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Thread: Genetic Genealogy and Ancient DNA in the News

  1. #501
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    Quote Originally Posted by Chad Rohlfsen View Post
    Bell Beakers are not 60-80% Corded Ware genetically. That is crazy. They hardly share any mtDNA. The two that are likely admixed are the 19% ones, as they do fall in between the two. You would need Bell Beaker to have loads of WHG (like 60-70%) before mixing. That just isn't parsimonious with what we know of MNE people in the area. Does anyone honestly believe we have European R1b coming from Iberia, popping up with 60-70%WHG? Come on now! It is far more likely that R1b picked up a good amount of WHG enroute to Germany. Or, if they were in Ukraine, they would likely have a decent amount of WHG on top of the EHG, prior to mixing with local farmers there and in Germany.
    Like I said, all one would need to get the Bell Beaker profile with direct Yamnaya input is a population sufficiently higher in WHG and Near Eastern than Yamnaya and with sufficiently lower levels of ANE and South Eurasian.

    Besides, and the more I think about it, the more likely I think it is, the Yamnaya people who moved west and north up the Danube valley to eastern Hungary probably did not have the exact same profile as the Volga-Ural Yamnaya we have from Haak et al anyway. So we would be starting with a different set of proportions to begin with.

    Another thing I mentioned before is that Beaker and Corded Ware were roughly contemporary, which would leave both of them with too little time to have a big genetic impact on the other that would show up in results from the 3rd millennium BC.
    Last edited by rms2; 03-06-2015 at 09:46 PM.
     


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  3. #502
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    Quote Originally Posted by rms2 View Post
    Like I said, all one would need to get the Bell Beaker profile with direct Yamnaya input is a population sufficiently higher in WHG and Near Eastern than Yamnaya and with sufficiently lower levels of ANE and South Eurasian.

    Besides, and the more I think about it, the more likely I think it is, the Yamnaya people who moved west and north up the Danube valley to eastern Hungary probably did not have the exact same profile as the Volga-Ural Yamnaya we have from Haak et al anyway. So we would be starting with a different set of proportions to begin with.

    Another thing I mentioned before is that Beaker and Corded Ware were roughly contemporary, which would leave both of them with too little time to have a big genetic impact on the other that would show up in results from the 3rd millennium BC.
    Exactly! Bell Beaker is related to Mako and Vucedol. And look at just how similar many of the Beakers are to BR1. It's not a coincidence. Kemi Oba was mixed with both Balkan and North Caucasus populations. They should have aDNA components from both. I seriously doubt that hunters in Ukraine were full EHG. They were probably quite mixed with WHG. These Beaker results are not surprising. BR1 is even more WHG than Beaker. It looks like Beaker was like BR1, then mixed with some farmers and Corded Ware to get to it's state represented in Germany.

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    In case some of our Board members haven't yet read it, both Patterson and Lazaridis commented on the Eurogenes blog. I think the post from Lazaridis provides some food for thought:

    Iosif Lazaridis (Broad) said... It's great that our data is finally out there, and I hope it will be useful to the wider community.

    Just a quick comment: There are significantly negative f3(Yamnaya; Near East, Karelia_HG) and f4(Karelia_HG, Yamnaya; Near East, Chimp) for many Near Eastern/Caucasus populations. We are clear in our paper that we don't think we have a good surrogate for the admixing population, and we mainly model Yamnaya with Armenians/Iraqi Jews because they top these statistics.

    You get a negative correlation like Fig. S9.20 with different Near Eastern/Caucasus populations. Percentages vary (39% BedouinB, 47% Druze, 48% Iraqi Jew, 53% Armenian, 68% Lezgin). African admixture (which many Near Easterners like BedouinB have, see Moorjani et al. 2011) reduces these estimates, while for populations like Lezgins (who have lower Near Eastern ancestry), you need proportionally more Lezgin input into the Yamnaya to account for the same amount of dilution. We estimated (Lazaridis et al. 2014) that Lezgins are 71% Near East, so .68*.71 = 48%, which seems about right.

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  7. #504
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    Anyone notice German Bell beaker in ANE K8 cluster with modern northwest Europeans? Irish in particular are closest to the avg. Beaker score. Umm.. Beaker had R1b-P312 and ~80% of Irish have R1b-P312, I wonder where Irish come from.

