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Thread: The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early Europea

  1. #481
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    Quote Originally Posted by Jean M View Post
    Would anyone who does not mind me using their real name care to confirm, especially the R1a1-M459* which I would be really, really grateful for sometime before I hand over text in October, unless we have some more published R1a from Dnieper-Donets before then. Desperate for this on the origin of Corded Ware.
    I now have the calls from the samples in this paper, courtesy of a member. Thank you! All results are now in my online tables.
    Last edited by Jean M; 02-13-2017 at 01:36 PM.

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  3. #482
    Quote Originally Posted by Romilius View Post
    I see, thanks for sharing... I think that ATP3 is really strange... You also stated he's got a lot of eastern admixture... do you think he is an early arrival in Iberia from the East?
    Yes.

    My discovery a year and a half ago that ATP3 was R1b-M269 is of the greatest importance. With a date of 3516–3362 BC, it's the oldest R1b-M269 sample that we currently have, older than the R1b-M269-Z2103 Pit Grave samples from Eastern Europe.

    My admixture analyses of the El Portalón samples, also going back to a year and a half ago, have shown that ATP2 (2899–2678 BC), ATP3 (3516–3362 BC), ATP7 (3345–2944 BC), ATP9 (1750–1618 BC), and ATP20 (2289–2050 BC) all had significant amounts of Eastern European admixture.

    The Y chromosome and autosomal evidence that I have produced prove that R1b-M269, Eastern European autosomal DNA, and Indo-European languages spread to Western Europe well before 3000 BC, not well after 3000 BC, as just about everybody claims.

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  5. #483
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    Genetiker,

    is there a way you could get raw data for samples from this study? More speciffically, I'm interested in sample NG21-10 (6600 ybp Male, Vinča culture). It has more than decent 339877 SNPs, so it's hard to believe it has only 8 positive calls on Y chromosome (4xBT, 2xCT, 2xF), according to Felix's data.

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  7. #484
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    Quote Originally Posted by genetiker View Post
    These claims made by Richard Rocca about PF6518 being "pretty useless", which ArmandoR1b has so enthusiastically repeated, and which have led to other commenters on other websites claiming that ATP3 was only R1b1a1a-P297 and not R1b1a1a2-M269, are completely false.

    The reason that Rocca observed the derived allele of PF6518 for 1000 Genomes samples not belonging to R1b is that he was looking at the phase 1 data for those samples, which consisted of short reads with low mapping quality (less than 30). What happened is that similar sequences from other parts of the genome were incorrectly aligned to the position of PF6518 on the Y chromosome, making it seem as though the non-R1b samples had the derived allele of PF6518, when in fact they didn't.

    The phase 3 data for the 1000 Genomes samples consists of long reads with high mapping quality (greater than 30), and if you look at that data for the same non-R1b samples that Rocca looked at, you'll see that they all have only the ancestral allele of PF6518.

    The read for ATP3 that's aligned to PF6518 is a long read (109 bases) with a high mapping quality (37), so the positive call for PF6518 for ATP3 is completely reliable.



    Do the search again. You'll see that the derived allele occurs only in C-V20*, G-FGC5672*, and R1b-M269. C-V20* is La Brańa 1 and G-FGC5672* is Ötzi. The apparent presence of the derived allele in those two ancient samples is due either to misalignment or DNA damage.
    Fair enough as long as Rocca agrees. We still don't know which if any of the 104 phylogenetic equivalents to PF6518 are positive and that includes M269. For all we know he could be on a branch that was negative for M269 or any of the other phylogenetic equivalents which would mean he is on a different branch from modern L23 people.

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  9. #485
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    Quote Originally Posted by genetiker View Post
    . . .

    My admixture analyses of the El Portalón samples, also going back to a year and a half ago, have shown that ATP2 (2899–2678 BC), ATP3 (3516–3362 BC), ATP7 (3345–2944 BC), ATP9 (1750–1618 BC), and ATP20 (2289–2050 BC) all had significant amounts of Eastern European admixture.

    The Y chromosome and autosomal evidence that I have produced prove that R1b-M269, Eastern European autosomal DNA, and Indo-European languages spread to Western Europe well before 3000 BC, not well after 3000 BC, as just about everybody claims.
    Well, it is well known that Marija Gimbutas posited three "kurgan waves" of steppe incursion into Europe west of the Dniester:

    Wave 1 - 4400 - 4200 BC
    Wave 2 - 3400 - 3200 BC
    Wave 3 - 3000 - 2800 BC

    If one reads David Anthony carefully, he will see that Anthony says pretty much the same thing. He just does not go quite as far with Waves 1 and 2 as Gimbutas does. Wave 3 is Yamnaya in the third millennium BC.

