D) Moon charts showing spatial distribution of ancestry proportions in European hunter-gatherers deriving from three deep Eurasian source groups; Italy_15000BP_9000BP; Ukraine_10000BP_4000BP; RussiaNW_11000BP_8000BP (source origins shown with coloured symbol). Estimated ancestry proportions are indicated by both size and amount of fill of moon symbols.“

    ReplyDelete
  78. @Davidski, these sort of results are actually hard to find in this paper. The results from their IBD modelling in Table IX provide the closest thing to deep autosomal modelling (what would be closest to a qpAdm deep analysis), but the samples there are provided only by sample ID and the IBD cluster they identify them to be part of, not their population grouping. So you have to cross match between the tables where they give archaeological context to work it out.

    Here's a specific excerpt for those 9 samples (albeit only the ones with good enough cover to get into their IBD analysis, so 7): https://imgur.com/a/kjWDYft

    It is a bit of a mess of a paper in a way. Shai Carmi is right that it should have been broken down. There's a good paper on "Stone Age Genomics" here, but also a lot of interesting stuff relating to IBD clusters and of contribution to each, through history, and its all a bit too much for people to give scrutiny to.

    Particularly there's some interesting stuff with the changes in contribution to BA and post-BA samples in Europe as well over time, but it's completely obscure actually when and where some of these samples in each cluster are actually from unless you're matching between tables. (And anyway questionable if this stuff belongs in this paper).

    ReplyDelete
  79. Thanks guys.

    If anyone can actually figure this out, where do the Neolithic Middle Don samples cluster in the West Eurasian PCA?

    ReplyDelete
  80. I believe they're the samples that are just above the steppe cluster based on Fig 1 and Fig 3 where they're the pink squares: https://imgur.com/a/kiAgX7w and https://imgur.com/a/gQaiXic

    The samples are only really labelled according to cluster (not even material culture!) in the PCA on Fig 3, and that only contains the highest coverage ones that I believe were used in the PCA inference stage. Whereas Fig 1 also contains the samples that were projected. Between them, I think that the Middle Don HG are basically this cline that leads from above where the steppe cluster is back to an intersection with the NW Russia HG.

    ....

    On the topic of IBD again; for example, here's another thing that's interesting in the IBD tables but kind of hidden by the labels.

    Under the models in Table IX, Globular Amphora from Poland and Funnelbeaker from Denamrk are combined under this label "FarmerEuropeE_late", to some extent broken down into a finer IBD cluster.

    But looking at the actual population labels, among all the samples they hold from the Neolithic from Europe with EEF component > 60% (e.g EEF), the Globular Amphora samples from Poland are quite distinguished from the others, because they have a small contribution from the Middle Don HG, about 8%: https://imgur.com/a/j14qnmf

    Which is *quite interesting* if the results are accurate. (I am not sure about this though; for one they suggest much higher contribution of WHG into Denmark samples compared to late Iberians. I'm not sure that this is consistent with qpAdm...)

    ReplyDelete
  81. @Davidski

    The PCAs appear to be located on page 36 of the PDF. The MiddleDon_7500BP samples cluster between the rest of the EHGs (RussiaNW_11000BP_8000BP, RussiaNW_7000BP_5000BP, and DonRiver 5800BP-5300BP), and Steppe_5000BP_4300BP, which seems to signify a gradual increase in CHG-like ancestry. There are a couple of RussiaNW_7000BP_5000BP HGs, and DonRiver 5800BP-5300BP HGs which drift towards the 5000-4300 BP steppe cluster (outliers perhaps?), which—to me anyway—indicates a gradual increase in CHG, just like the Middle Don samples from 7500BP. Interestingly, the Eurasian PCA shows a WSHG-related sample that’s west of MA1. Unfortunately, they didn’t utilize Afontova Gora, only Mal’ta and Yana_31000BP.

    ReplyDelete
  82. I've made a simulated coordinate by substracting trypilia ancestry from the Yamnaya average and then I made two others by substracting 50% Vonyuchka and Progress from that simulated coordinate.

    With progress substracted you get 30% CHG, with Vonyuchka 24%. I'll work out some stuff and report on my blog.

    Very similar to what I suspected what happened more than a year ago tbh:
    https://eurogenes.blogspot.com/2021/03/against-conventional-wisdom.html?m=1

    Also @Davidski I guess most of the previews of ancient samples you gave me back then such as the Don samples or iron age volga samples are from this study. So the next time you say "coming soon" I'll put it in my 2023 calendar!

    Awesome that you are back by the way, the return of the King!

    ReplyDelete
    Replies
    1. Can you please share the simulated coordiantes here? Thank you in advance.

      Delete
  83. I'll try to break up this thing into several blog entries targeting key points.

    But it'd be a lot easier if they just released the data publicly so that I could stick the samples into the G25.

    ReplyDelete
  84. @Davidski

    „where do the Neolithic Middle Don samples cluster in the West Eurasian PCA?”

    I can see interesting possibilities for Poland on this PCA:

    https://postimg.cc/JH3vnksm

    ReplyDelete
  85. In case anyone is interested in Iberia, the latest papers by Villaba, Patterson and Allentoft have given us a large number of genomes from the Mesolithic to the Iron Age. Surprising that from 6.000 BC there are Iberian HGs with good percentages of Ukrainian HGs blood ???- It is noteworthy, that it has been demonstrated again the genetic continuity between the BB culture and the historical peoples of the Iron Age-El Argar (2.200-1500 BC) is identical in uniparental markers (Df27) and autosomal composition to the Edetanos, Ilerkavones, Indiketes and Layetanos (Mediterranean Iberians)-In addition, it has been possible to demonstrate the genetic continuity between the Chalcolithic peoples of the Cantabrian mountain range (Asturias and Cantabria) with their Astures and Cantabrian descendants (also DF27) subdued by Augustus in 29 BC-Basque-Iberianists are still celebrating because the linguistic implications are important (few Spanish linguists doubt the linguistic continuity between the BBC and the Iron Age Iberians). Moreover, the results in Etruria (72% R1b, including 35% U152, two cases of Df27 and NO Z2103) show that also the Etruscans were R1b-P312 and spoke a NON-Indo-European language. The Etruscans were not Levantine, not Africans or Greco-Anatolians (except for three or four outliers) but a western people genetically very similar to the Iberians, northern Italians and Spaniards. The linguistic debate is going to be exciting because someone has told me that there are advanced studies on the Iron Age-Iberia especially focused on Celtiberians and people of doubtful linguistic affiliation (Vettones, Vacceans and Carpetans). The leaks speak of many surprises for Harvard, so if we are patient we will have interesting things to discuss.

    Regarding the CWC, I thought the R1a guys would be celebrating the results because they already have R1a-M417 in the Middle Don along with CHG ancestry. Just a little EEF blood and they have the Yamnaya-CWC mystery solved. Despite being siblings, the lives of R1a and R1b are parallel and have rarely crossed in the prehistory of Europe (Bohemia is an anecdote and also L51 is much earlier in Bohemian deposits than R1a and the rest of the steppe lineages (Q and Z2103)-

    I do not forget the Ukrainians, we pray for them every day. Forza Ucrania

    ReplyDelete
  86. All DF27 descend from a single P312 person. All P312 people descend from a single R-L151 person. All R-L151 people descend from a single R-L52 person. All R-L52 people descend from a single R-L23 person. None of those have been found in western Europe without Steppe autosomal DNA. These are the data points that matter. Not the language or what was found once these markers made their way to western Europe.

    ReplyDelete
  87. NEO310 from 4600bce from south turkmenistan is the oldest sample from SC asia yet. It is Y-HG L1a. Paper says.


    "The Neolithic individual from Turkmenistan (~6,500 BP) clusters close to Neolithic Iranians."

    If indeed this sample is without AnatoliaN unlike later samples from the region, then we likely have the first sample with the IndiaN sort of ancestry which split from the ancestors of IranN > 12ky ago.

    ReplyDelete
  88. This Turkmenistan ancestry will fit as the source for the later 35% ancestry into steppe :).

    ReplyDelete
  89. Twenty Late Neolithic pre-Corded Ware Bohemian males from a handful of different sites from Papac et al (2021) and not a single sign of R-L51 nor steppe ancestry:

    I2a1 - Sample: I7197
    G2a2a1 - Sample: I4893
    I2a1b1a - Sample: NER001
    I2a1b1b1a - Sample: I7187
    I - Sample: BRZ001
    I2a1a2a - Sample: I14167
    I2a1a2 - Sample: I14170
    R1b - V88 - Sample: I14169
    C1a2 - Sample: I14174
    T1a1 - Sample: KOB003
    H2 - Sample: I6677
    I2a1 - Sample: VLI006
    T1a1 - Sample: KOB007
    R1b - V88 - Sample: I14176
    G2a2a1a - Sample: I7192
    R1b - V88 - Sample: I14173
    I2a2a2 - Sample: I7272
    H2a1 - Sample: TUC003
    H2a1 - Sample: TUC004
    G2a2 - Sample: TUC005

    Those Western-European-homer types that heavily touted R-L51's origin in Iberia and, when that didn't work out, pushed it further east to France then Germany, and are now attempting to push it to Bohemia, when we already have proof it wasn't there. Not sure who they are trying to convince, besides other feeble-minded homers. Fortunately the rest of us that have even the most basic non-biased deductive reasoning skills are still here and calling bullshit on their nonsense.

    ReplyDelete
  90. Plot all the L51+ samples 3000 BCE - 2800 BCE. 0 in Northern Europe, all around the Alps and end of the Danube. They don't call you Alpine Race for nothing!

    ReplyDelete

  91. @Dospaises

    Single person L51 actually has its origin in Bohemia (3.000 BC), P312 single person has its origin in Germany (2.500 BC), U106 (Bohemia (2.900 BC), U152 Germany-2.500 BC, L21 (England (2.400 BC), DF27 Occitania (2.350 BC)-The steppes? Don't make me laugh, you have long since believed the fairy tale you have been told. Steppe ancestry? I can also make programs and models that demonstrate genetic compositions that favor my interests.

    ReplyDelete
  92. Even the SGC samples are obviously from the South and not the East because they are more Unetice like autosomally than Baltic CWC or Battle Axe

    ReplyDelete
  93. Dear friend Rocca, long time no hear from you, I see you are still as rude and disrespectful as before the pandemic. Remember that, if someone thinks differently than you, you should not insult, nor lie and of course you should not ban that person, you should simply show convincing arguments. And that is precisely what you lack. Besides, you do not have enough intelligence to understand that you will be making a fool of yourself for many years to come. I suppose that it will be profitable for you to adopt the position of guardian of the Kurganist orthodoxy, but remember that you are not only insulting me but also prestigious western scientists (archaeologists, geneticists, linguists and anthropologists) who do not agree with the Harvardian theory that you are defending.

    Having said that, I have to remind you once again that you should not act like a weasel and put in my mouth words that I have never said. I have always defended the same as now, that is to say a western origin of P312 (probably in the French-Cantabrian region-Pyrenees, Occitania, Aquitaine), an Iberian origin of Df27, the non-existence of L51 in Yamnaya, the existence of BB migrations linked to the Iberian BB culture, the genetic continuity in Iberia since the Chalcolithic, etc. I have been right in all the predictions, maybe that's why you have banned me in anthrogenica-When you have no arguments you have to silence the enemy at any cost.

    7 years ago the Kurganists were looking for routes for the arrival of the Yamnaya culture to mainland Europe and its transformation into the BBs of the eastern domain. Last year Papac and colleagues had no choice but to liquidate the Yamnaya culture as the origin of the R1b-L51 marker. Ha Ha Ha, I was right. I know it is painful for you to recognize it, but I have to remind you that educated gentlemen recognize their mistakes and congratulate their opponents. You have too much arrogance and not enough humility to recognize your mistakes. The Bohemian L51's do not belong to the CWC and you know it. They are too old and come from archaeological contexts typical of Czech neolithic cultures. Besides, their autosomic signal related to the Baltic, places them to the north, not to the east of Bohemia. The longer you take to recognize this, the harder the fall will be

    Regarding the Western European Neolithic, I already have a list of 9 samples (5,000-3,000 BC) that undoubtedly belong to R1b-L754>M269, so tell your fairy tale to whoever wants to believe you. I'm sure you know them, but I guess you're not educated enough to debate it calmly.