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  9. #505
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    Quote Originally Posted by Krefter View Post
    Anyone notice German Bell beaker in ANE K8 cluster with modern northwest Europeans? Irish in particular are closest to the avg. Beaker score. Umm.. Beaker had R1b-P312 and ~80% of Irish have R1b-P312, I wonder where Irish come from.
    Yeah, I called that. The Irish had a four-fold increase in population during the LNE/EBA. I think it is safer to say that they descend from those that are mixed with Corded, in the Netherlands. So, they should be similar to the Quedlinburg Beakers. We need something closer to 20% ANE to cover the change.

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    Quote Originally Posted by everest59 View Post
    The ones that Chad gave me all produced +ve f3 stat. Here are some others that I just tested:
    result: Yamnaya Dai Sindhi -0.006478 0.000533 -12.142 236964
    result: Yamnaya Dai Pathan -0.007256 0.000525 -13.812 236729
    result: Yamnaya BedouinB Armenian -0.003075 0.000414 -7.421 225089
    result: Yamnaya BedouinB Pathan 0.002317 0.000434 5.336 237400
    result: Yamnaya BedouinB Sindhi 0.005813 0.000452 12.867 237713
    result: Yamnaya Armenian Lezgin -0.003189 0.000410 -7.771 221623

    For those that produced -ve f3 stats, here are the qpBound results:

    Yamnaya Dai Sindhi -0.006478 -12.142 -nan -nan
    Yamnaya Dai Pathan -0.007256 -13.812 -nan -nan
    Yamnaya BedouinB Armenian -0.003075 -7.421 0.171 0.650
    Yamnaya Armenian Lezgin -0.003189 -7.771 0.153 0.501

    Obviously, Dai does not represent ASI, so that did not work.
    As for Armenians and Lezgins, it worked, and I see a big range. Lezgins as a mixture of Yamnaya and Armenian have anywhere from 15% to 50% Yamnaya admixture. Yamnaya,BedouinB; Armenian on the other hand is 17-65%.

    Actually, it worked with Papuan. It appears, it came up with a range for ANI:
    Yamnaya Papuan Sindhi -0.005436 -8.018 0.551 0.851
    Yamnaya Papuan Pathan -0.005507 -7.620 0.592 0.847

    Obviously, it isn't very accurate given what we would expect (i.e. Pathans should have higher ANI than Sindhis). The bigger difference is in the lowerbound.
    Thanks Everest!

    For what it's worth, I'm not sure how we should interpret the Yamnaya percentages for Pashtuns and Sindhis. Based on what we currently know, they seem much too high, even the lower bounds. The HGDP Pashtuns are, for all intents and purposes, approximately 0% WHG. Not only do they lack the WHG found in Europeans, but they even seem to lack the residual WHG we see in certain West Asian populations (I'm basing this on David's K8). By contrast, the Yamnaya seem to be around 35% WHG. Even if the HGDP Pashtuns are only around 60% Yamnaya-admixed (the lower bound), the WHG-portion just can't be figured into it. With time, I guess we'll figure it all out.

    Although, it is notable that most of the Yamnaya samples are as ANE-admixed as the HGDP Pashtun samples. The Yamnaya average for ANE is 34%, while the HGDP Pashtun average is also around 34%. Perhaps the approximately equal amounts of ANE ancestry is inflating the similarity (not to mention shared ENF ancestry), even though the actual genetic contribution from Yamnaya to Pashtuns is significantly smaller?

    To test this, I think you should try "Yamnaya, Papuan, Iranian". This might give us an idea of what we are actually seeing.

    Just for the fun of it, could you eventually run "Lezgin, Papuan, Pathan", when you find the time (I wish we had the Onge, but Papuan seems to have worked reasonably well)? Also, I was hoping you could use only these HGDP samples, for this qpBound experiment:

    HGDP00213
    HGDP00243
    HGDP00244
    HGDP00259
    HGDP00262

    Thanks in advance.

