Wednesday, January 20, 2021

Good Start to Year.. SGC DNA

Eurogenes' prediction that the Single Grave Culture is the root source of pan-European Bell Beaker lineages is starting to show some fruit.

A new paper is on the street, Genomic Steppe ancestry in skeletons from the Neolithic Single Grave Culture, by Egfjord et al, 2021.

Here, we have our first SGC Y-profile from Gjerrild, in Jutland and he is indeed R1b.


But there is an exciting twist.  He's R1b-V1636!?

If we assume that this peculiar lineage wasn't pushed to the front of a queue of SGC genomes awaiting release because of its weirdness, the simple probability is that the Single Grave Culture did indeed harbor the cradle from which founders would begin emerging.

This doesn't mean we won't eventually find V1636 in some random Beaker, or much later in Medieval Europe, just that it was not a particularly successful lineage in a sea of exploding L51's.  As Davidski comments, given that V1636 can be more concretely tied to the Eneolithic Steppe, this is not an insignificant link between the Steppe and West European lineages specifically.  

The real question then is what this means for the understanding of the CWC in this area.  

What does this do for Kristiansen's linguistic hypothesis for the emergence of proto-Germanic?  I was skeptical in that post, but would this and subsequent results strengthen his hypothesis?  Interestingly, it almost seems as if the original isogloss between East and West European speech is becoming a harder and darker lineage between these Eastern and Western tribes cut from the same roots.

Citation: Egfjord AF-H, Margaryan A, Fischer A, Sjögren K-G, Price TD, Johannsen NN, et al. (2021) Genomic Steppe ancestry in skeletons from the Neolithic Single Grave Culture in Denmark. PLoS ONE 16(1): e0244872. https://doi.org/10.1371/journal.pone.0244872


28 comments:

  1. Replies
    1. Thats why Tutankahmen's father married his sister.

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  2. It shouldn't really be a surprise to find SGC as a root source of pan-European Bell Beaker lineages. This would already have been expected some years ago from examining Kyndelose and Bell Beaker autosomals.

    We must be careful not to be driven by wish fulfilment though. V1636 is not L51, which is much closer to Volgan Z2103, Atapuercan M269, Bulgarian M269xL23 and even Latvian pre-M73. V1636 is more in the realms of Iberian V88, Blatterhohle V88 and Villabruna L754. All it really reinforces is the realisation that R1b was not imprisoned in the Steppe before Bell Beaker.

    As Eurogenes points out, most human remains between Holland and Denmark "have been eaten up by the acidic soils that exist in this area", so we have little or no evidence to determine which yDNA was here when.

    My curiosity is more how and why L51 skirted around or cut through Neolithics and Corded Ware to get here, and again some of the clues to this come from examining SGC autosomals.

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  3. The L51 missing link is still missing. R-V1636 is not at all closely related to R-M269>L23>L51. M269's phylogenetic equivalent block has about 96 SNPs. That's a long time. V1636 and V88 are not closely related to each other for that matter.

    The lineage that is ancestral to the vast majority of R1b in Europe, R1b-L151, is L51>P310>L151. We have P310* way out in Afansievo/Mongolia. We have the earliest L151 that I know of at Aesch, Switzerland in Corded Ware. Where is the L51* and P310* in between????

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    1. The interest in V1636 is that it can be firmly placed in the Eneolithic Steppe in the millennia before the emergence of the SGC in Northern Europe. So while it is not closely related to 310 and L51 per se, it is from a milieu of lineages that come from the Steppe and not somewhere else. (and this would make sense given the cultural affinities with the Steppe)

      Exactly when it left the Steppe is a different issue, but it must have been within the same timeframe as L51 because if it existed in a previous archaeological culture of Northern Europe whose male lines didn't survive, it wouldn't be in the first or second SGC body rolled out of a grave.

      As to P310 and L51. No idea, it still boggles my mind that it has been so elusive. It will be interesting if the SGC starts turning up surprising lineages like Z2103, and for whatever reason, became dwarfed by some insignificant tribe of L51's that were at war with everyone, even in the bedroom.