    ReplyDelete
  94. @ vasistha
    Nice. But isn’t Y-hg L1 found in one of the Majkop & AreniC samples ? Seems that CHG in steppe correlates with J1 instead
    I’d place origin of L1 in Mesopotamia

    ReplyDelete
  95. R1a-M417, R1b-M269/L51, and Q1b-FT380500 were all contemporaneous to one another and were found together in early Bohemia Corded Ware; some were even found together at the same sites:

    PNL001, Plotiště nad Labem_LX, Bohemia Corded Ware (Bohemia_CW_Early), 2914-2879 calBCE, mtDNA: U5a2a1, Y-DNA: R1b-U106

    PNL002, Plotiště nad Labem_221B, Bohemia Corded Ware (Bohemia_CW_Early), 2869-2573 calBCE, mtDNA: H3b, Y-DNA: R1a-M417(xZ645, S2846, Z2461)

    VLI011, Vliněves_4214A, Bohemia Corded Ware (Bohemia_CW_Early), 2881-2669 calBCE, mtDNA: W3a1c, Y-DNA: R1b-L151(xU106, xP312)

    VLI015, Vliněves_4757, Bohemia Corded Ware, 2881-2669 calBCE, inferred (kinship with VLI011), mtDNA: N2, Y-DNA: R1b-L151(xU106, xP312), notes: *this sample has been directly dated without Accelerator Mass Spectrometry (AMS) [CRL-9198 BP:4247 ±:80 cal2Sigma 3085-2581 BCE], but AMS date from father/son (VLI011) is preferred

    VLI075, Vliněves_1071, Bohemia Corded Ware (Bohemia_CW_Early), 2900-2500 BCE, mtDNA (inferred): L3'4, Y-DNA: R1a? (low coverage, xZ651)

    VLI081, Vliněves_2891, Bohemia Corded Ware (Bohemia_CW_Early), 2900-2500 calBCE, mtDNA (inferred): L1'2'3'4'5'6, Y-DNA: R1b-P310 (low coverage, no coverage at L151, P312, U106 or Z2103)

    VLI085, Vliněves_4307, Bohemia Corded Ware (Bohemia_CW_Early), 2862-2576 calBCE, mtDNA: J1c2m, Y-DNA: R1b-L151(xU106, no coverage at P312)

    VLI092, Vliněves_9566A, Bohemia Corded Ware (Bohemia_CW_Early), 2882-2669 calBCE, mtDNA: N1a1a1a2, Y-DNA: R1b-L151(xP312, xU106)

    KO1002, Kolín I_3013, Bohemia Corded Ware (Bohemia_CW_Early), 2835-2485 calBCE, mtDNA: X2b4, Y-DNA: R1b-L151(xU106, xP312)

    KON003, Konobrže_26A/91, Bohemia Corded Ware (Bohemia_CW_Early), 2900-2500 calBCE, mtDNA (inferred): L1'2'3'4'5'6, Y-DNA: R1b-L151(xP312, no coverage at U106)

    KON005, Konobrže_26/94, Bohemia Corded Ware (Bohemia_CW_Early), 2868-2586 calBCE, mtDNA: U, Y-DNA: R1b-M269 (low coverage, no coverage at L151, U106, P312 or Z2103)

    STD002, Stadice_29, Bohemia Corded Ware (Bohemia_CW_Early), 2882-2673 calBCE, mtDNA: I1a, Y-DNA: R1b-L151(xP312, xU106)
    TRM001, Trmice_4/87, Bohemia Corded Ware (Bohemia_CW_Early), 2900-2500 calBCE, mtDNA (inferred): L1'2'3'4'5'6, Y-DNA: R1a (low coverage)

    TRM006, Trmice_109/82, Bohemia Corded Ware (Bohemia_CW_Early), 2859-2576 calBCE, mtDNA: R1b1, Y-DNA: R1a-M417(xZ645, xZ647)

    DRO001, Droužkovice_20B-2, Bohemia Corded Ware (Bohemia_CW_Early), 2872-2633 calBCE, mtDNA: H2b, Y-DNA: Q1b-FT380500

    Vasilyevskiy kordon 17 has R1a, R1b, and J1 together; Khvalynsk had R1a, R1b, I2a, J1a, and Q1a; Karavaikha has R1a and R1b together; and in Sakhtish IIa (Sakhtish in general), I2a, Q1b, R1a, and R1b were all found together. R1a, R1b, and Q1 are ANE derived lineages in EHGs, and they spread to the rest of Europe via EHG derived groups.

    ReplyDelete
  96. @Gaska

    No one has found the very first R-L51 or the first R-L52, or the first R-L151 or the first R-P312. But we do know that because of how Y-DNA phylogeny works that in order for a R-P312 person to have existed that a R-L151 person was an ancestor to all R-P312 people. Not all R-L151 people were ancestors to all R-P312 people but all R-L151 people and all R-P312 people are descendants of the very first R-L151 person. This is the same of each subclade and the next upstream clade.

    Those first people are the "single" people I mentioned. Each of those single first people are the patriarchs of each subclade.

    All of the people that you mentioned - L51 Bohemia (3.000 BC), P312 Germany (2.500 BC), U106 (Bohemia (2.900 BC), U152 Germany-2.500 BC, L21 (England (2.400 BC), DF27 Occitania (2.350 BC) are descendants of the very first person to have the R-L51 mutation. They all also have Steppe autosomal DNA. There is not a single one of them that don't have Steppe autosomal DNA. This only means one thing. Their ancestors descend from people that had Steppe autosomal DNA.

    ReplyDelete
  97. @Gaska "Regarding the Western European Neolithic, I already have a list of 9 samples (5,000-3,000 BC) that undoubtedly belong to R1b-L754>M269"

    I have news for you. None of those people are derived for R-L23 or any of the R-L23 subclades and they lived after R-L51 came into existence. So we couldn't care less about your 9 samples.

    ReplyDelete
  98. “CHG in steppe correlates with J1 instead ”

    And counter-current / back-diffusion of R1b-V3616 & Q1

    ReplyDelete
  99. But J1 appears in EHG and, for example, at Vasilyevskiy kordon 17, where CHG is minimal.

    On the other hand, there's a lot of CHG at Golubaya Krinitsa where there's no J1. It seems to me that there must be some sort of mtDNA U4 link with CHG in these sorts of populations.

    There are also CHG/Caucasus mtDNA lineages in Yamnaya and Corded Ware, but no J1. So CHG in the steppe mostly correlates with female lineages.

    ReplyDelete
  100. Found an interesting post online.
    What do you guys make of it?

    Syrian texts 2500bce

    Hittite personal name
    Hu-da-Su
    Vedic equivalent
    Su-da-sa


    Hittite
    Hasauwant
    Sanskrit equivalent
    Asuvant/Asumant

    ReplyDelete
    Replies
    1. Link please! There are many of these correspondences. The phonology of Anatolian languages is an artifact of our interpretation of the cuneiform, same with Persian.

      Delete
  101. @Dospaises said-“All of the people that you mentioned - L51 Bohemia (3.000 BC), P312 Germany (2.500 BC), U106 (Bohemia (2.900 BC), U152 Germany-2.500 BC, L21 (England (2.400 BC), DF27 Occitania (2.350 BC) are descendants of the very first person to have the R-L51 mutation. They all also have Steppe autosomal DNA. There is not a single one of them that don't have Steppe autosomal DNA. This only means one thing. Their ancestors descend from people that had Steppe autosomal DNA”

    Yeah, and they also have WHG and EEF autosomal DNA. There is not a single one of them that don’t have WHG or EEF autosomal DNA. This only means one thing. Their ancestors descend from people that had WHG and EEF autosomal DNA.

    @Dos paises said “I have news for you. None of those people are derived for R-L23 or any of the R-L23 subclades and they lived after R-L51 came into existence. So we couldn't care less about your 9 samples.”

    And I have news for you, any of these samples could be the parent or grandparent of R1b-L51, however, there are no cases of R1b-L754>M269 in Ukraine or Russia, so there is not even the possibility of finding the ancestors of L51 in that region. Ergo if you don't care about them is your problem, you will always be wrong.

    ReplyDelete
  102. Time for the bizzare question.

    1 man on a fair day migrates from Location A to Location B. Marries local women and has 10 female children.

    These women marry local men and each reproduce 4 children on average.

    Now we have 40 samples in matter of less than a century with 25% ancestry from Location A without any apparent change in archaeological culture and absolutely no change in X&Y haplogroups.

    A generation later we find 100+ such samples with 12% location A input.

    How are geneticists able to determine that this 12% ancestry was an outcome of large migration or just 1 male or 1 female having highly successful sexual relationship ;)

    ReplyDelete
  103. @Simon Stevin-

    You are wrong, R1b-L51/U106 and women with steppe ancestry predate R1a-M417 and Q1b in Bohemia by at least 250 years, ergo they are only contemporary and appear in the same sites when the steppe lineages arrive. There are only two possibilities

    1-R1b-L51 is a typical marker of the Czech neolithic cultures (Baltic origin, Narva signal in all these samples and the reason why Max Planck liquidated the Yamnaya culture) and acquired their steppe signal by exogamy.

    2-They traveled separately-In this case you need two different origins in the steppes or in the forest steppe. But in the case of R1b-L51 you need a culture with Baltic signal that does not exist in that region.

    *VLI076 (2.959 BC)-Vlineves, Bohemia-FEMALE-mtDNA-N1a1/a1a/2 +steppe
    *PNL001 (2.896 BC)-Plotiště nad Labem_LX, Bohemia-HapY-R1b-U106-mtDNAU5a2/a1 +steppe
    *OBR003(2.893 BC)-Obritsví, Bohemia-HapY-R1b-L151-mtDNA-No data-U5a1/b1 ?? +steppe
    *VLI090 (2.831 BC)-Vlineves, Bohemia-FEMALE-mtDNA-Jb1a/1 + steppe
    *VLI088 (2.789 BC)-Vlineves, Bohemia-FEMALE-mtDNA-HV +steppe
    *STD002 (2.777 BC)-Stadice, Bohemia-HapY-R1b-L151-mtDNA-I1a
    *VLI011 (2.775 BC)-Vlineves, Bohemia-HapY-R1b-L151-mtDNA-W3a1/c
    *VLI015 (2.775 BC)-Vlineves, Bohemia-HapY-R1b-L151-mtDNA-N2
    *VLI092 (2.755 BC)-Vlineves, Bohemia-HapY-R1b-L151-mtDNA-N1a1/a1a/2

    And then miraculously CWC/Yamnaya (steppe or steppe forest) appears.

    *DRO001 (2.752 BC)-Droužkovice-HapY-Q1b2a-mtDNA-H2b
    *PNL002 (2.721 BC)-Plotisté nad Lebem-HapY-R1a-M417-mtDNA-H3b

    Do you understand? First R1b-L51 and steppe females, 250 years later typical steppe male markers. If you add to this that the grave goods of the L51 men have absolutely nothing to do with Yamnaya or the CWC (remember that there is only one type A battle axe in the R1b sites and that type of weapon originated in Jutland not in the steppes)-Battle axes existed in Bohemia 2,000 years before the arrival of the CWC.

    The samples you mention in Khvalynsk etc are R1b-V1636, none of them is R1b-M269>L51, so you can go looking for other arguments because the lives of R1b-M269 and R1a-M417 are parallel and never came together in European prehistory.

    ReplyDelete
  104. @Gaska

    The early Corded Ware males from Bohemia with R1b-L51/U106 have a lot of steppe ancestry.

    Are you arguing that they don't?

    ReplyDelete
  105. In regards to the deep origins of Germanic languages, it seems now that proto-Germanic developed in the contact zone between the more northerly R1a-rich Battle Axe and more southerly R1b-rich Single Grave populations (or their descendants).

    There was also some pre-Indo-European I1 in this milieu, and eventually it made a big impact via a founder effect.

    I'll write this up soon in a new blog post.

    ReplyDelete
  106. @ Davidski


    ''But J1 appears in EHG and, for example, at Vasilyevskiy kordon 17, where CHG is minimal.

    On the other hand, there's a lot of CHG at Golubaya Krinitsa where there's no J1. It seems to me that there must be some sort of mtDNA U4 link with CHG in these sorts of populations.

    There are also CHG/Caucasus mtDNA lineages in Yamnaya and Corded Ware, but no J1. So CHG in the steppe mostly correlates with female lineages.''


    The relationship is not mutually exclusive. J1 would have been originally CHG related during Late Paleolithic, but autosomally washed away by the time it got to Karelia




    ''In regards to the deep origins of Germanic languages, it seems now that proto-Germanic developed in the contact zone between the more northerly R1a-rich Battle Axe and more southerly R1b-rich Single Grave populations (or their descendants).

    There was also some pre-Indo-European I1 in this milieu, and eventually it made a big impact via a founder effect.''