    Edit: In addition to "Yamnaya, Papuan, Iranian", and "Lezgin, Papuan, Pathan" (with "Pathan" consisting of HGDP00213, HGDP00243, HGDP00244, HGDP00259, and HGDP00262), another thing to try would be "Yamnaya, Paniya, Pathan"+"Yamnaya, Paniya, Sindhi" (same Pashtun samples). The Paniya are around 40%-50% West Eurasian, so they aren't a good ASI reference. But, they definitely don't have Yamnaya ancestry, because they have 0% Baloch/Gedrosia (and 0% NE Euro). As a result of this, we might see more reasonable Yamnaya estimates for Pashtuns and Sindhis. Not to mention that the Paniya's West Eurasian admixture would make them a more accurate surrogate for the actual South Asian parental population involved with Sindhis and Pashtuns in relation to Yamnaya.
    Last edited by Sein; 03-07-2015 at 04:18 AM.

  12. #507
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    Quote Originally Posted by everest59 View Post
    The ones that Chad gave me all produced +ve f3 stat. Here are some others that I just tested:
    result: Yamnaya Dai Sindhi -0.006478 0.000533 -12.142 236964
    result: Yamnaya Dai Pathan -0.007256 0.000525 -13.812 236729
    result: Yamnaya BedouinB Armenian -0.003075 0.000414 -7.421 225089
    result: Yamnaya BedouinB Pathan 0.002317 0.000434 5.336 237400
    result: Yamnaya BedouinB Sindhi 0.005813 0.000452 12.867 237713
    result: Yamnaya Armenian Lezgin -0.003189 0.000410 -7.771 221623

    For those that produced -ve f3 stats, here are the qpBound results:

    Yamnaya Dai Sindhi -0.006478 -12.142 -nan -nan
    Yamnaya Dai Pathan -0.007256 -13.812 -nan -nan
    Yamnaya BedouinB Armenian -0.003075 -7.421 0.171 0.650
    Yamnaya Armenian Lezgin -0.003189 -7.771 0.153 0.501

    Obviously, Dai does not represent ASI, so that did not work.
    As for Armenians and Lezgins, it worked, and I see a big range. Lezgins as a mixture of Yamnaya and Armenian have anywhere from 15% to 50% Yamnaya admixture. Yamnaya,BedouinB; Armenian on the other hand is 17-65%.

    Actually, it worked with Papuan. It appears, it came up with a range for ANI:
    Yamnaya Papuan Sindhi -0.005436 -8.018 0.551 0.851
    Yamnaya Papuan Pathan -0.005507 -7.620 0.592 0.847

    Obviously, it isn't very accurate given what we would expect (i.e. Pathans should have higher ANI than Sindhis). The bigger difference is in the lowerbound.
    Would using Han as an East Asian stand in help any? What way can we use this to test for EHG in the Karitiana? I'm interested to see if EHG is a better fit for the non-East Eurasian part than MA-1. Would an f4 be best, and how would you set that up?

  13. #508
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    Chad are you implying that German Beakers had no Iberian input whatsoever? Need I remind you that Both the Beaker sample and the Benzigerode sample's lowest resnorm for the N=2 case do not include Yamnaya in the mixture instead they include 75.2% Spain_MN and 71.2% Spain_MN with 24.8% Karelia_HG and 26.9% Karelia_HG.

  14. #509
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    Quote Originally Posted by Chad Rohlfsen View Post
    ... I'm interested to see if EHG is a better fit for the non-East Eurasian part than MA-1. ...
    Karelia EHG is too downstream (abt 17000years), but it almost certain that ancestors of Karelia EHG were closer to the "non-East Eurasian" portion of the Karitiana than MA-1 was. The f stats as well as admixture point to that.

    (I have put non-East Eurasian in quotes since ~24000 ybp both ANE and EHG were also East Eurasian, and in fact what we now know of as East Eurasian could have still been further to the west in the Tibet-Nepal-SW China-Burma area.)

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    Given their WHG and Cordeds lack thereof, does show any Iberian input is minimal. Secondly, there is no pure EHG migration to back your continued support for Iberia. Spain MNE wasn't higher than German MNE for drift. You would need those Iberians to mix with something almost pure WHG before mixing with Corded. Again, not possible.
    Last edited by Chad Rohlfsen; 03-07-2015 at 04:20 AM.

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