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    2. V88 was also in the Eneolithic Steppe, but probably arrived in North Western Europe (e.g. Blatterhohle) completely separately to L51.

      Whether they find it or not, I'm pretty sure that L51 was in SGC though, as SGC autosomally is the clear springboard for L51 Bavarian Bell Beaker. It wouldn't be at all surprising for some Z2103 to be found there as well, but that wouldn't necessarily mean that L51 arrived with it. SGC looks genetically like a mix of peoples coming in from all angles - a time of flux.

      We already have likely L51 early samples in Smyadovo (M269xZ2103) and Atapuerca (M269>Y17204); low coverage is probably all that stops them from being identified as such. Most of the places where L51 may be findable are still sparsely tested - e.g. the Adriatic/Southern Italy and Western France. At least recent tests in other likely locations (the Alps and North Western Europe) are starting to rectify these omissions.


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    3. What a mystery... Could it be that thje L-51 people belonged to a culture that practiced cremation and that's why the remains are so scarce?

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    4. That's an interesting possibility. Never heard that mentioned before. I think probably it was just a very minor lineage. A somewhat similar problem with the CW R1a lineages.

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  4. Is there any R1b-V88 in early Iberian Bell Beakers?

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  5. All R1b lineages known to us so far are typical of WHGs including R1b-M269 and R1b-V88 which were incorporated as other male markers into the farming communities. From the Balkans they migrated to the west and east, therefore all eastern markers R1b-V88 (Dereivka), R1b-Z2103 (Yamnaya) and R1b-V1636 (Khvalynsk, Eneolithic Progress, Yamnaya) migrated back to mainland europe with the steppe migrations. We have already found V1636 in SGC and Z2103 in the BBs. We also have three cases of neolithic Swiss farmers R1b-L51 and in addition (as Nicolas says) we have Smyadovo and ATP3 which are R1b-M269. So the obstinacy of the Kurganists to keep linking R1b-L51/P312 with the steppes through the CWC is another lie.

    By the way, we already have the oldest Df27 in a BB site in Narbonne (Occitania) in a site with Pyrenean style pottery (which as everyone knows has decorative motifs identical to the Ciempozuelos style). We already have the marauder mesetans traveling through France 4,500 years ago with their V-perforated buttons, and their copper weapons.

    Assigments-2.500 genomes Reich Lab-EHU002 belongs to R1b1a/1b1a/1a2a/7-

    El hundido site (Monasterio de Rodilla, Burgos, Castilian Plateau-2,434 BC) also contains Ciempozuelos style pottery, so it seems clear where the BBs from the south of France come from, doesn't it? EHU002 is positive for A12032/S24844 (under Df27).Yet, the anthrogenica and eurogenes naysayers, after years of lying about Quedlinburg-I1806 as the first Df27 in Europe (it is positive for a U152 marker) will never acknowledge that there were BB migrations from Iberia to many regions of western Europe. The longer they take to recognize it, the more ridiculous they will be.

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  6. Another famous Kurganist myth recently debunked is Afanasievo-I6222

    https://reich.hms.harvard.edu/downloadable-genotypes-worlds-published-ancient-dna-data
    Sample-I6222 3320-2918 calBCE (4415±31 BP, OxA-36222) Mongolia_Chalcolithic_Afanasievo_1_contam R1b1a1b1a1 25 R .. .. [0.815,0.861] 0.042 .. 22 n/a (<200 SNPs) n/a (<200 SNPs) n/a (<200 SNPs) -0.039 0.056 Model_Misspecified [0,0.071] ds.half S6222.E1.L1 QUESTIONABLE_CRITICAL (damage.ds.half=0.042, mtcontam=[0.815,0.861])

    Another garbage sample used to try to link Yamnaya to P310. They will never find this lineage in the steppes and if they do, they will be WHGs without steppe ancestry like the samples to be released from Volosovo.

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  7. And regarding the linguistic issue, the Bb culture never spoke an Indo-European language. If what we have to take into account is the genetic continuity of both male and female unipersonal markers, then it has been clearly demonstrated that the Bb culture at least in Iberia and southern France spoke Ibero-Basque. This is the evident proof of what I am saying.