    In terms of the Bronze Age, that seems to be the case. Also pertinent would be original location of I1 groups to help fine tune this geographically.
    However, the final Germanic genesis was in pre-ROman Iron Age. The Bronze Age pastoral / metal chiefs lost power (internally) to households and individuals with new focus on agriculture, land tenure and eventually a neq warrior identity via ideas gained from La Tene world, often via Poland (e.g. Przeworsk culture).

    ReplyDelete
  107. @Assuwatama, well, that sort of thing basically becomes really improbable at a large scale. How likely is it for even one male to have ten surviving daughters and no surviving sons in the first place? Not very likely. How likely is this to happen *a* lot so that a large population ends up having that happens to have a particular pattern? Even less likely!

    But the sort of patterns of differences between autosome, X chromosome, mtdna and Y dna you talk about generally, those could happen, however there must be some social structure reason or large scale events that make it happen like that.

    Like, let's say 5 men from pop A migrated to a foreign culture Pop B where there are open to accepting them, and 4 of them managed to find local wives and reproduce successfully. Then they had a mix of sons and daughters, but there are few local partners, so these children must migrate elsewhere in Pop B. There, unfortunately the men are a lot more patrilocal and the sons would have no luck finding partners, being socially disadvantaged in some way, and only the daughters are able to migrate out and reproduce successfully.

    Then you'd find that, although the initial migration was male, there would be no Y or mtdna signal left, and you'd only have an autosomal signal left (about 25%). If there is some systematic social force that led to this outcome, it might get reproduced again and again (or if the population's small enough it might not need to get reproduced that many times).

    Or you could have some twist of the above where the male children (finding themselves with no luck finding more wives from Pop B) backmigrated to the father's culture and took wives there, which would lead to the same situation where the father's culture (Pop A) starts to have 25% admixture but again, no change in Y dna or mtdna haplogroups.

    So this kind of thing can happen, but it is more a case of large scale good/bad luck, or social forces, rather than it is likely to be due to driven by individual luck or chance. Social institutions like bride price, sex specific young age mortality, or sex specific migration, can be the cause of some of these events.

    ReplyDelete
    Replies
    1. Thanks.

      I have come across some social practices where brides who can't get grooms are sold in market place. Also kinda similar practice has been documented by ancient scholars who called it asura vivha/marriage.

      Polygamy was a common practice among elites. Could explain it far better than my previous example.

      Also we have a mythological figure head in Vedic culture who had 60 daughters and from his daughter's like Danu came danavas and from Aditi came adityas.

      Interestingly some tales narrate that his sons took to celibacy.

      Kinda mirrors swat valley samples which show 18% steppe input with 2 in 44 male samples being R1a and if I am not wrong they aren't the andronovo type either, right?

      Males dying on battlefield will result in higher proportion of females. Such events would lead to more children from single male.

      Delete
    2. Matt - well my family is an example. Paternal grandfather had 9 children, and is daughtered out with the next generation of something like 30 or 40 descendents. BTW we are Nordic BA I1. Not a bad run.

      Delete
  108. @Davidski
    It's interesting that you're so hellbent on associating U4 with CHG when you also have U4 lineages in EHG where CHG autosomal input is either minimal or non-existent. And correlating J1 with EHG is like denying that R1b in Copper Age Anatolia is from the Steppes, very dishonest.

    ReplyDelete
    Replies
    1. We have 2 800ce samples from India with R1a and zero steppe input.

      Highest steppe input of 25% or more is associated with J2b & J2a.

      Around 15% steppe guys are R2.

      Delete

  109. @Davidski

    Of course not, they have steppe ancestry (and WHG, and EEF ancestry), BUT they also have 10-15% signal from Narva culture-Are you arguing that they don't? Do you agree that this signal is incompatible with Yamnaya?, do you agree that this is the reason why Max Planck has renounced the Yamnaya culture as the origin of R1b-L51 (and even of R1a-M417)?-Those R1b-L51 are some kind of outliers within the CWC. Many mitochondrial lineages in the Bohemian CWC are from the steppe (not Baltic), do you agree that females also passed on that autosomal signal?

    ReplyDelete
  110. @Gaska

    If you continue to misrepresent data and/or lie, I see no reason as to why David shouldn’t ban you once again. Early Bohemia Corded Ware has both R1a-M417 and R1b-M269. These samples are all contemporaneous (they date to the same time periods), they’re located at the same sites (or they are proximal to one another), and every single one has Yamnaya related ancestry, that is EHG + CHG. Every single sample we have with R1b-L51/M269 and R1a-M417 has CHG + EHG autosomal DNA. That means their ancestors are from Eastern Europe. It also means they share a common ancestry with Yamnaya and Afanasievo. None of the Narva HGs had M269; those Baltic HGs also have large amounts of EHG autosomal DNA and Y-DNA (R1a, Q1b-Y2700*, and R1b-Y13200/M73). R1b is not a WHG or EEF marker, it’s an EHG marker—it’s derived from ANE—just like R2, R1a and Q.

    And this is what the Planck paper said: “CW individuals were shown to be genetically distinct from culturally pre-CW people, having ~75% of their ancestry similar to Yamnaya individuals from the Pontic-Caspian steppe (3, 4, 23–27). This Yamnaya-like “steppe” ancestry then spread rapidly throughout Europe, reaching Britain, Ireland, the Iberian Peninsula, the Balearic Islands, Sardinia, and Sicily before the end of the third millennium BCE (5, 28–32)…Therefore, despite their sharing of steppe ancestry (3, 4) and substantial chronological overlap (45), it is currently not possible to directly link Yamnaya, CW, and BB groups as paternal genealogical sources for one another, particularly noteworthy in light of steppe ancestry’s suggested male-driven spread (23, 41–43) and the proposed patrilocal/patriarchal social kinship systems of these three societies (46–48)…the addition of either Latvia_MN (57 of 95 supported models), Ukraine_Neolithic (53 of 95 supported models), or PittedWare (32 of 95 supported models) to the sources drastically increases the number of supported models (table S17). These results show the presence of excess Latvia_MN/Ukraine_Neolithic/PittedWare-like ancestry in Bohemia_CW_Early relative to all known Yamnaya and central European Neolithic groups. Our models suggest that this ancestry accounts for ~5 to 15% of the Bohemia_CW_Early gene pool (table S17).”

    ReplyDelete
  111. This is the data on Baltic HGs, they have significant EHG, they also don’t have any R1b-M269, only M73/Y13200, which was found in the Samara EHG.

    Mittnik et al. (2018): “Using the qpWave/qpAdm framework, we modelled the Baltic Mesolithic hunter-gatherers as a two-way mixture between EHG and WHG (Fig. 3), which reveals a difference in mixture proportions between the more northern individuals from the Latvian site (65–76% WHG with 24–35% EHG; Supplementary Table 3) and the samples from the Lithuanian sites to the south (88–100% WHG with 0–12% EHG; Supplementary Table 3)…Using qpAdm, we confirm the previously published result of SHG being formed by admixture of WHG and EHG (57 ± 2% WHG with 43 ± 2% EHG)…Both EHG and SHG share a non-negligible component in ADMIXTURE analysis that is maximized in some modern Native American populations which points towards ANE ancestry, as represented by the MA1 and AG3 samples from Palaeolithic Siberia (maroon component in Fig. 2a, Supplementary Fig. 4). Indeed, D-statistics show that EHG and SHG share significantly more alleles with MA1 and AG3 than WHG…Similarly to the Baltic Mesolithic, the later Eastern Baltic Neolithic hunter-gatherers of the Narva culture exhibit varying proportions of EHG (0–46%) and WHG (54–100%) ancestry (Fig. 3 and Supplementary Table 3)…The later individuals attributed to the Baltic MN CCC exhibit a significantly higher affinity to EHG with the ancestry proportion estimated at 68–99% EHG and 1–32% WHG (Fig. 3, Supplementary Table 3).”

    Lamnidis et al. (2018) found the following: 63.3% EHG and 19.8% Yamnaya for CCC/Pit-Comb Ware, 45.5% EHG in two PWC Sweden HGs, 40.8% EHG in two SHGs, 15.5% EHG in two Narva HGs, 5% and 17.2% EHG in two Kunda HGs, 19.7% and 26.2% EHG in two Latvia HGs, 20.7% EHG in a Latvia MN sample, and 31.5% Yamnaya in another Latvia MN sample. Jones et al. (2017), and Matthieson et al. (2018) got practically the same results (30% EHG in Kunda, Narva, and 65%-100% EHG in CCC). VK531 was like the SHGs and the CCC HGs; he had a significant amount of EHG ancestry, and that’s where his R1b-M73 comes from

    ReplyDelete
  112. @KikuyuBulalba

    J1 is found in European hunter-gatherers, so there's no need to correlate it with the CHG influx into the steppes, especially in groups that lack J1.

    On the other hand, R1b-V1636 is obviously a steppe lineage that couldn't have possibly existed in Anatolian hunter-gatherers, so it represents recent steppe influence in Anatolia.

    We'll probably be able to work out which maternal lineages were associated with CHG ancestry in the steppe when the R1b-rich Khvalynsk and R1a/I2-rich Sredny Stog samples are published.

    I'm betting that with high enough resolution, there will be a Caucasus-specific mtDNA U4 lineage involved.

    ReplyDelete
  113. So Bohemia CWC could have Ukraine Neolithic ancestry instead of Latvia_MN, and Latvia_MN has samples with 20.7% EHG and 31.5% Yamnaya related ancestry.

    ReplyDelete

  114. @SS

    Unfounded accusations (misrepresent data, lies), bans, this is how the Holy Inquisition worked, the Kurganist dogma has become a religion for some ignorant people. It is not worth responding to you, just a recommendation, read Luka Papac's paper again, these are his words, if you accuse me of lying it is that you simply do not know how to read, or you do not know how to interpret what you read

    “Steppe ancestry is also present in BB individuals; however, they predominantly carry R1b-P312, a Y-lineage not yet found among CW or Yamnaya males. Therefore, despite their sharing of steppe ancestry and substantial chronological overlap, it is currently NOT POSSIBLE TO DIRECTLY LINK Yamnaya, CW, and BB groups AS PATERNAL GENEALOGICAL SOURCES for one another, particularly noteworthy in light of steppe ancestry’s suggested male-driven spread and the proposed patrilocal/patriarchal social kinship systems of these three societies”

    “In addition, when modeling early CW individually as “standard” three-way mixtures of Anatolia_Neolithic, WHG, and Yamnaya_Samara (3), we find that in 37% (10 of 27) of cases, the model lacks strong support (P < 0.05 or infeasible). To explore why two-way proximal models between any Yamnaya and a European Neolithic source are insufficient in explaining Bohemia_CW_Early genetic diversity, we tried adding a THIRD SOURCE to obtain better model fits. We find that when either one of LATVIA_MN, Ukraine_Neolithic, or PittedWare is added as a source, almost all (280 of 285) model fits (P values) improve and most of them by several orders of magnitude (table S17)”.

    “These results show the presence of excess Latvia_MN/Ukraine_Neolithic/PittedWare-like ancestry in Bohemia_CW_Early relative to all known Yamnaya and central European Neolithic groups. Our models suggest that this ancestry accounts for ~5 to 15% of the Bohemia_CW_Early gene pool (table S17)”

    “Modelling Bohemia_CW_Early as a two-way and three-way mixture using proximal sources-Interpretation: known Yamnaya groups are an UNSATISFACTORY source for "steppe" ancestry in Bohemia-CW-Early-

    “FINDING LATVIA__MN-like ancestry in early CW, in conjunction with the absence of Y-chromosomal sharing between early CW and Yamnaya males, suggests a LIMITED OR INDIRECT role of known Yamnaya in the origin and spread of CW to central Europe.

    “It is likely that GAC and CW/Yamnaya individuals spoke different languages, meaning that early CW society in Bohemia encompassed people who had demonstrably different histories, likely originating from ideologically diverse cultures, who spoke different mother tongues”.

    “In contrast to BB males from England, several of whom are derived at R1b-L21 (R1b1a1a2c1), showing that English and Bohemian BB males cannot be descendants of one another, but rather diversified in parallel. A scenario of R1b-P312 originating somewhere between Bohemia and England, POSSIBLY IN THE VICINITY OF THE RHINE, followed by an expansion northwest and east is compatible with our current understanding of the phylogeography of ancient R1b-L151–derived lineages”

    ReplyDelete
  115. IMO-“The pull of early CW towards the WHG is really obvious>Yamnaya totally debunked and therefore also Afanasievo and your fantasies about L52 in Mongolia”

    You are wrong, early CWC Bohemia is L51 NOT R1a-M417 or Q1b, anyone who knows mathematics is capable of making the average of the dates, you just have to read the Papac tables well. If you are unable to recognize that L51 (2.896 BC) is older than M417 (2.721 BC) you are trying to fool the people reading these comments. EXACTLY 175 years (8-9 generations) both in the same deposit- Plotiště nad Labem. You get it? L51 was either there or he came before.


