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Thread: Kinship-based social inequality in Bronze Age Europe

  1. #11
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    Quote Originally Posted by MitchellSince1893 View Post
    Congrats!
    So the oldest U106 to date is Bell Beaker? Well, that is a game changer.
    Not necessarily a game changer. Given the vast number of ancient Bell Beaker already published, it is clear U106 did not play a significant role in the Bell Beaker Culture.
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    Quote Originally Posted by Wing Genealogist View Post
    Not necessarily a game changer. Given the vast number of ancient Bell Beaker already published, it is clear U106 did not play a significant role in the Bell Beaker Culture.
    IMO, It's a big deal. Until today, many argued that U106 had to originate in Battle Axe as the previously oldest U106 sample was from Battle Axe/Sweden site. So how is an older U106 sample found in a different culture not a significant discovery?

    The vast majority of Corded Ware samples have been R1a; and until today, it has been successfully argued that L51 and descendants weren't part Corded Ware. The discovery of L151 in CW...even if it's a contemporary of the oldest P312 means that argument is no longer valid.

    I've heard that same line of argument used for U106 not being part of Bell Beaker. Today's discovery of the oldest U106 in Bell Beaker shows that U106 was part of BB...even if it was a small part...just like L151/L51 may have been a small part of Corded Ware.
    Last edited by MitchellSince1893; 10-11-2019 at 02:02 AM.
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    Quote Originally Posted by Wing Genealogist View Post
    As reported in another thread, the supplementary information can be downloaded from: https://science.sciencemag.org/conte...ce.aax6219.DC1

    For me, the Bad News is that out of 53 males tested, only 1 was U106+ (HUGO_180sk1) and the test yielded poor results (many SNPs missing, and the SNPs reported almost universally had only a single read).
    The Good News is this appears to be the oldest U106 found to date. The paper reported the Median date as 2335.5 calcBCE with a 2 sigma age range 2562–2039 calBCE.

    This is reported as a Bell Beaker grave site, so it is also the first confirmed U106 in Bell Beaker.

    I am not sure if this result is legit, because it's based on a single read, it's a low quality sample and many SNP's are missing like you said.

    Last year, there were two similar cases: two Bell Beakers, a Hungarian and a Czech one, were thought to be known as Z18 and Z9 respectively. However, these findings were not confirmed by Williamson. Williamson suggested that it was a result of deamination, which happens for aDNA, and results in spurious C->T (and G->A in results) mutations.

    Apparently, the authors of this paper were not confident enough to classify HUGO_180sk1 as U106/M405, but rather as just R1b1a2. In this case, the best thing to do is to let an expert like Willamson take a look at this sample to confirm or deny/doubt that he is U106 IMO. Are there any BAM files available?
    Last edited by Radboud; 10-11-2019 at 02:00 PM. Reason: typo

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    Quote Originally Posted by Radboud View Post
    I am not sure if this result is legit, because it's based on a single read, it's a low quality sample and many SNP's are missing like you said.

    Last year, there were two similar cases: two Bell Beakers, a Hungarian and a Czech one, were thought to be known as Z18 and Z9 respectively. However, these findings were not confirmed by Williamson. Williamson suggested that it was a result of deamination, which happens for aDNA, and results in spurious C->T (and G->A in results) mutations.

    Apparently, the authors of this paper were not confident enough to classfiy HUGO_180sk1 as U106/M405, but rather as just R1b1a2. In this case, the best thing to do is to let an expert like Willamson take a look at this sample to confirm or deny/doubt that he is U106 IMO. Are there any BAM files available?
    You are correct in this caution, as the U106 mutation (C->T) is subject to deamination, so a single read is anything but conclusive. Additionally, there are no reads for the vast majority of clades below M269, so we cannot rule out this individual being P312+ or some other clade below M269. We do really need a close examination of the BAM file by an expert.

    Being human, it's hard not to get excited when a somewhat surprising result (such as U106 in Bell Beaker) shows up. Hopefully the BAM file will show up results for SNPs not documented in table S8 and we are able to more confidently place this sample.

    EDIT: It appears the researchers have discovered a way to differentiate between a true thymine call and a false call due to the deamination process. Thus the single read for U106 was likely not due to deamination. Even so, a single call is still not enough evidence to state with ANY confidence the call is legitimate. There are a number of other reasons where a single call is in error.
    Last edited by Wing Genealogist; 10-11-2019 at 07:56 PM.
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    Quote Originally Posted by MitchellSince1893 View Post
    IMO, It's a big deal. Until today, many argued that U106 had to originate in Battle Axe as the previously oldest U106 sample was from Battle Axe/Sweden site. So how is an older U106 sample found in a different culture not a significant discovery?

    The vast majority of Corded Ware samples have been R1a; and until today, it has been successfully argued that L51 and descendants weren't part Corded Ware. The discovery of L151 in CW...even if it's a contemporary of the oldest P312 means that argument is no longer valid.

    I've heard that same line of argument used for U106 not being part of Bell Beaker. Today's discovery of the oldest U106 in Bell Beaker shows that U106 was part of BB...even if it was a small part...just like L151/L51 may have been a small part of Corded Ware.
    I agree, it opens up all kinds of possibilities, even if it was a minor clade amongst them. Assuming, that is, that it's not an extinct subclade of U106
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    The authors were very careful with the Y-hg classifications in this paper, and did a good job, unlike what we've seen in other papers.

    So if the results don't say U106, then it's unlikely to be U106.

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    Am I reading Table S9 correctly? It looks like Tauber CWC is just above 1/3 steppe while Lech BB is around 1/2 steppe.