    *GBVPK (2.380 AC)- Grotte Basse de la Vigne Perdue, Narbona-HapY-R1b1a/1b1a/1a2a/1-Z195-
    *I3494 (1.836 AC)-Coveta del Frare, Valencia-Bronce Valenciano-HapY-R1b- DF27-ZZ12-Hap Mit-J1c1/b
    *I1312d (1.782 AC)-Can Roqueta, Barcelona-Bronce Nordeste-HapY-R1b-Df27-Z195-Hap Mit-HV0@195
    *I3397 (1.741 AC)-Lloma de Betxí, Valencia-Bronce Valenciano-HapY-R1b-Df27-Z195-Hap Mit-K1a2/b
    *I3487 (1.675 AC)-Cabezo Redondo, Alicante-Cultura del Argar-HapY-R1b-P310-Hap Mit-H1e1/a
    *I4559 (1.600 AC)-Galls Carboners, Tarragona-HapY-R1b-P311- Haplogrupo Mitocondrial-J1c1
    *I4563 (1.600 AC)-Galls Carboners, Tarragona-HapY-R1b- Df27-Z195-Haplogrupo Mitocondrial-H1/H84
    *I3486 (1.600 AC)-Cabezo Redondo, Alicante-Cultura del Argar-HapY-R1b-P297-Hap Mitocondrial-H1q
    *I3488 (1.600 AC)-Cabezo Redondo, Alicante-Cultura del Argar-HapY-R1b-M269-Hap Mit-HV0@195
    *Pir001 (1.600 AC)-Cueva del Pirulejo, Córdoba-Cultura del Argar-HapY-R1b-L23-Hap Mit-K1a13
    *I1836 (1.593 AC)-Cova del Gegant, Barcelona-Bronce del Nordeste-HapY-R1b-L151-Hap Mit-U5a2/b3
    *I8570 (1.400 AC)-Tossal Mortorum, Castellón-HapY-R1b-L151- Haplogrupo Mitocondrial-J1c3
    *I3315 (861 AC)-Naveta des Tudons-C.Talayótica-HapY-R1b-P312-Hap Mit-U5b1@16189@16192
    *I12641 (665 AC)-Can Revella, Barcelona-Cultura Íbera-Layetania-HapY-R1b-M269-Hap Mit-HV0d
    *I12640 (618 AC)-Can Revella, Barcelona-Cultura Íbera-Layetania-HapY-R1b-P312-Hap Mitocondrial-H1t
    *I8211 (475 AC)-Ampurias, Gerona-Cultura Íbera-Indiketes-HapY-R-Hap Mitocondrial-HV0@195
    *I8344 (450 AC)-Ampurias, Gerona-Cultura Íbera-Haplogrupo Y-R1b1a/1a-Haplogrupo Mitocondrial-H3
    *I12410 (445 AC)-Mas Den Boixos, Barcelona-Cultura Layetana-HapY-R1b-P312-Hap Mitocondrial-H
    *I12877 (445 AC)-Mas Den Boixos, Barcelona-Cultura Layetana-HapY-R1b-M269-Hap Mitocondrial-J1c1
    *I8210-(425 AC)- Ampurias (Gerona) Cultura Íbera-Indiketes- HapY-R1b1a/1a2-Hap Mitocondrial-U5b3
    *I8209 (425 AC)-Ampurias, Gerona-Cultura Íbera-Indiketes- HapY-R1b-P312- Hap Mitocondrial-U1a1/a
    *I8212 (425 AC)-Ampurias, Gerona-Cultura Íbera-HapY-R- Haplogrupo Mitocondrial-H27@16093
    *I8341 (425 AC)- Ampurias, Gerona-Cultura Íbera-HapY-R1b-P312-Haplogrupo Mitocondrial-H1
    *I3323 (284 AC)-Puig de Sant Andreu, Gerona-Cultura Ibérica-Indiketes-HapY-R1b-L151-Hap Mit-X2b
    *I3324 (276 AC)-Puig de Sant Andreu, Gerona-Cultura Ibérica-Indiketes- HapY-R1b-DF27-Hap MitH1
    *I3496 (250 AC)-Turó de Can Oliver, Barcelona-Layetanos-HapY-R1b-Df27-Hap Mit-H1e1/a
    *I3326 (225 AC)-Puig de Sant Andreu, Gerona-Cultura Ibérica-Indiketes-HapY-R1b-P297-Hap Mit-J1c
    *I3327 (225 AC)-Puig de Sant Andreu, Gerona-Cultura Ibérica-Indiketes-HapY-R1b-L52-Hap Mit-J2b1/a
    *I3321 (200 AC)-Els Estrets-El Racó de la Rata, Castellón-Ilerkavones-HapY-R1b-P312-Hap Mit-U3a
    *I3320 (200 AC)-Els Estrets-El Racó de la Rata, Castellón-Ilerkavones-HapY-R1b-Df27-Z225-Hap Mit-I1
    *I8206 (200 AC)-Ampurias, Gerona-Cultura Ibérica-Indiketes-HapY-R1b-Df27-Z195-Hap Mit-H7a1