    @SS

    You said-“R1b is not a WHG or EEF marker, it’s an EHG marker—it’s derived from ANE—just like R2, R1a and Q.” and then you said-Baltic HGs-R1b-M73/Y13200, More northern individuals from the Latvian site (65–76% WHG with 24–35% EHG), Lithuanian sites to the south (88–100% WHG with 0–12% EHG), SHG being formed by admixture of WHG and EHG (57 ± 2% WHG with 43 ± 2% EHG)…

    That is, Latvian R1b-HGs 70.5%-WHGs, Lithuanians-R1b-HGs-94%-WHGs and Scandinavian HGs-57%-WHGs and your interpretation is that R1b is a typical marker of EHGs?, Ha Ha Ha- Also the Balkans, Italy and France have R1b totally WHGs. My advice is that you would save time if you leave this hobby and dedicate yourself to writing children's stories.

    ReplyDelete
  116. @Davidski

    NEO163 has a noticeable amount of CHG ancestry, and instead of making a dishonest roundabout remark that it's "European hunter-gatherer", you can instead admit the truth that it's directly related to CHG, especially given the fact that the Karelian EHG J1 was very much related to Satusrblia.

    Now take a look at NEO174 with W6a, this mtDNA is likely associated with this CHG population because you can find archaic W6 clades in Iran and South Asia. You cannot say the same about U4 in Iran, South Asia or the Caucasus, the lineage there is recent and is extremely unlikely to be associated with pure CHG.

    And if NEO174 had W6a, a clearly non Euro-HG lineage, why don't we see said lineages in the Middle Don samples?

    ReplyDelete
  117. If the I1 were still predominantly fishermen, it might explain why they survived and the I2 hunter-turned-farmer of central Europe many not have had the population density when they tried to expand northwards and were unsuccessful. There isn't really any other area where I1 outside Sweden/Finland could have been hiding out in the Bronze Age now that so much of Europe has been studied. It's also clear they didn't arrive from anywhere else like Spain, Ukraine, Britain, or France...etc

    ReplyDelete
  118. @Gaska

    There is an easy explanation for this. The western most group of R1b were L754* and merged with other I2 groups in the Balkans when the WHG formed during and after the re-expansion from the LGM. There were other offspring to a L754+ man who were successful and most definitely further east to the Balkans, possibly north of the Caucasus or a more eastern refugia. These R1b survivors were not WHG, but most closely resembled the ANE ancestor. When it was hospitable to re-expand northwards, the hunters did so and merged with other groups who had been in the Balkans, this is how you get the Baltic groups who were P297+ and splits of WHG-EHG. THe M269+ ancestor also descends from one of the groups in the more eastern refugia, and of course the earliest split of R1b with PH155 being somewhere in Mongolia or Kazakhstan where they most closely resembled ANE as late as 1000 BC in China.

    ReplyDelete
  119. So you are saying that the earliest Bohemian R-L151 males (2914-2875 BC) are continuous with the Bohemian Neolithic, even though both are typical Corded Ware flexed Easy-West, right sided burials and one of them is buried with a Corded Ware pot and a Corded Ware battle axe? And because they have 10-15% ancestry from Narva, which is from the Baltic and nowhere near Bohemia, they are now native EEFs from Bohemia? And of course you just completely ignored all the Y-DNA samples I posted that were all the very same Bohemian Neolithics that you are trying to pin these L151s on and none are even R-M269, let alone R-L151. Can you once and for all show us the pre-Corded Ware samples you know of that have R-M269 and no steppe ancestry? Without that, you are just spitting into the wind.

    ReplyDelete
  120. Hum... this is a huge freaking paper. The supplements are 600 pages. It introduces several new statistical techniques that should have been solo papers. So two questions to start with. 1) Why the huge paper? Is there something happening in the aDNA research community that drove the decision? 2) Why are the diagram such low resolution? Has anyone found an alternative site for the diagrams?
    Cheers,
    Guy

    ReplyDelete
  121. This comment has been removed by the author.

    ReplyDelete
  122. @Gaska
    You could have spared us all from your poorly written, grammatically disastrous, schizophrenic drivel, if you actually made a single coherent point. Haplogroups are not people, stop referring to L51’s “life,” that makes no sense. If you’re going to write in English, it has to make sense in English. Regardless, you seem to have missed the part where the authors said that this excess affinity in Bohemia CWC could be Ukraine Neolithic or Pitted Ware: “the addition of either Latvia_MN (57 of 95 supported models), Ukraine_Neolithic (53 of 95 supported models), or PittedWare (32 of 95 supported models) to the sources drastically increases the number of supported models (table S17). These results show the presence of excess Latvia_MN/Ukraine_Neolithic/PittedWare-like ancestry in Bohemia_CW_Early relative to all known Yamnaya and central European Neolithic groups.”

    So there we are, Bohemia CWC is 75% Yamnaya-like, with 5-15% ancestry that resembles Latvia_MN or PittedWare or Ukraine_Neolithic. You are saying it is derived directly from one of these three sources, when the authors are stating that it is “like” those sources—you are misrepresenting and/or lying about the data. There’s a difference between Yamnaya-like and Yamnaya proper, and Latvia_MN-like and Latvia_MN proper. Furthermore, all of these reference sources have significant amounts of EHG, hence the R1 and Q1b Y-DNA lineages. Latvia_MN samples have around 20.7% EHG and 31.5% Yamnaya-like admixture; Pitted Ware has roughly 45.5% EHG. Mathieson et al., 2018 found the following: “We find (Supplementary Data Table 3) that Mesolithic and Early Neolithic individuals (Latvia_HG) associated with the Kunda and Narva cultures have ancestry intermediate between WHG (~70%) and EHG (~30%), consistent with previous reports. We also detect a shift in ancestry between the Early Neolithic and individuals associated with the Middle Neolithic Comb Ware Complex (Latvia_MN), who have more EHG-related ancestry (we estimate 65% EHG, but two of four individuals appear to be 100% EHG in PCA).” They also found that Ukraine_Neolithic is 39.3%-43.7% WHG vs 49.8%-60.7% EHG; Latvia_MN is roughly 32.6%-35.1% WHG and 63.4%-67.3% EHG. So Bohemia CWC has excess WHG/EHG on top of what Yamnaya-like admixture brings. Not only that, but the best fitting source population (Latvia_MN), has the highest amount of EHG out of the other two, which means a higher proportion of overall EHG ancestry. What’s more, R1b still came from Eastern Europe, and M269 always comes with Yamnaya related ancestry, every single time. There is not one sample with M269 that lacks EHG or EHG + CHG/steppe related autosomal DNA. You have no evidence, no samples, nothing. You’re oddly asserting M269’s origin in the Baltic, even though those populations have significant EHG, especially Latvia_MN, which is one of the three source populations in the Planck study. Moreover, Baltic HGs only have I2a, R1b-M73/Y13200, Q1b-Y2700, and R1a(xM198), and no M417 or M269; all their R1 and Q1 lineages are EHG derived. Do R1a and Q1b come from the Baltic now? They’ve never been found in Yamnaya. That’s basically your fallacious “thinking.” Corded Ware and Yamnaya share a common ancestry, which explains their common Y-DNAs. Neither derives from the other, just like the Vikings don’t derive from the Saxons or Franks. They share a common EHG + CHG ancestry, with some minor EEF and WHG. R1a and R1b come from EHGs, which is why Corded Ware and Yamnaya have it—they’re predominantly EHG paternally. R1b-M269 was spread by Yamnaya-like populations from Eastern Europe; it doesn’t derive from Yamnaya proper. At this rate, you’ll be saying L51 originated in Finland or Siberia, that’s how often you cope and shift goal posts, anywhere but the Pontic-Caspian and East European forest steppes. Hypothetically speaking, even if L51 comes the Baltic, Basques still paternally derive from Baltic HGs with EHG autosomal DNA and Y-DNA. Utter fail.

    ReplyDelete
  123. Additionally, the latest paper on the Sicilian Mesolithic, demonstrated EHG ancestry in a Late Mesolithic sample of Sicilian hunter gatherers, and in Villabruna. This explains where Villabruna’s R1b-L754* came from; EHG + WHG admixture events in the Balkans, produced EHG admixed, R1b-L754* bearing groups; these groups migrated further west, towards regions such as modern day Italy and France.

    ReplyDelete
  124. SHG invented blonde haired blue eyed fair skinned women thousands of years before the Farmers or swarthy Steppe people stole the formula.

    ReplyDelete
  125. @Davidski,

    yHG J1 is for sure Southwest Asian origin. Its presence in a few hunter gatherers in Europe should one or way another be from geneflow from Southwest Asia. It should be specifically from CHG.

    ReplyDelete
  126. @Genos

    The question is this: which uniparental markers were associated with the perceptible rise of CHG-related ancestry on the steppe?

    You must be giving the answer to another question, because there's no obvious correlation between J1 and the CHG-related ancestry on the steppe, since EHG has none of the perceptible/excess CHG-related ancestry seen in Yamnaya.

    Keep in mind that there's J1 in EHG, but not in Yamnaya.

    ReplyDelete
  127. I don't care about this but reminder there is a J1 in Afansievo which is basically Yamnaya

    ReplyDelete
  128. @ Davidski

    J1 is probably associated with CHG originally, like in Late Paleo
    On the steppe things get more complex , because you can have CHG rich Yhg Q1 and V3616 guys, like in Khvalynsk, and CHG poor guys in karelia due to “autosomal washout”.

    MtDNA U4-9 looks like something deeper / more ancient than CHG

    ReplyDelete
  129. Yeah, J1 might have been a CHG marker originally, but on the steppe its spread may have been entirely mediated by EHG.

    On the other hand, U4 may have been a steppe marker originally, but females from the North Caucasus with U4 may have been the main source of CHG-related ancestry on the Neolithic/Eneolithic steppe.

    So what I'm saying is that in this case I'm not interested in the deep associations between uniparental markers and CHG, but rather in the associations that led to such a high level of CHG-related ancestry on the steppe during the Bronze Age.

    ReplyDelete
  130. @Davidski,

    I can be answering both.

    The J1 in Karelia could be from the Mesolithic CHG influx that gave Lower Don Neolithic so much CHG ancestry. But by the time the CHG geneflow reached northern Russia it became undetectable.

    ReplyDelete
  131. @Genos

    I've considered that, but from what I've seen (published and unpublished), the Russian Neolithic and Eneolithic samples with the highest levels of CHG ancestry don't belong to J1.

    They actually belong to steppe Y-DNA lineages like I2a, R1a and Q, but with potentially Caucasus-related mtDNA lineages like U2, U4 and W6.

    This is in line with the high ratio of Caucasus-related mtDNA lineages in Yamnaya, but no Y-DNA J1.

    Ergo, even if J1 entered the steppe with people heavy in CHG, I think that female mediated gene flow from the North Caucasus is the main explanation for the CHG-related ancestry on the steppe.

    ReplyDelete
  132. @SS & Wood

    I know my English is a mess, my apologies, at least we try to communicate in a language that is not our mother tongue. I hope this is grammatically correct and everyone understands it-

    Bla bla bla bla bla bla bla

    The truth is that;

    1-R1b are a typical lineage of WHGs and also of the Russian HGs (which according to Allentoft have nothing to do with the Eastern, Ukrainian or Siberian HGs and which did not contribute genetically to the formation of Yamnaya_CWC).

    2-R1b-L51 is at least 175 years older than M417 in the Czech deposits so either it is already there or they traveled separately.

    3-Yamnaya and Afanasievo debunked because the Narva signal is absolutely incompatible with those cultures.

    ReplyDelete
  133. U5, U4, U2e - neither of these look like original CHG mtDNA. I agree that they were Steppe lineages associated with ANE and WHG rich populations. But if the Steppe CHG population was rich in those lineages, what does this imply in regards to their admixture? Wouldn't it be likely that they were enriched in European forager ancestry, thus explaining their tendency to have U4, and now also U2 and later probably U5 which are now bizarrely seen as CHG mtDNA?

    A friend of mine made several simulations that give a simplified version of what might have been going on.