    Then, EBA and MBA Lech tends to be even higher in steppe.

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    Quote Originally Posted by nuadha View Post
    Am I reading Table S9 correctly? It looks like Tauber CWC is just above 1/3 steppe while Lech BB is around 1/2 steppe.

    Then, EBA and MBA Lech tends to be even higher in steppe.
    Good catch, I'd say they simply entirely transposed the columns in that table:

    TauberCWC:
    Globular_Amphora 0.68
    Yamnaya 0.32

    The other way round that would make perfect sense and would be a typical CWC result and would fit figure S8:

    Fig. S8.f4-statistics showing differences in ancestry in populations grouped by period..JPG

    "Fig. S8.f4-statistics showing differences in ancestry in populations grouped by period. (A) An increase in affinity to ancestry related to Anatolia Neolithic over time. Males and females grouped together shown as upward and downward pointing triangles, respectively.( and (C) f4-statistics of the form f4(Mbuti, Test; earlier Lech population, later Lech population) become significantly positive when Test is a Neolithic or Chalcolithic population, indicating progressive admixture from populations with comparatively more Neolithic-related ancestry."

    Table S9 certainly disagrees with any other table or text in that PDF:

    "Modeling with qpAdm the period groupings as three way mixtures of WHG, Anatolia_Neolithic and Yamnaya_Samara using the parameters allsnps: YES, we observe an increase over time in the proportion of Middle Neolithic ancestry in the southern German population and correspondingly, a slight decrease in steppe ancestry over time (Fig. 2, table S7).

    To examine if we could more accurately identify the Middle Neolithic genetic stratum involved in the admixture event that formed the Lech populations we explicitly tested two-way admixture models with qpAdm, using Yamnaya” from Samara as first source and different European Middle Neolithic and Chalcolithic populations as second source. The best fitting models were obtained with the farmers of the Globular Amphora culture, the Middle Neolithic population of France and Chalcolithic Iberia, who all gave p-values over 0.05 for the Lech BBC, EBA and MBA populations when used as a source (table S9)."


    And not even the description of table S9 is correct, it's obviously not a three-way admixture model and the above text that references it clearly states it's a two-way model.

    They have some very obvious technical mistakes in the Supplementary Information, unfortunately. Just look at Fig. S5, too. The sample and culture names are entirely unreadable.
    Last edited by Chnodomar; 10-11-2019 at 05:31 PM.
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  15. #19
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    Everyone including myself is now toying with the idea that Yamnaya wasn't directly involved in the Indo-Europeanization of Europe, but the exact process is elusive. I've tried to do some nMonte modelling of all the extant CWC and Bell Beaker samples using Eneolithic steppe (ie, non-Yamnaya/pre-Yamnaya) proxies. But CWC/BBC requires BOTH:

    a) a "North Pontic" source like Sredny Stog (Sredny Stog_En_II is I believe from Alexandria, Ukraine; alternatively the Dereivka_En_1/2 samples are nearby), AND
    b) an "East Pontic"/Caucasus steppe source like Progress/Vonyuchka

    Now Progress/Vonyuchka is basically contemporary with the Alexandria sample (~4000-4200 BCE). The Dereivka_En_I and Dereivka_II samples are dated 3200 BCE, temporally closer to CWC, but these produce worse fits with the CWC/BBC samples. They look basically like WHG-shifted versions of the Alexandria sample.

    Using distal models, Progress is 2/3 Samara HG and 1/3 CHG; Sredny_II (Alexandria) is more like 2/3 Samara and 1/3 ENF. Removing either Progress OR Sredny Stog severely damages all the fits for CWC/BBC samples. I think David has speculated on this before, but the Repin Culture seems geographically midway between Sredny Stog and Progress.

    Current theory:
    - One Repin group carrying R1a-M417 rapidly worked northwest thru the forest-steppe circa 3500 BCE, while the cousins they left behind were folded into Yamnaya on the steppe proper
    - And the big surprise: this splinter Repin group bumped into the remnants of the Dnepier-Donets hunters somewhere near the Ukraine-Belarus border; DD guys contributed R-L51 to the mix

    (bold rows below indicate poor fits at >3.5% distance)


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    Alas, the Y haplogroup data as depicted in Supplementary Material Table S8, with the Y haplogroups presented both as ISOGG letters and numbers, and as supposed terminal SNPs, has a vast number of "holes". There is really little to be learned until a true expert (e.g., "Williamson") "reads" the associated BAM files and confirms what is and is not correct. Just looking at R-U152 related SNPs, U152 is "greyed out" (not working up to defined standard), although two individuals in the sample group were a "hit" on one run. Oddly the most common downstream SNP, L2, is not even included - although downstream Z367 was ("worked" but no individuals positive for this SNP - and further downstream the relatively common L20 is grayed out). The handfull of other U152 - related SNPs include many I don't recognize, although L4 worked well (no derived samples), but as I recall is confined to the Ashkenazi population and not likely to be "ancient". I am beginning to doubt that this paper will end up being in the same league as the other major Bell Beaker study, Olalde et al., 2018. Perhaps the soil conditions were not as conducive to being able to avoid deamination issues (e.g., more acidic?). Hopefully as I type this, someone is assessing the BAM file and we will soon have more clarity. It was interesting to note that another Bell Beaker candidate SNP, L21 (predominant today in for example Ireland), worked relatively well, but zero samples appear to have been derived for this SNP.
    Last edited by falconson1; 10-11-2019 at 09:18 PM.

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