    In other words, genetic continuity is the whole Iberian territory from BB culture to the Iron Age peoples. The Iberian language spread from Andalusia to Herault (France) along the Mediterranean coast and the Pyrenees. Who can prove that the Iberians changed their ancestral language? What were the reasons for doing so? Can the Kurganists demonstrate such an obvious genetic continuity between any Steppe culture and the Iron Age in Europe? Evidently the answer is NO, even if the Harvardians keep analyzing thousands of genomes in Russia and Ukraine they will never find R1bM269 and L51 there.



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    1. how do you explain this?

      "...by ~2000 BCE the replacement of 40% of Iberia’s ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry."

      https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6436108/

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    2. I'm not quite sure why you want me to explain Olalde's statement because in reality, if R1b-P312/DF27 has its origin in the steppes and massacred the neolithic Iberian farmers, its genetic continuity in Iberia until the Iron Age would lead us to the absurdity of saying that neither the BBC nor the CWC nor the steppe cultures spoke an IE language, but some kind of Ibero/Basque-like language. So far, the only thing we know for sure is that the Iberians (DF27-Z195 and ZZ12) spoke Iberian and also Basque and that none of these languages are Indo-European

      Or do you think they changed their language when they arrived in Iberia because they found beautiful women waiting for them on paradisiacal Mediterranean beaches. It could be, but I don't think our copper age ancestors had time to sunbathe with their women.

      Dr. Reich and his Harvardians have a theory and an agenda to defend and to do so, despite the fact that they have no idea about European Chalcolithic, they have to use any argument at their disposal. They have failed in their attempt to demonstrate the continuity of the R1b male lineages and their relationship to the spread of the IE language, they have also failed in claiming that the proportion of men who participated in the migrations was much higher than that of women, when in fact several dozen female lineages have already been identified in both the CWC and the BBC. All they have left is the autosomal argument, the famous steppe ancestry (formerly Yamnaya ancestry)and something is really wrong with this type of autosomal component.

      1-It is true that there are male lineages related to the WHGs (C1a2), or to the Neolithic farmers (H2, R1b-V88) that apparently became extinct from Iberia during the Chalcolithic, but others such as I2 and G2 have not only been documented in the Bronze Age, but have reached our days in significant percentages. So 100% replacement-Ha Ha Ha Ha
      2-The Bb culture was very heterogeneous in terms of male markers not only in Western Europe, but also in the Eastern domain. It was also heterogeneous in relation to its autosomal composition. There is R1b with no autosomal steppe component (Spain. England) and G2 with an appreciable percentage of this component (France, Hungary, etc). That is to say, Harvard is wrong again to link this steppe ancestry exclusively with the R1b-M269/P312 lineage, because other male lineages were involved and because women also contributed significantly to change the European genetic landscape.
      3-The vast majority of Iberian BBs can be perfectly modeled without using samples from the Yamnaya culture. But even if we could not do so, it is evident that part of the Yamnaya genome was shared with Neolithic farmers from all over Europe (after all, EHGs have an important part of WHGs, and the Yamnaya culture has a good proportion of EEF coming from the Balkans (Wang et al), i.e., it is normal that Iberian and steppe populations shared at least 10-15% of their autosome, without having to resort to migrations. There are non biased guys who can do serious autosomal studies on the BBs of the western domain.
      4-Olalde's autosomal studies are clearly improvable, he uses at his convenience certain populations that serve to justify this alleged invasion, depending on this, everything will be more or less Yamnaya.