    The Copper Axe method was followed for this one, coordinates are - Middle_Don_Neolithic_ghost,0.1354802,0.0855646,0.07169953,0.14669236,-0.02376309,0.05600136,0.00671083,-0.00019196,-0.06084604,-0.09073494,-0.00442323,-0.0010949,0.00122882,-0.02292617,0.05414585,0.0323214,0.00373099,-0.00149713,-0.00870126,0.02412682,-0.00278455,-0.00230396,0.01915916,0.04154561,-0.00690892

    Target: Middle_Don_Neolithic_ghost_(R1_I2&U5_U4_U2e)
    Distance: 9.6419% / 0.09641940
    61.2 RUS_Samara_HG
    28.2 GEO_CHG
    10.6 UKR_Meso


    This population in itself is likely a 50/50 of two different populations, as things usually are. Chip off some European HG ancestry and you'll get this

    Target: CHG_Steppe_population_(J1&U5_U4_U2e_W6)
    Distance: 19.9949% / 0.19994862
    58.4 GEO_CHG
    37.4 RUS_Samara_HG
    4.2 UKR_Meso

    So now you can model the first simulation with the one above, which easily explains the peculiarities of the uniparentals.

    Target: Middle_Don_Neolithic_ghost_(R1_I2&U5_U4_U2e)
    Distance: 0.0095% / 0.00009489
    48.2 CHG_Steppe_population_(J1&U5_U4_U2e_W6)
    43.2 Samara_HG_(R1_Q&U5_U4_U2e)
    8.6 UKR_Meso_(I2_R1&U5_U4_U2e)

    ReplyDelete
  134. This comment has been removed by the author.

    ReplyDelete
  135. @Rocca

    1-Excusatio non petita, accusatio manifesta-“You know that the main problem with the Papac`s paper is the inconsistency in the dating (too old to belong to the CWC), and the absence of grave goods associated with the CWC. For this reason, the guardians of Kurganist orthodoxy (you among them) were quick to point to the existence of that battle-axe as irrefutable proof that L51 in Bohemia was associated with the CWC. However, you know that the type A battle axes have their origin in Jutland, and that in Bohemia the Neolithic cultures used this type of weaponry thousands of years before the CWC appeared-In addition, the rest of the tombs with L51 men are considered as "Preceramic" and cannot be associated with the CWC. In my opinion, archaeologically these L51 men do not belong to the CWC.

    2-Plus Ultra-The age of L51 and steppe women in the Bohemian deposits is 175-250 years before the arrival of Q1b, R1a-M417 and Z2103, so it is evident that they did not travel together, because in the rest of the regional varieties of the CWC (Baltic, Poland, Sweden) we only have M417 and NEVER L51. There is also no L51 in the early Danish SGC (only R1a and I2a). It is therefore common sense to think that L51 in Bohemia is a local issue that cannot be generalized to the rest of the CWC.

    3-Alea Jacta Est-The Narva signal is especially associated with L51 men and is absolutely incompatible with Yamnaya. Max Planck understood the coming disaster and tried to save the steppe theory from the bonfire by looking for alternatives. In order to gain time (at the moment Harvard and Max Planck are only fighting to preserve their egos), they have introduced into the debate the Ukrainian forest steppe where an autosomal signal similar to the Narva signal could exist. They have mobilized all their resources-Archeologically Volker Heyd has searched for solutions to link CWC ceramics with those of the forest steppe, Patterson et al have developed DATES to increase the time the famous Yamnaya signal reached mainland Europe, Anthony et al have studied Khvalysnk in depth, Allentoft has published dozens of Ukrainian and Russian genomes and specialized genetic pages have kept hope alive so that the Kurganist troop will not be demoralized. Nothing to criticize, it is their obligation as scientists to propose a theory and then try to prove it, we just have to thank them for the effort they are making, as long as they do it in an honest way. The drama is that after so much effort there is still not a single case of M269-L51>P312 in Ukraine or Russia (Lyalovo, Volosovo, Khvalynsk, Siberian cultures, Eneolithic Caucasus, Maykop, Dnieper-Donets, Sredni Stog, Repin, Yamnaya, Afanasievo, Fatyanovo, Catacomb etc etc etc)-Nothing (except Z2103, I2a-L699, V1636 ) that can link the steppe cultures with the BB culture and Western Europe, nothing that can prove that these people were responsible for the spread of IE .

    ReplyDelete
  136. 4-Quod erat demostrandum-I do not ignore anything because the data you have published have been known to us for months. Evidently there is no M269>L51 in the Czech Neolithic (Papac et al), nor is there L51 in the Danish (except one R1b-L754-3.500 BC) or Swedish Neolithic, nor in Poland, Ukraine or Russia. Nobody knows where we are going to find the ancestors of the Bohemian L51-Certainly the Baltic and the Balkans are a possibility. Seven years ago there was not a single R1b west of the Dnieper River and since R* is in Siberia everyone naturally accepted that R1a and R1b are Siberian markers related to EHGs. However, 7 years later we have more than a hundred R1b-WHgs or neolithic farmers (including many V88) all over continental Europe. Haak and Allentoft were seriously mistaken in assuming that the mass migrations linked to M417 and L51 brought the IE to mainland Europe. Olalde et al were seriously mistaken in saying that M269-P312 was the only one responsible for the introduction of the steppe signal in Western Europe.

    5-Numantia Victrix-We already know that for the guardians of the Kurganist orthodoxy it is almost an obligation to try to ignore or discredit any case of R1b-M269>L51 that appears in Western Europe in order to keep the steppe theory alive. Sometimes it is the archaeological contexts, other times the dates, other times the quality of the genomes etc etc etc... However, we already have conclusive evidence of the existence of M269 and L51 in Western Europe prior to the arrival of the CWC. Whenever you want we can talk about the Cueva de las Lechuzas (I think you have talked with Villaba about the dating of that site), or we can also talk about Fichera's thesis and the cases of R1b in Belgium. Obviously we still have to demonstrate genetic continuity up to P312 and BB culture, but it is our obligation to study that possibility. Time will tell who is right-And once again the steppe ancestry in M269 IS NOT definitive proof of its origin.

    ReplyDelete
  137. @KikuyuBulalba

    It seems to me that many people assume that CHG actually made it into the steppe. But this is unlikely.

    More likely is a scenario where a population rich in CHG-related ancestry spread this ancestry north of the Caucasus.

    So, obviously, such a population would have to have been something like an EHG/CHG mixture, and thus not necessarily rich in classic CHG uniparental markers.

    ReplyDelete
  138. @Gaska
    Yamnaya and the CWC descend from Western Russian hunter gatherer groups; the vast majority of Russian HG ancestry is EHG. Where do you think WSHs/PIEs got their EHG from? The fucking sky?

    R1b is not a typical WHG lineage, it’s a minor lineage in majority WHG groups, one that was acquired via admixture with early EHGs; only L754* and V2219/V2219>V88 have been found in majority WHG derived specimens. R1b-M73/Y13200 is the only R1b lineage found among Baltic HGs (no M269 has been found among them). Furthermore, the Samara EHG was R1b-M73/Y13200, so even if L51 came from the Baltic, it’s EHG in origin, just like P297>Y13200/M73. Anywhere there is M269, there is EHG and CHG. Not one M269 sample—let alone a sample bearing L51—has been uncovered without EHG or EHG + CHG autosomal DNA. There is not one non-steppe admixed, Baltic sample with R1b-M269. The vast majority of Mesolithic Baltic HGs have EHG DNA; all of the Neolithic Baltic samples have significant EHG ancestry—some even have steppe/Yamnaya-like admixture.

    You’re claim that it’s Narva admixture is fallacious. It’s Latvia_MN-like, not Narva-like, though Ukraine_Neolithic is an equal possibility (a mixture of both is also possible). Additionally, Latvia_MN is not even close to being pure WHG, they’re a mix (32.6%-35.1% WHG and 63.4%-67.3% EHG). So your ace in the hole, is the population with the most EHG out of the three (Latvia_MN is the best fit); moreover, steppe ancestry is present in at least one of the Latvia_MN samples. The fuckin irony. Additionally, the Afanasievo sample I6222 belongs to R1b-L51>P310*, so that debunks your bullshit right there.

    As for the Bohemia CWC dates, these are C14 age range estimates. The oldest R1a guy has a range of 2882-2673 BCE, while the oldest L151 guy has a range of 2914-2879 calBCE, so it’s possible that the R1a guy dates to the same time as the oldest sample with R1b-L151—they’re age ranges just barely cross over. This doesn’t matter anyway, because the R1a-M198, R1b-M269, and Q1b-FT380500 bearing males of the Bohemia CWC, all have identical autosomal profiles; all of them have Yamnaya-like ancestry. Are Q1b and R1a Baltic, WHG lineages now lol? These samples all have around 5-15% Latvia_MN/Ukraine_Neolithic/PittedWare-like ancestry, and R1a/Q1b have never been found in Yamnaya. Q1b and R1a being WHG is consistent within your fallacious, illogical framework. I’ll say it again, you have no evidence, no samples, no nothing. R1a, R1b, and Q1 arrived with ANE autosomal DNA, and they were spread throughout Europe by EHG derived groups (EHGs were the first HGs in Europe with ANE). There is not one, ancient R1b-M269 bearer without steppe related ancestry. Wherever M269 pops up, there’s EHG/steppe autosomal DNA. Keep it up with the Basque nationalist fairytales, your coping and goal post shifting is beyond incorrigible.

    ReplyDelete
  139. Is this schizo typing up his Basque nationalist manifesto on your blog? Who is he speaking for, he keeps saying “we,” like is he a spokesman for a Basque political party?

    ReplyDelete
  140. L51 and Z2103 both derive from L23, and L23 has a TMRCA of 3500-4800 BCE (median of 4100 BCE). So all Z2103 and L51 males share a L23 ancestor (one who lived around 3500-4800 BCE), this includes the Z2103 bearing Yamnaya males. Basically, if you’re arguing for a WHG or Narva origin for L51, you also have to argue for a WHG/Narva origin for Z2103. But seeing that we haven’t found one M269 sample without steppe related ancestry, the chances of an WHG origin are close to zero. All majority WHG specimens with R1b, have V2219/V88.

    ReplyDelete
  141. @Guy, really anyone's guess what the internal politics are... Possibly there's similar going on at other labs, so although they didn't really have a good schedule to release a lot of these papers, they have Frankensteined it all together to sort of get it out there before others. Or that the techniques all depended on samples they've only released here, but then I still would expect it to be multiple papers. It really should have been split up.

    The lack of scaleable vector graphics in the PDF is indeed a huge problem in its own right but particularly given that this how they present many results, without tables. (The data supplement is pretty limited for a paper with so many results!). It seems like a rushed export job that saved the graphics as unscaleable forms.

    I also think using their IBD clusters for the graphics can be quite confusing, since it's fairly cryptic where and when the samples in each cluster date from.

    For an example of contrasting this, I've done a few graphics using the results from their Table X that aim to show what they showed in Fig 5J, about how the initial Corded Ware Late Neolithic (and similar like early Beaker and Battle Axe) is 2 way mix between GAC_Poland and Steppe_EMBA, but other and later populations are diluted by admixture:

    https://imgur.com/a/nClJpSJ

    There are spatial and temporal patterns where the 2 way admixture of GAC_Poland and Steppe_EMBA remains strongest in the Scandinavian region, in their model, and is more diluted in other parts of Europe (although the total amount of Steppe ancestry is not always necessarily diluted). But it's really hard to see this from Fig 5J, which obscures a lot of this behind the IBD cluster labels, and then doesn't even put a copy of the IBD cluster legend by the figure!

    Its an interesting pattern that gives credence to the notion that most of the steppe admixture in Europe probably came via Corded Ware/early Single Grave cultures, but its quite obscure to understand via their presentation.

    (Also noticed while doing this, on an unrelated note, that they're put the Bronze Age Iberian sample COV20126 who is unusual for having I2 and steppe ancestry, who was dated at 1600 BCE in its original publication, 2000 years earlier in the Neolithic. Minor error.).

    ReplyDelete

  142. @simon stevin

    the debate between ANE and WHG as a source of the typical PIE y lines is outdated.
    We now know that ANE is predominantly a west eurasian cluster and in fact most of its ancestry is from deep in Europe ( aurignacian technocomplex) Basically ANE is
    75% aurignacian ( Goyet-Kostenki like). since aurignacians arrived in Europe through the balkans and the central mediterranean the logic conclusion is that most of ANE is just an older layer of WHG from a geographical point of view. proto ANE is intrusive in the eastern european palin just like WHG ( which ultimately derives from aurignacians too).
    ex oriente lux is a myth that has been crushed by ancient dna.

    one of the last paper on the subject

    "Beringia and the settlement of the Western Hemisphere"
    V V Pitul'ko, John F Hoffecker, E.Y. Pavlova.

    quote

    The HE 4 cold interval (40–38 ka) was followed by a protracted interstadial (GI 8) that apparently promoted rapid human population growth in the most biologically productive area of northern Eurasia. People in southwest Europe expanded eastward <38 ka and occupied the central East European Plain 38–32 ka (e.g., Kostenki)20. Their earliest known representatives in Northeast Asia (Ancient North Siberians [ANS]) are found at the Yana River site complex in western arctic Beringia dating to ~34–32 ka21 (see Figure 3). Younger representatives of the same lineage (Ancient North Eurasians [ANE]) are found in southern Siberia during and after the LGM at Mal’ta (~24 ka) and Afontova Gora (~17 ka).

