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Thread: DF27 aDNA Discussion Thread

  1. #31
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    Quote Originally Posted by Mikewww View Post
    You guys have plowed through the "The genomic history of the Iberian Peninsula over the past 8000 years" by Olalde, right? I found this in the supplement trying to find more info R1b-P312 people.

    "Only one Bronze Age male, esp005.SG (7), had DNA sequences overlapping R1b-DF27 (R1b1a1a2a1a2a) and he was positive for the mutation. Two Bronze Age males, I6470 and I3997, had DNA sequences overlapping R1b-Z195 (R1b1a1a2a1a2a1), with I6470 being negative and I3997 positive. Eleven Bronze Age males had DNA sequences overlapping R1b-Z225 (R1b1a1a2a1a2a5), with only VAD001 being positive for the mutation (one Iron Age male, I3320, is also positive for this mutation). We thus detect three Bronze Age males who belonged to DF27 (154, 155), confirming its presence in Bronze Age Iberia. The other Iberian Bronze Age males could belong to DF27 as well, but the extremely low recovery rate of this SNP in our data set prevented us to study its true distribution."

    Almost any of these studies that show R1b-P312 people may not be picking up DF27 nor ZZ12. There could be a lot of folks that are ZZ12 that look like P312.
    As I have posted in this thread, and in threads in the past, I already knew about the issue of a lot of specimens not getting calls on DF27, and subclades of DF27, but I hadn't personally analyzed the files since it didn't seem necessary. Due to other comments in this thread I have been looking at the BAM files. So far I have seen what we have known about the previous Olalde et al. 2018, and what you quoted, that most of them don't have calls for Z195. However, I have found one specimen I12209 dated 1368–1211 BCE from La Requejada, San Román de Hornija, Valladolid, Castilla y León that has a derived (positive) read for DF27. Probably another example of a G->A mutation being ignored due to possible deamination. He has a no-call for Z195 and is ancestral for Z274 and Z272. I would really like some other people to look at this specimen.
    Last edited by ArmandoR1b; 10-01-2020 at 02:01 AM.

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  3. #32
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    Quote Originally Posted by ArmandoR1b View Post
    I have found one specimen I12209 dated 1368–1211 BCE from La Requejada, San Román de Hornija, Valladolid, Castilla y León that has a derived (positive) read for DF27. Probably another example of a G->A mutation being ignored due to possible deamination.
    I feel kind of vindicated... although 15 or so would have been better. I remember that I0806 was sequenced twice, and Rocca found the DF27+ call only in one of the BAM files. Sheer luck, I think. Likewise with the downstream clades that the chip tests may occasionally find -- they aren't using a very robust list. But there might easily be extinct DF27 subclades, that could be picked up by a chip test but be unrecognized as such. Practically speaking, we only know the phylogeny below DF27 from testing men alive in the 21st century -- whose ancient (or young) YDNA lines have not daughtered out.

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  5. #33
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    Quote Originally Posted by ArmandoR1b View Post
    As I have posted in this thread, and in threads in the past, I already knew about the issue of a lot of specimens not getting calls on DF27, and subclades of DF27, but I hadn't personally analyzed the files since it didn't seem necessary. Due to other comments in this thread I have been looking at the BAM files. So far I have seen what we have known about the previous Olalde et al. 2018, and what you quoted, that most of them don't have calls for Z195. However, I have found one specimen I12209 dated 1368–1211 BCE from La Requejada, San Román de Hornija, Valladolid, Castilla y León that has a derived (positive) read for DF27. Probably another example of a G->A mutation being ignored due to possible deamination. He has a no-call for Z195 and is ancestral for Z274 and Z272. I would really like some other people to look at this specimen.
    That sample was called as P312 by Kolgeh, here: https://anthrogenica.com/showthread....l=1#post672282.

    However, it was called as ZZ12>BY15964 by R.Rocca, here: https://anthrogenica.com/showthread....l=1#post556114

    Hence my observation of the possibility of Z195 and Z225 being captured on the 1240K tests because R. Rocca determined a number of the samples from the Iberian paper were Z195. The two Sicilian BB samples were called as Z195 by Reich. Then sample, VAD001, DF27>Z225, 1867–1616 cal BCE (3400±35 BP, Ua-36345) ... C_Iberia_BA, Cogotas I, La Requejada, San Román de Hornija, Valladolid and this sample from the French Paper, OBE3626-1, Eastern France (Bas-Rhin, Alsace): 3505 +/- 35BP, 1926-1701 BC (c. 1813 BC), ZZ12 >Z229. So it might be that the location of Z229 is captured on the 1240K test as opposed to Z225.

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  7. #34
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    Quote Originally Posted by Webb View Post
    That sample was called as P312 by Kolgeh, here: https://anthrogenica.com/showthread....l=1#post672282.
    Even the authors had caught that is was P312. They listed it as R1b1a1a2a1a2(xR1b1a1a2a1a2c,xR1b1a1a2a1a2b1,xR1b1a 1a2a1a2a5) which is P312 (xL21,xL2,xZ225). Notice here they don't mention Z195 or U152. That is because it does not have a read for Z195. I was more interested in the call for DF27.

    Quote Originally Posted by Webb View Post
    However, it was called as ZZ12>BY15964 by R.Rocca, here: https://anthrogenica.com/showthread....l=1#post556114
    It's hard to tell from that post if he also saw that I12209 had a derived read for DF27. Veering off the subject a bit, BY15964 has also been found in men from Mexico and from Portugal. It is a phylogenetic equivalent of R-BY15963 You have to drill down to the subclades of R-BY15963 to see all of them.