      In other words, my opinion is that Olalde and Reich's claim is risky and unconvincing. In a few years it will be remembered as another great scientific failure. They will have to accept the criticism, and the only way to prove their theory is to find R1b-M269/L51/P312 on the steppes for once and for all. If they don't do that then they'd better go back to speculating about Martian genetics and if they do, we will have to congratulate them for having solved the great mystery of our origin.

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    3. My explanation is that the statement is simply misleading, whether deliberately or otherwise.

      The study actually compares Iberian ancestry to 'Central European Beaker/Bronze Age-related ancestry', not Iberian ancestry to Steppe ancestry.
      And if it had compared Iberian ancestry to Bronze Age-related ancestry just North of the Pyrenees, it would have provided an even better fit.
      The major changes were much less striking (local to Western Europe), and in any case the study itself shows that they didn't occur until 1,900 BC - over a thousand years after the Steppe migrations took place.

      The Single Grave study is similar. It is presented as a demonstration of 'genomic Steppe ancestry', whereas the study itself shows that these genomic profiles were already present in the Danish Neolithic before Single Grave arrived, and that when Single Grave did arrive, it came from the West (the opposite direction to the Steppe) and from people who had no Steppe ancestry at all (only Caucasian).

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    4. You are right Nicolas, but the big question is; why does Olalde and his team use the central European samples and not the ones they have available from the steppes?

      BBs from Iberia and Germany share many female markers that are identical in both regions, this could explain at least female migrations from Iberia and also the autosomal similarity without having to resort to R1b-P312 (unless Harvard thinks that females do not transmit steppe ancestry). However Olalde in his paper (2018) denied this possibility arguing that the H3 lineage did not exist in Iberia and therefore Iberian migrations had to be totally ruled out. I have never seen such a poor argument and so badly used because H3 has been in Iberia since the Neolithic. This shows that Olalde has not done his job well, he just forced the results to make everything fit.

      How can they continue to deny small Iberian migrations (even male) when you have Z195 in Sicily and Occitania in deposits with typically Iberian pottery and when those males can only be satisfactorily modeled using Iberian samples. Population movements were abundant, men and women crossed the Pyrenees in both directions, the story is much more complicated than the simplistic explanation of mass migrations from the steppes. Sooner or later they will have to recognize it.

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  8. So can we say that Gimbutas was right about steppe migrations? Evidently yes because R1b-Z2103 and V1636 (surely some other minority lineage in the steppes too) reached mainland europe, but what is a major mistake is to think that those migrations were able to change the language of the European neolithic farmers. Neither were they massive migrations (we have Swiss neolithic farmers R1b buried in dolmens) nor did the steppe male lineages reach western europe (R1a-M417 because it never joined the BB culture and R1b-L51/P312 because it was already in Europe when Z2013 and V1636 returned). So it is time for Anthony and other archaeologists to start thinking that Indo-European languages in Western Europe are a Bronze and Iron Age issue, not a BB culture issue.

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  9. Looking at the V1636 sample in more detail:
    1. Its autosomal profile matches the Eastern Danish Kyndelose sample (2,671 BC) more closely than it does the Corded Ware samples, so its genetics look to have been indigenous to Denmark from 500 years previously, rather than derived from Corded Ware.
    2. These genetics were already present in Eastern Danish Kyndelose before 2,600 BC when the Single Grave Culture arrived from the west (Western Jutland), so they predate the Single Grave Culture and do not appear to have derived from it.

    Single Grave Culture genetics do not appear to be of Yamnayan origin. Of the two earlier Single Grave samples, one has no Yamnayan in it whatsoever - it simply has a Caucasus insertion, and a Central Steppe component is completely absent.