    ANE and WHG came from the same regions with the obvious difference that ANE has also east eurasian ancestry that lacks in WHG.
    It is over.

    ReplyDelete
  143. @Old Europe

    My understanding is that WHG (Villabruna) is mostly Dzudzuana-like, with around 15% Vestonice, and minor ANE. ANE on the other hand, is mostly Kostenki/Sungir-like, with some minor ancestry related to Tianyuan. I don’t recall anything about ANE having Aurignacian, as in GoyetQ116-1 related ancestry. We can differentiate WHG and ANE ancestry, and Y-DNA P lineages don’t show up in Europe until after ANE autosomal DNA arrives. Tianyuan and IUP related groups, had Y-DNA K2 as well. A shared descent through Sungir/Kostenki-like populations, doesn’t negate genetic differentiation or the genetic distinctions between ANE and WHG. Drift, founder effects, selection, bottlenecks, common population specific genetic markers, and novel/rare population specific genetic markers produce discrete populations, even among deeply related groups. We can detect Anglo-Saxon admixture via the autosomes and sex chromosomes, despite their close genetic relationship with the British Celts. What’s more, we’ve yet to see a Y-DNA P bearer among Gravettians and Aurignacians.

    ReplyDelete
  144. The article Old Europe linked suggests a dual route into North America, with Yana-like lineage being earlier, then a more ANA-related group moving in after 17,000 bp. I did not pick up discussion there about WHG -ANE relations.

    ReplyDelete


  145. kostenki is an aurignacian site and also we the Siuren ( Crimea) site that is aurignacian too that reinforce the eastward spread of the aurignacian dna. Inside the aurignacians there were three genetic signals
    Villabruna like
    Goyet like
    Kostenki like

    the western side of ANE obviously was from a combination of all these.
    As per the relation between Dzudzuana and Villabruna you have got things the wrong way. There is Villbruna in Dzudzuana not the other way round. This is clear also as per the 2019 paper on the gravettians origins.

    The origin of the Gravettians: genomic evidence from a 36,000-year-old Eastern European
    View ORCID ProfileE. Andrew Bennett, Sandrine Prat, Stéphane Péan, Laurent Crépin, Alexandr Yanevich, Simon Puaud, Thierry Grange, Eva-Maria Geigl


    Quote
    The absence of the “Common West Eurasian” ancestry, as represented by Villabruna, in BuranKaya3A marks a key genetic distinction between the Gravettian inhabitants of Buran-Kaya III, possibly including the broader populations of EUP Eastern Europe as well, and the UP populations of Western and Central Europe, which is characterized by a West-to-East reduction in “Common West Eurasian” ancestry (seen in Extended Data Figure 10)


    This means that at 36000 BC Villabruna dna was in western europe but not in eastern europe ( let alone the caucasus). In fact you can model the Vestonice cluster as a mix of Villabruna and Kostenki which makes a lot of sense geographically.

    the y dna is still unsolved. there were rumors of a finding of P in the gravettian era Bacho Kiro sample BK1653 ( 33000 BC) but it has not been confirmed yet.

    ReplyDelete

  146. R1b-L754 Villabruna is Epigravettian (12.000 BC) and everyone knows that Gravettian>Epigravettian

    So you have the oldest case of R1b linked to WHGs and yet there are people who are unable to accept it. When you find an R1b in Russia, Siberia or Ukraine older than Villabruna then you will be able to say that it is a typical lineage of the eastern HGs, meanwhile you will have to accept the reality.

    ReplyDelete
  147. The preprint by Marchi (https://www.biorxiv.org/content/10.1101/2020.11.23.394502v2 - "Demogenomic modeling of the timing and the processes of early European farmers differentiation") which we've discussed on here before, has now been published in Cell:

    https://www.cell.com/cell/fulltext/S0092-8674(22)00455-X

    I believe some folks on here were critical of this paper for the model showing split of WHG and Anatolian HG at around the time of Dzudzuana. I wonder if this has any more credence given models from the recent "Genomics of Stone Age Eurasia" that modelled WHG as mostly from the Dzudzuana population, or if that model just still seems really bad.

    I think there model here, which proposes Iran_N as an unadmixed population in a clade with one ancestral to ANF, may be contradicted by the data from Dzudzuana Cave.

    ReplyDelete
  148. So the Corded Ware samples that were radiocarbon dated by a reputable lab (Curt-Engelholm-Zentrum Archaeometrie in Germany) are too "early" for your liking because they go against your argument. That has got to be the weakest genetics counter-argument of all time.

    Hum, should we trust the reputable scientists at the reputable Max Planck Institute or some arm-chair blogger that has shown a bias towards Western Europe, time and time again? C'mon man.

    ReplyDelete
  149. Gravettian and Aurignacian are mostly C/F/I Male with M1 and U2 Females. Similar to AASI in South Asia like C/F/H with M and R Females.

    ReplyDelete
  150. @Old Europe

    That’s making the assumption that Villabruna is a pure, un-admixed component, which is pretty unlikely all things considered. For one, it has ANE related ancestry and R1b-L754. Secondly, Villabruna can be modeled as a mix of Dzudzuana, Vestonice, and ANE. Thirdly, Villabruna dates to 12268-11851 calBCE. So we’re supposed to believe that for over ten thousand years, 100% pure Villabruna-like populations spawned out of the Balkans/Italy, and received no admixture from other HGs, but they admixed into much older groups sporadically (Vestonice and Dzudzuana)? Seems fallacious, heavily presumptuous, and anachronistic to model much older populations as being partly derived from much younger (over ten thousand years younger), “pure” populations/components. There is not one Gravettian and Aurignacian sample with K2b or P. I’ve also never seen Kostenki14 referred to as an Aurignacian—I believe the Sungir samples are classified as Eastern Gravettian. The only confirmed Aurignacian sample I’ve seen with Y-DNA, is GoyetQ116-1 (33678-32771 calBCE). Regardless, I don’t think the Aurignacian archaeological label helps that much, especially when we consider the genetic discreteness between the Kostenki-Sungir clade, the Goyet clade, and the Bacho Kiro IUP/Oase clade. These IUP/UP HGs could share an industry/material culture, and still be genetically distinct from one another (novel/rare and common population specific SNPs, drift, selection, etc.), and they are genetically distinct—though related—from one another.

    @Gaska

    Villabruna has ANE admixture, and is negative for P297, V1636, and PF6323 (V2219). He has no calls for L389 either, so he is in no way relevant to M269 or P297. Villabruna dates to 12268-11851 calBCE, while P297 formed from 15600-11800 BCE (median: 13600 BCE), and its TMRCA is 12900-9800 BCE (median: 11300 BCE); L389 formed around 16900-13300 BCE (median: 15100 BCE) and its TMRCA is 15600-11800 BCE (median: 13600 BCE). So if he was relevant, he should have at least carried P297—which existed right before Villabruna—but he didn’t, he didn’t even have calls for L389. R1b-L754 formed around 21300-15500 BCE (median: 18400 BCE), and its TMRCA is 16900-13300 BCE (median: 15100 BCE), so Villabruna lived at least 3300 years after the first L754 bearer. That’s plenty of time for admixture to arrive from eastern, ANE admixed populations (EHGs), you know, the same hunter gatherers who were geographically closest to where the ANEs lived—ANEs are the oldest R/Q bearing populations on record too. Furthermore, 21300-15500 BCE is around the time R1b-L754* ended up in the WHG gene pool (via ANE admixed populations (EHGs) from further east); the paper “Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily“ (2022), uncovered EHG gene flow into Sicilian WHG populations—this started around 6800 BCE at least.

    ReplyDelete
  151. @ AWood


    ''of course the earliest split of R1b with PH155 being somewhere in Mongolia or Kazakhstan where they most closely resembled ANE as late as 1000 BC in China.''

    Were are these 'long lost Tarim-ANE'ans '' ?

    Pre-Afansievo Mongolia & the Altai region lack Y-hg R. The 2 new HGs in this featured Study from Sayan-Altai region belong to Y-hg C & Q1.

    ReplyDelete
  152. Here’s another reminder to our slow Basque friend: Villabruna has ANE. Villabruna is negative for FGC21012 (V2219 equivalent), P297-equivalents, and V1636-equivalents. He has no calls for L389. Therefore, Villabruna is not relevant to P297, since it already existed before him, and he didn’t belong to it (he didn’t belong to L389 either lol). Just because a sample is found somewhere with a certain lineage, doesn’t mean that lineage originated there, especially when we consider autosomal DNA, formation dates, and the clade’s TMRCA. R1a-YP4132 (formation: 10200 BCE, TMRCA: 4200 BCE) didn’t originate in the Andronovo sample I4773 (1463-1568 BCE), despite the fact that he’s the first sample we’ve found with YP4132. So Villabruna man is a genetic dead end with ANE. He is not relevant to M269, L754, L389, or P297. Just because he was found in northern Italy with L754*, doesn’t mean that’s where those lines originated. EHG has a lot of ANE. R1 comes from ANE ultimately, so deductively it makes that this clade originated in the most ANE rich groups, located in Eastern Europe, which is the area of Europe closest to where ANEs lived (Siberia/North Asia).

    Oh and the Balkans HGs with R1b have significant EHG ancestry, which is where the EHG autosomal signal in the LM Sicilian HGs and Villabruna likely came from. From Mathieson et al. (2018): “Modeling Iron Gates hunter-gatherers as a mixture of WHG and EHG (Supplementary Table 3) shows that they are intermediate between WHG (~85%) and EHG (~15%). However, this qpAdm model does not fit well (p=0.0003, Supplementary Table 3) and the Iron Gates hunter-gatherers show an affinity towards Anatolian Neolithic, relative to WHG (Supplementary Table 2). In addition, Iron Gates hunter-gatherers carry mitochondrial haplogroup K1 (7/40) as well as other subclades of haplogroups U (32/40) and H (1/40) in contrast to WHG, EHG and Scandinavian hunter-gatherers who almost all carry haplogroups U5 or U2. One interpretation is that the Iron Gates hunter-gatherers have ancestry that is not present in either WHG or EHG. Possible scenarios include genetic contact between the ancestors of the Iron Gates population and a NW Anatolian-Neolithic-related population, or that the Iron Gates population is related to the source population from which the WHG split during a re-expansion into Europe from the Southeast after the Last Glacial Maximum.17,37.” Oops sorry buddy…they have EHG too. So sad. You’ve been refuted once again.

    ReplyDelete

  153. ''My understanding is that WHG (Villabruna) is mostly Dzudzuana-like, with around 15% Vestonice, and minor ANE. ''


    The 'problem' with the latter position is that it doesn't square up with uniparentals. Of course, genome-wide data is 'more powerful' for analysis & simulations, but uniparental data provides a straighforwrad ''sanity check''
    The Buran Kaya genome from Bennet et al - dead end lineage
    Duzudzuana - dead end lineage
    the Kotais_23K - J2b. the mtDNA U4/9 is interesting, although not exactly pathognomonic of WHGs

    In sum, no clear evidence of sweeping migration from Caucasus to Europe c. 26,000 bp in the archaeological or uniparental record.

    If you take away the ANE-related R1b which appears in Epigravettians, the prevalent lineages (Y-hg I & mtDNA U5) were already present in the Vestonice Gravettians, although the spcific Vestonicians evacuated central Europe and shifted to Hungary, the northern Balkans and west Ukraine.
    This means that genome-wide analysis is potentially insensitive to ''real-life'' events which entailed a series of demographic events, resulting in significant G-W 'shifts' due to a multipleier effect phenom. Insensitive, that is, if the analyist doens;t incorporate other evidence and takes their stims at face value as something representing reality



    ''https://www.cell.com/cell/fulltext/S0092-8674(22)00455-X

    I believe some folks on here were critical of this paper for the model showing split of WHG and Anatolian HG at around the time of Dzudzuana. I wonder if this has any more credence given models from the recent "Genomics of Stone Age Eurasia" that modelled WHG as mostly from the Dzudzuana population''


    I see what they're saying now, seems like theyve modified their suggestion, images are nice. European & West Asian populations split by 26,000 , due to diconnection resulting from 'Ice Age', rather than positing a migration from West Asia into Europe 26,000. However, Eurasian populations weren't just 'budding off' repeatedly, but also re-joining, migrating, admixing etc. Hence, although imperfect, qpGraph has the potential to sketch out a more 'realistic', longue-duree, reticulating typology of populations.
    One error here is their calling Loschbour/ Bichon as 'West European I' in western Europe 20K BP. But at this time in western Europe you had the Goyet-Q2/ El Miron group, ignored in this study. The Bichon group only arrived after 14,000 bp, as documented in Posth & Fu, meaning the West Euro I & II only split c. 14,000 bp, not 20,000 bp, although some gene-flow between the 2 occurred (because Goyet -Q2 isn't simply Goyet-Q116).