    Anyway, your ideas in this regard are not way out in left field, not if Gimbutas was right.
    Last edited by rms2; 02-13-2017 at 04:59 PM.
     


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  11. #486
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    Quote Originally Posted by genetiker View Post
    My admixture analyses of the El Portalón samples, also going back to a year and a half ago, have shown that ATP2 (2899–2678 BC), ATP3 (3516–3362 BC), ATP7 (3345–2944 BC), ATP9 (1750–1618 BC), and ATP20 (2289–2050 BC) all had significant amounts of Eastern European admixture.
    Only ATP9 has a significant amount of Eastern European admixture. The others have exactly none.

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  14. #488
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    Quote Originally Posted by Generalissimo View Post
    Only ATP9 has a significant amount of Eastern European admixture. The others have exactly none.
    Have you now done analysis on a higher quality ATP3 sequence to conclusively discount an eastern admixture?

    Davidski: "So does this mean that ATP3 also lacks Yamnaya-related ancestry? Probably, but not necessarily. Large-scale population turnovers were common in ancient Europe, and ATP3 may have been the result of an early migration from the east that didn't leave a lasting impact on Sierra de Atapuerca. I'll need a higher quality sequence of ATP3 to sort this out properly." http://eurogenes.blogspot.com/2015/0...rian-atp2.html

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  16. #489
    D-statistics support the results of my admixture analyses showing Eastern European admixture in ATP3, ATP7, ATP9, and ATP20, and also suggest the presence of such admixture in ATP16 and ATP17:

    Code:
    Pop 1          Pop 2              Pop 3         Pop 4        D stat   Z
    El Mirador CA  El Portalón 2 CA   Pit Grave CA  Mbuti Pygmy  0.0019   0.503
    El Mirador CA  El Portalón 3 CA   Pit Grave CA  Mbuti Pygmy  −0.0169  −1.119
    El Mirador CA  El Portalón 7 CA   Pit Grave CA  Mbuti Pygmy  −0.0173  −1.210
    El Mirador CA  El Portalón 9 MBA  Pit Grave CA  Mbuti Pygmy  −0.0085  −1.552
    El Mirador CA  El Portalón 12 CA  Pit Grave CA  Mbuti Pygmy  0.0000   0.013
    El Mirador CA  El Portalón 16 CA  Pit Grave CA  Mbuti Pygmy  −0.0039  −0.904
    El Mirador CA  El Portalón 17 CA  Pit Grave CA  Mbuti Pygmy  −0.0084  −0.566
    El Mirador CA  El Portalón 20 CA  Pit Grave CA  Mbuti Pygmy  −0.0445  −2.028

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  18. #490
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    Quote Originally Posted by genetiker View Post
    D-statistics support the results of my admixture analyses showing Eastern European admixture in ATP3, ATP7, ATP9, and ATP20, and also suggest the presence of such admixture in ATP16 and ATP17:

    Code:
    Pop 1          Pop 2              Pop 3         Pop 4        D stat   Z
    El Mirador CA  El Portalón 2 CA   Pit Grave CA  Mbuti Pygmy  0.0019   0.503
    El Mirador CA  El Portalón 3 CA   Pit Grave CA  Mbuti Pygmy  −0.0169  −1.119
    El Mirador CA  El Portalón 7 CA   Pit Grave CA  Mbuti Pygmy  −0.0173  −1.210
    El Mirador CA  El Portalón 9 MBA  Pit Grave CA  Mbuti Pygmy  −0.0085  −1.552
    El Mirador CA  El Portalón 12 CA  Pit Grave CA  Mbuti Pygmy  0.0000   0.013
    El Mirador CA  El Portalón 16 CA  Pit Grave CA  Mbuti Pygmy  −0.0039  −0.904
    El Mirador CA  El Portalón 17 CA  Pit Grave CA  Mbuti Pygmy  −0.0084  −0.566
    El Mirador CA  El Portalón 20 CA  Pit Grave CA  Mbuti Pygmy  −0.0445  −2.028
    In that case, shouldn't the D-stats be at the very least Z -2 for ATP3, ATP7, ATP9, and ATP20? They all look insignificant, which might be due to a lack of power, but in that case you need to prove this some other way.

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