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  10. The 18th Dynasty R1b study has been published (in a book). A pdf is available here:

    'Maternal and Paternal Lineages in King Tutankhamun's Family' (Gad et al. 2020)

    https://www.docdroid.net/EC8uFeh/gad-et-al-hawass-fs-final-2020-pdf



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  11. Bell Beaker ancestry in the Guanches:

    https://anthrogenica.com/showthread.php?22741-Ancient-genomes-from-North-Africa-evidence-prehistoric-migrations-to-the-Maghreb-from&p=737848&viewfull=1#post737848

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  12. What the archaeology and admixture in this study seem to show is that Single Grave was a cultural development within an indigenous population that had already received genetic input from elsewhere some time previously. And to a greater degree than I expected, this earlier input was Caucasian, rather than Steppic.

    This would appear to suggest that much of any new DNA in Western Europe came directly from the Caucasus region through the Balkans or Mediterranean, rather than through the Steppe. It's all there for anyone to see in the admixture chart, regardless of how they spin it.

    It would also explain how elements of the new genetics and culture also appeared in ancient Egypt and the Mahgreb, as A indicates.

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    1. are you saying most of the supposed steppe DNA in western Europe is actually just 'caucasian' DNA? (CHG?)

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    2. I didn't think it was (it differs from other studies), but that is what the admixture analysis in the SGC study shows, probably based on using different reference samples.

      This could be quite revealing, as it appears to indicate a more particular origin point for DNA that looks intrusive to Western Europe - i.e. Northern Caucasus/Southern Steppe, rather than Ukraine or middle Volga.

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  13. I have just tried replicating the approach of Olaide's Iberian paper by using the Egfjord study's own data to estimate the percentage contributions to the Single Grave samples of prior-dated Danish Late Neolithic and prior-dated Corded Ware, and it comes out with the following result - 100% Danish Late Neolithic, 0% Corded Ware.

    It is clear to me that when the Single Grave culture moved into Eastern Jutland from the West, it represented a cultural transition within an existing Danish population that involved little or no migration from Corded Ware areas to the South and East. If L51 were found within Single Grave, there would appear to be no sign that it came via Corded Ware.

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    1. I haven't read that paper and I don't know if this is applicable, but one thing to be careful of is that "Late Neolithic" in Jutland or adjacent areas often refers to what is essentially the early metal age. It's kind of like the absence of the Chalcolithic in Britain is more how periods of certain areas are defined historically by archaeologists.

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    2. Yes, I agree. The Late Neolithic in Denmark differed from the Early Neolithic genetically as well as culturally. My point is that these changes in genetics preceded the Single Grave Culture and did not occur with it. If L51 was in SGC, the data indicates that it was almost certainly there before SGC and was not brought into Denmark with SGC from Corded Ware.

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  14. More good news: One of the oldest (Dutch) Beakers has been identified as a subclade of P312>DF19. DF19 burials hadn't been found _anywhere_ at all until one dated to ~200AD, so it was a good bet it was hiding in an area with hostile soil conditions, or an area not heavily researched.
    Noord-Holland
    aDNA: I5748
    MDKA Birth: Netherlands
    Bell Beaker, PRJEB23635. 2579-2211 calBCE (3945±55 BP, GrN-6650C). Noord-Holland, Oostwoud, De Tuithoorn Netherlands.
    R-P312/S116 > DF19/S232 > Z302/S233 > Exact position not yet finalized

    From Alex Williamson's Big Tree, you can see I5748 as the green "Noord Holland" box below Z302 at
    https://www.ytree.net/DisplayTree.php?blockID=183

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  15. Trying again, my comment a month or so ago never appeared. The oldest of Oostwoud's "Beakers" - who was buried below the layer containing beaker fragments - is now reported by Alex Williamson (and confirmed by yfull) to be P312>DF19>Z302. So we have a "grandkid" of P312 before Beaker culture really blooms in greater Frisia, and it looks autosomally similar to the L21 Beakers in S. England.

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