    ReplyDelete
  154. also RE: Marchi et al. The view that pre-27K populations are 'hardly structured" doesnt ring consistent with other studies.

    ReplyDelete
  155. @Rocca

    No one has doubted the published dating on Bohemia, quite the contrary, because they reinforce the hypothesis that R1b-L51 males and some steppe women (exogamy) arrived 175>250 years earlier than M417, Q1b and Z2103 males. If 51 arrived from the east, he did not arrive in the same migration as the rest of the male lineages. And of course, we must trust Max Planck, in fact they has published the best genetic paper I have read in a long time, among other things because he has given me the reason on issues that I have long defended-Western origin of P312 and BB culture, genetic difference between BB culture and CWC, and the recognition that the Yamnaya culture is not the origin but the sink of R1b- There is no way to connect Yamnaya, CWC and BBC by male lineage. That is, if you trust Max Planck, you also trust Gaska, I am afraid that many supporters of the steppe theory do not agree with these conclusions because they still defend the origin of M417 and L51 in Yamnaya-Afanasievo.

    Do you think that these lineages originated in the forest steppe (Sredni Stog) as Papac and colleagues advocate?

    ReplyDelete
  156. @ Rob

    I see what you’re saying, and I’m not interpreting these genetic relationships literally. I don’t think Villabruna has direct admixture from the Dzudzuana samples, but there is some connection to an older source population—a common ancestor to both samples. I’ve also read that Villabruna man lacks Basal Eurasian, and Basal Eurasian was found in Dzudzuana, so that alone discredits direct admixture. “Dzudzuana-like” and “Vestonice-like” are more appropriate and descriptive. By the way, do you have a link to any of your models concerning WSHG?

    ReplyDelete
  157. Rob: "One error here is their calling Loschbour/ Bichon as 'West European I' in western Europe 20K BP. But at this time in western Europe you had the Goyet-Q2/ El Miron group, ignored in this study. The Bichon group only arrived after 14,000 bp, as documented in Posth & Fu, meaning the West Euro I & II only split c. 14,000 bp, not 20,000 bp, although some gene-flow between the 2 occurred (because Goyet -Q2 isn't simply Goyet-Q116)." .

    Yes they do ignore samples without high coverage whole genome data which likely misses lots. Though even El Miron at 18.7 KYA itself though actually already seem to have some "WHG/Iron_Gates" ancestry at 40% (per Fu's model) compared to previous populations in Europe, and note that El Miron I believe actually has more of this than some samples from further north (as you say, HohleFels49 at 15 KYA), which offers some minimal support to a cline of this ancestry in Europe. Not just a continuation of prior groups from earlier Upper Paleolithic.

    There's some reason to doubt that this ancestry was that persistent in Iberia even by the Mesolithic or Late Upper Paleolithic, as the main HG I'm aware of that showed good evidence of persistence of this was I10899, and there seems to be uncertainty about its date (I10899 was called Iberia_Meso and given a date of 9700-5500 BCE in its original paper... But Reich Lab's anno which implies there's a higher coverage unpublished version and that this one is contaminated, gives a ridiculous date range of 40000-5000 BCE!). The sample BAL051 by 13KYA BCE is much more of a regular Late UP / Mesolithic European HG person. (And likewise the sample NEO694 at 11KYA from Spain in the new Willerslev group paper is also like this).

    We also have the oldest HG in Italy, Tagliente at 16.7 KYA who is a fairly representatively Late UP / Mesolithic European HG person and has some features of being genetic ancestral to later Western European HG specifically (not an undifferentiated sample). He's nicely supplemented by San Teodoro 3 from the Willerslev paper from 16.8 KYA who seems the same.

    The paper on Tagliente also suggests that this change can be associated with the Epigravettian in Italy - https://www.biorxiv.org/content/10.1101/2020.08.10.241430v1.full - at "about 18-17 ka ago at the beginning of southern Alpine deglaciation" (which is later than their 23 kya split albeit!).

    That in mind, I don't think it's impossible to think that the "WHG like" population may have replaced others in Italy and split off by 20,000 YBP. (Whether we can appropriately call Italy Western WHG or not, another question). So a model of a structured "Italian" and "Ukraine/Balkan" HG beginning by around this period might not be tenable, with the latter maybe undergoing slightly less drift and slightly more admixture from ANE and into Near East HG. As proposed by the Willerslev group preprint. Then these populations expand after LGM and the mixed El_Miron like cluster becomes some minor admixture into the expansion from Italian refugium. There's not any actual direct evidence for WHG in Italy or Ukraine/Balkan region during or just prior to the LGM though, but its not a crazy inference.

    (end p1)

    ReplyDelete
  158. (cont p2) The Marchi paper here is proposing that the broader WHG group (ancestral to "Italian" and "Ukraine/Balkan" refugium) underwent a large shared founder effect early on (expanding from a few founders), due to climatic change, but thereafter maintained a fairly high population size, so the effects of separate drift between "Italian" and "Ukraine/Balkan" HG were not that large relative to the time they'd actually been separate before we begin to see first samples with differentiation (about 6,000 years?), which is kind of an interesting suggestion. They beleive they can separate time from when the largest founder effects take place, better than f-stats can. I don't know if y-dna or high resolution mtdna can further help sort this stuff out at all! (What are the estimated time splits in the I2 clades? etc)

    Regarding the Near East side, there does seem like a potential big problems in them:

    1) suggesting that early Iran_Neolithic represents a population that is relatively undrifted and is close to the ancestral population for Near Eastern populations. That's kind of an inconsistency with the 'PopGen of Stone Age Eurasia' which shows that the sample projects on PCA fairly close to the centre of the West Eurasia PCA (https://imgur.com/a/M8569OW) overlapping close to Europe today and without a position overlapping Iran_N. Seems wrong.

    2) their suggestion for the formation of the Anatolian genome at 12.9 KYA is obviously already contradicted because Pinarbasi HG already exists at 15.7 kya, and most likely would represent a gene pool that formed at least a couple of thousand years before this.

    I also repeat my objection (which I commented to the authors on their Biorxiv) around their model fitting that they have no excuse not to include at least Ust Ishim in the graph fitting. He's high quality, whole genome, and should drive the emergence / non-emergence of Basal Eurasian, and test how much it works to have an unstructured proto-West Eurasian population that expands at 26 KYA. So it's very strange not to include him.

    ReplyDelete
  159. @Gaska - Maybe the problem with the large current population of R1b in western Europe is simpler than all this. Maybe the question is where did they all come from?
    Might also be a question about R1a, too.

    What's come back from these papers is that this was not a simple migration from someplace in the east and we see they moved into the west. It wasn't Yamnaya moving from the steppes to Ireland. So who was it is an honest question. Yes, they were related, but it wasn't them.

    We can look at the people who currently live in US or North America and pretty much say that they are the direct descendants of people who lived in Europe or Africa a thousand years ago. But you can't seem to do that with R1b.

    It doesn't seem to work with R1b. It wasn't here they are in 3000 BCE and they "migrated" and here they are in western Europe and here the ones who stayed behind. Not like you can say the Irish migrated to America from Ireland and look there are still Irish in Ireland and they are directly related.

    Gaska - if you put it that way, you may be getting closer to the real mystery about all this.

    ReplyDelete
  160. Gaska... When the first DNA samples of Yamnaya and Corded Ware came out, it seemed like a matter of time before R-Z2103's sibling R-L151 would be found in Yamnaya as well. However, as the R-Z2103 samples kept piling up, I was the first one to really start to question that and pointed at Corded Ware as the real mover for R-L151, and then David produced the autosomal evidence to back it up. The most realistic conclusion is that the earliest Corded Ware clans to move west included R-L151 from the Forrest Steppe zone with some kind of mixing with Baltic and/or GAC populations. From an archeological viewpoint, the triangle bone belt clasps seem like the breadcrumbs to track these movements as they appear in Bohemia, Germany Poland and the Baltic. The males that were buried with these and tested so far are R-L151(xU106,P312), R-U106, R-M269 (low quality) and I2a1. In this case, I2a1 seems like an early Corded Ware mover as well.

    ReplyDelete
  161. Back on the main comment paper:

    Steppe Ancestry from Supplementary Table X Crossplot Against Sample Date - https://imgur.com/a/64COjpM

    Similar pattern to what we see in previous papers (e.g. in data from Papac 2021); entry of steppe ancestry to Europe west of the Pontic-Caspian steppe around 3000/2900 BCE, then dilution over time to around 60% by 2500/2300 BCE. So from that time scale about an average of 3 - 1.7% reduction per generation (between 1/30 surviving reproductions per generation to 1/59).

    Btw, question to the commentariat here; what do you guys think of the sample NEO792? He's the Danish sample with the highest tested steppe ancestry, though he's not earliest (around 2500 BCE), but he has I2a1a2 and was buried in a Megalithic burial (with a trepanation), and also carries an mtdna under U2 which they state is closely related to some individuals on the steppe.

    Does his y haplo this seem like steppe or farmer (ultimately via HG) I2a1a2 to you guys? I'm tempted to explain his y-dna as being linked to the early phase of steppe ancestry introduction into Europe west of the steppe where Papac described there being a little bit more diversity in y-dna that was reduced later on, but maybe this is trying to hard to fit it into a model.

    ReplyDelete
  162. @Davidksi

    David what’s your take on the Marchi paper only using high quality whole genomes? Is that really necessary when modeling populations and figuring out their genetic structure?

    ReplyDelete
  163. @ Matt


    ''Yes they do ignore samples without high coverage whole genome data which likely misses lots. Though even El Miron at 18.7 KYA itself though actually already seem to have some "WHG/Iron_Gates" ancestry at 40% (per Fu's model) compared to previous populations in Europe, and note that El Miron I believe actually has more of this than some samples from further north (as you say, HohleFels49 at 15 KYA), which offers some minimal support to a cline of this ancestry in Europe. Not just a continuation of prior groups from earlier Upper Paleolithic.''

    Vilalba-Muoco re-sequenced Goyet-Q2, with higher coverage. they might have missed that. But you dont really need super high coverage to understand that the Goyet-Q2 genuinely is distinctive to the so-called Villabruna cluster. Paleolithic archaeologists are pretty onto it (not having been softened by post-modernism ) , and the uniparental data (mtDNA U8a vs U5b_) is also supportive. Therefore its a major error they have committed. Even if they excluded data (a dubious approach), they appear to have misunderstood the chronologies withn their claims


    ''There's some reason to doubt that this ancestry was that persistent in Iberia even by the Mesolithic or Late Upper Paleolithic, as the main HG I'm aware of that showed good evidence of persistence of this was I10899, and there seems to be uncertainty about its date (I10899 was called Iberia_Meso and given a date of 9700-5500 BCE in its original paper...)''


    I do not have much doubt that Iberia is distinctive, regardless of the dating of I10899. We have post-14K genomes from Balma Guilanya which have elevated Goyet-Q2 related ancestry. Even though the Mesolithic Iberians were inundated by WHG, they still have preserved elevation of Goyet-Q2 ancestry with qpAdm, some as much as 50%, eg Portugal mes (Which is shy papers like Rivollat used that feature as a means of sifting though different neolithic waves)
    So Iberia is different to rest of Europe - early WHG ancestry in El Miron (although this could be something different), whilst Northwest lacks it, then followed by preserved G-Q2 whilst it dropped precipitously north of Pyrenees after 14K bp. Agains, this is consistent with uniparentals, as Iberian HGs feature Y-hg I1 and C1a, missing in Italy and post-14K northwest Europe. Lastly, Iberia's distinctive is supported by paleodemographic models.

    The ancestry in LUP Italy is entirely expected, because they are epigravettians. But Italy isnt in western Europe, and Iberia isn;t epigravettian, so it doesnt change the errors in Marchi it el.
    In short- the WHG cluster did begin to split already at 25K, but it only reached NWE after 14K.


    ''their suggestion for the formation of the Anatolian genome at 12.9 KYA is obviously already contradicted because Pinarbasi HG already exists at 15.7 kya, and most likely would represent a gene pool that formed at least a couple of thousand years before this.'''

    I think Pinarbasi is fairly distinctive to Neolithic Anatolians

    ReplyDelete
  164. ''their suggestion for the formation of the Anatolian genome at 12.9 KYA is obviously already contradicted because Pinarbasi HG already exists at 15.7 kya, and most likely would represent a gene pool that formed at least a couple of thousand years before this.''


    Also, I think Feldmen et al were way off when they painted ANF as 90% Pinarbasi. A lot of the blogosphere has uncritically accepted these claims
    I'd say the continuity is closer to 30-40%

    ReplyDelete
  165. @Simon

    The peer reviewers of that paper should've asked the authors to back up their strange findings with a different method and with uniparental markers before letting it through.

    But I guess they were too stupid and/or lazy to do so.

    ReplyDelete
  166. Boncucklu_N is 87% Pinarbasi + 13% IranN (https://pastebin.com/peKLqXLf)
    Barcin_N is 76% Boncuklu_N + 3% Iran_N + 21% Levant_PPN. (https://pastebin.com/n0P4Mvvd)

    P-values are not great but for proportions, the models should suffice.

    ReplyDelete
  167. @Rob: The Balma Guilanya at 12kya in NE Spain does look like it could be modelled as 50% El_Miron and 50% OrienteC HG. Following Fu's model then probably we'd expect it to be 70% from the "WHG/Iron_Gates" ancestry clade and 30% previous Goyet Q116.

    Later in the Mesolithic we then get La Brana in NW Spain that dilutes this by 50% again (something like 85% "WHG/Iron Gates", 15% GoyetQ116), and some El Miron blends survive only in the far NW and SW (Moita de Sebastiao) and Chan do Lindeiro.

    (Specific excerpts: https://imgur.com/a/dYZEzql)

    My point wasn't to defend exactly the authors' map, which in terms of where the think populations were is largely supposition that ignores the shotgun or lower quality capture dna. But to point out that the geneflow makes it more plausible that the WHG group had already expanded and was split at this time and slowly expanded over time. Whereas you were suggesting that the Balkan (West II) and non-Balkan/Italian (West I) branches split "only split c. 14,000 bp, not 20,000 bp" - e.g. which seemed to imply some kind of late scenario where there's only one unstructured refugium alone largely repopulates Europe after the LGM.

    If the suggestion is instead different on the split dates and like your subsequent post where you have said now: the WHG cluster did begin to split already at 25K, but it only reached NWE after 14K, then that I'm in agreement with that and don't dispute that.

    Pinarbasi might not be a member of a broader population that was 100% ancestral to Boncuklu and Barcin (only 30-40% just intuitively seems like a stretch though), so fair enough, but I think it does directly evidence that the formation process for the population and its principal distinctive genetic drift was earlier than their model suggested.

    ReplyDelete
  168. This comment has been removed by the author.

    ReplyDelete
  169. @ Matt

    We knew that ElMiron (@ 18kyBP, so considerable after end of LGm) has some WHG admixture due to the original publications. And that was some precocious co-mingling coming via Italy, not a separate refuge (although Western Europe was indeed separate, but nothing to do with WHG).
    Even Italy was “not separate” at 20kyBP, but part of the same “community”. If we want to speak about separation, then it’s after 15 kyBP; when epigravettians truly began to split - some moving ever southward to Italy and Greece, others north into central Europe , & the rest increasingly fragmented in the homeland which became increasingly forested


    “ which seemed to imply some kind of late scenario where there's only one unstructured refugium alone largely repopulates Europe after the LGM.”

    No such implication was made because i made numerous references to the western refuge (GQ2 pops)
    But WHG came from one (broad) region which did not encompass Western Europe until fairly late on, ElMiron considered

    ReplyDelete
  170. This comment has been removed by the author.

    ReplyDelete
  171. @Rob, at this point, this discussion ends to await further fossils and dna, of samples of the age of Tagliente but outside Spain and Italy, and identify directly how much substructure actually existed at this time, which cannot be known without such samples.

    Re; Pinarbasi, I just want to note that I don't have a strong preconception that Barcin itself isn't immediately derived to some large degree from some population outside of NW / Central Anatolia. This is possible, but it would have to some degree to represent a reflux of a population that was derived from the developing Anatolian population, rather than merely a "dilution" of Pinarbasi by Iran_LUP, Natufian.

    ReplyDelete
  172. @Mr Slow Stevin-

    WHGs does not only refer to their geographical location (Western Europe), but also to their autosomal composition. All HGs can be modeled as a mixture of western and eastern HGs, and depending on their percentages they are classified in one or the other category - it is evident that even in geographically located areas in eastern Europe the HGs were mostly western (Baltic-Lithuania>90 % and Balkans-Iron Gates>85%) and all of them were overwhelmingly R1b (regardless of their subclade). Even the Ukrainian-HG have a strong Western component (>40% according to Patterson, 2.021). The only subclades of R1b older in Ukraine/Russia than in the West are V1636 and Z2103 and neither of them is relevant to the history of L51>L151>P312. I have already told you many times in order to consider R1b as a typical lineage of the HGs you need samples older than Villabruna, meanwhile Bla bla bla bla bla. Your theory that R1b is the typical lineage of the EHGs is hilarious, your efforts to qualify Villabruna as irrelevant to the genetic history of M269 are pathetic and pretending that you can give genetics lessons to me or anyone else only shows your ignorance. A person who thinks that P310 has its origin in Mongolia is genetically illiterate.

    ReplyDelete
  173. Mr Rocca-

    You have changed Steppe-Yamnaya to Forest Steppe-CWC, but you still can't find R1b-M269>L51. I wish you luck, you're going to need it.

    ReplyDelete
  174. im getting some surprising results for Okunevo with qpAdm. Damgaard quoted a mere 20-30% Afansievo levels (but they did not compute with qpAdm)
    I'm getting up to 50% Afansievo, 50% Shamanka_BA (Fairly standard set up). Although they are almost all Y-hg Q1a. Seems like a male mediated takeover

    ReplyDelete
  175. @Gaska (not sure if this is unacceptably off topic or not, but…)
    Surely the linguistic evidence of Etruscan, not DNA, are what show whether Etruscan was an IE or non-IE language?

    ReplyDelete
  176. @Davidski
    There is some good evidence that a specific subset of Germanic words have a common root up and down the Atlantic coasts, from the late bronze age Iberian culture package that also resulted in stelae in Scandinavia that reproduce the same themes as the Iberian ones. (The chariots, weapons etc).
    E.g. see “Rock art and Celto-Germanic vocabulary: Shared iconography and words as reflections of Bronze Age contact” — John T Koch.

    ReplyDelete
  177. @vAsiSTha

    The only Anatolian Neolithic samples that can be modeled with Pinarbasi with a decent fit are some from Boncuklu (024, 001, 031). They are also very close geographically and quite possibly had actual ancestry from the local population represented by the Pinarbasi sample.

    Also you should be careful using Levant_PPNB as a source for this purpose, because they are heavily Anatolian admixed (Natufian + Anatolian, with Anatolian in the 30-50% range or so), so their affinity to Anatolian N samples might due to the source of Anatolian in Levant PPNB and not the other way around.

    We should consider that Pinarbasi was possibly not typical for its time among ancient Anatolians.

    I tried something: I substracted Villabruna from Pinarbasi with a 0.075 weight in G25 nMontes and included it in the test. It could be probably done better (with different WHG and different assumed admisture ratio), I just made a shot in the dark, but all Anatolian N and Levant PPN samples picked this artificial "sample" against actual Pinarbasi overwhelmingly or even exclusively, except Boncuklu. So Pinarbasi might had a WHG ancestry that was otherwise missing from the contemporary ancestors of most Neolithic Anatolians, except Boncuklu that had ancestry from the WHG admixed Pinatbasi population.

    ReplyDelete
  178. This comment has been removed by the author.

    ReplyDelete
  179. This comment has been removed by the author.

    ReplyDelete
  180. @Gaska "And I have news for you, any of these samples could be the parent or grandparent of R1b-L51, however, there are no cases of R1b-L754>M269 in Ukraine or Russia, so there is not even the possibility of finding the ancestors of L51 in that region."

    Why do you have such a hard time grasping Y-DNA phylogeny? The R1b-L51 block descends from R1b-L23 which is at least from 6100 ybp or about 4140 BC. Any of your 9 samples that are that old or younger that do not have R1b-L23 or an equivalent cannot possibly be an ancestor to R1b-L51. So your samples that from 4140 BC or younger are definitely not positive for R1b-L23 because they would be known. You even admit that you don't have proof that all of your 9 samples are definitely positive for R1b-M269. Go ahead and post your samples that are older than 4140 BC that you think are positive for R1b-M269 so we can see your proof of the existence of these important specimens and their eye-opening results.

    ReplyDelete
  181. @ Matt

    “ await further fossils and dna, of samples of the age of Tagliente but outside Spain and Italy, and identify directly how much substructure actually existed at this time, which cannot be known without such samples.”

    Sure but you’d need to look to the balkans and south EE, not France / the rhine (as drawn in this study)
    And it won’t really change the fact that between 25-15kbp, the epigravettian was still one social organism/ mating network

    ReplyDelete
  182. This comment has been removed by the author.

    ReplyDelete
  183. @Gaska "The only subclades of R1b older in Ukraine/Russia than in the West are V1636 and Z2103 and neither of them is relevant to the history of L51>L151>P312."

    You still have no understanding of what we have explained to you. Z2103 and L51>L151>P312 descend from L23. There has never been a specimen from western Europe dated to before 3500 BC that has been found to be positive for a subclade of L23. Additionally, there has never been a specimen positive for a subclade of L23 that did not have Steppe autosomal DNA. Since you keep repeating your nonsense we will keep repeating facts.

    ReplyDelete
  184. @slumberry

    "Also you should be careful using Levant_PPNB as a source for this purpose, because they are heavily Anatolian admixed (Natufian + Anatolian, with Anatolian in the 30-50% range or so), so their affinity to Anatolian N samples might due to the source of Anatolian in Levant PPNB and not the other way around."

    I dont think so. Levant_PPN samples are dated to around 8000-7000bce. Boncuklu dated to 8000bce (they dont show levantine input) and Barcin to 6500-6000bce. I dont think theres any direct barcinN input into PPN, that would be anachronistic.

    "We should consider that Pinarbasi was possibly not typical for its time among ancient Anatolians."

    Maybe something similar to Pinarbasi, but not exactly, was the true ancestor of neolithic anatolians.

    @Rob
    "None of 3 samples had C14, but presumed to be 2500-1500. Means virtually unadmixed Srubnaja reached as far down as Samarkand"

    The latest anno file has 2 of the 3 samples dated to 1700bce and 1400bce respectively.


    ReplyDelete
  185. @Rob, yeah, that's where you would have to sample to find out if there's any differentiation already.

    ReplyDelete
  186. For discussion, I have the L51 phylogenetic tree:

    http://www.tropie.tarnow.opoka.org.pl/images/ancient-cwc.l-51malopolska-podkarpacie-czechy.jpg

    ReplyDelete

  187. "I dont think so. Levant_PPN samples are dated to around 8000-7000bce. Boncuklu dated to 8000bce (they dont show levantine input) and Barcin to 6500-6000bce. I dont think theres any direct barcinN input into PPN, that would be anachronistic.

    Yes, of course. I meant that the Anatolian ancestors of Levant_PPN were not symmetrically related to the _ancestors_ of the other Anatolians and Pinarbasi. More specifically I think that in the time-depth of the Pinarbasi sample the Anatolian ancestors of levant PPN were closer to the ancestors of Barcin N and the other similat groups than to Pinarbasi.
    If we would like to determine southern input into Anatolian Neolithic, it is "cleaner" to use Natufians.

    "Maybe something similar to Pinarbasi, but not exactly, was the true ancestor of neolithic anatolians."

    Similar, one main difference being the WHG mixture that is present in Pinarbasi, but is not present (or at least significantly smaller) in the ancestors of Barcin N, Catalhoyuk, Kumtepe, Tepecik_Ciftlik and Levant PPNB. That might be the reason why Pinarbasi as an ancestor results in bad fit for those populations. Because the Paleolithic WHG admixture (that was pointed out by the original Pinarbasi paper too) was not universal or was at least uneven.
    (This also suggests that the Pinarbasi / Boncuklu group was possibly a bit of an isolated pocket, as there is an apparent population continuity for several millennia.)

    ReplyDelete

Read the rules before posting.

Comments by people with the nick "Unknown" are no longer allowed.

See also...


New rules for comments

Banned commentators list