    Quote Originally Posted by Webb View Post
    Hence my observation of the possibility of Z195 and Z225 being captured on the 1240K tests because R. Rocca determined a number of the samples from the Iberian paper were Z195. The two Sicilian BB samples were called as Z195 by Reich. Then sample, VAD001, DF27>Z225, 1867–1616 cal BCE (3400±35 BP, Ua-36345) ... C_Iberia_BA, Cogotas I, La Requejada, San Román de Hornija, Valladolid and this sample from the French Paper, OBE3626-1, Eastern France (Bas-Rhin, Alsace): 3505 +/- 35BP, 1926-1701 BC (c. 1813 BC), ZZ12 >Z229. So it might be that the location of Z229 is captured on the 1240K test as opposed to Z225.
    There is a difference between a test including an SNP and a specimen having DNA at the position that the SNP exists. Most of the samples definitely did not get a read on Z195 and Z225 due to decay of the DNA. That was the point made by the statement by the authors of Olalde et al. 2019 that Mikewww quoted. It is an accurate statement made by the authors. Therefore it doesn't matter if the test includes an SNP when the specimens have damaged DNA due to decay at the specified position. I'll keep working on getting a list of specimens with a call for Z195 and Z225 in Olalde et al. 2019 and the Viking World study. In the meantime I suggest taking a look at again at my post #28 in this thread where I pointed out which specimens in Olalde et al. 2018 do not have a read on Z195. Only 2 out of 32 have a read on Z195. This proves it is hard to get a result for that SNP in a lot of the ancient specimens. Even if it is done with the petrous bone such as I12209, VK261 and VK329. Those last two didn't even have a read for Z225. The lack of a read is very important especially since so many people don't understand that a lack of a positive read of a specific SNP many times is because of DNA decay and not because the specimens were negative for the SNP. A lack of evidence is not evidence.

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  9. #35
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    Maybe this is simplistic, misguided, or totally irrelevant but I'm going to ask it anyway:

    After looking at the VK samples, does it seem like a possibility that DF27 could have been carried by "Germanic" peoples?
    Perhaps its a question of opinion, but could part of the high DF27 percentages in Spain and France be attributed to a group such as the Visigoths?

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  11. #36
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    Quote Originally Posted by sktibo View Post
    Maybe this is simplistic, misguided, or totally irrelevant but I'm going to ask it anyway:

    After looking at the VK samples, does it seem like a possibility that DF27 could have been carried by "Germanic" peoples?
    Perhaps its a question of opinion, but could part of the high DF27 percentages in Spain and France be attributed to a group such as the Visigoths?
    Many many years ago I had a theory about DF27 and Goths, but Razyn laughed at me. So I never brought it up again. My emotional wounds were starting to heal, but thanks to your post, I have just called to make an appointment with my therapist. Joking aside, while I think most DF27 in Spain predates Goths, I am starting to speculate that our Germanic tribes who went wandering, were a conglomerate of many various haplogroups. We now have quite a few Bronze Age DF27 samples from Spain, so we know it was there early. The oldest sample, however, is still the Quedlinburg, Germany sample, from around 2500 B.C., which is in the heart of Germany. One of the questions not yet answered, is how far North did P312, in this case DF27 get during P312's maximal geographic spread? Was DF27 a large factor in the Belgic tribes? We have the DF27 Alsace sample from around 1900 B.C., which is close. The Rhine Delta has flooded and been cleared and repopulated many times, and there is evidence of flooding mitigation as early as 500 B.C.. Were the Belgae a mixed bag of haplogroups, the Frisians, then the Franks? I know that I wasn't as surprised by the CTS4065 sample as I was the M167/SRY2627 samples.

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  13. #37
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    Quote Originally Posted by Webb View Post
    I had a theory about DF27 and Goths, but Razyn laughed at me.
    Visigoths. I was only laughing at the Visi part. But anyway, speaking of absurd theories from the distant past, I suggested Ukraine and Poland in this post from seven years (and three days) ago: https://anthrogenica.com/showthread....ll=1#post15080

    And I have suggested Pinsk more recently than that, but still without any hard evidence -- except what I see on northern and eastern European men's haplotree results, and don't see early enough in the Hungarian Plain, squeezing through the Iron Gates, etc.

    In these latter days, saints preserve us, Generalissimo is theorizing about Corded Ware / SGC guys spreading their autosomes into Hungary and Moravia from the north; and hinting at papers he can't talk about yet with ancient DNA of L51, L11, P312 or some of those guys in the suburbs of Moscow.

    I think we are getting closer to finding out, but I'm still not sure. I just continue to look farther east than most do, for our YDNA origins.

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  15. #38
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    Quote Originally Posted by sktibo View Post
    Maybe this is simplistic, misguided, or totally irrelevant but I'm going to ask it anyway:

    After looking at the VK samples, does it seem like a possibility that DF27 could have been carried by "Germanic" peoples?
    Perhaps its a question of opinion, but could part of the high DF27 percentages in Spain and France be attributed to a group such as the Visigoths?
    The high DF27 percentages in Spain and France is definitely not due to a group such as the Visigoths. That is a group that arrived in Spain in the Roman period. DF27 was already in Spain thousands of years prior to them and any group that could be defined as Germanic. The hot spot of DF27 in France is in the southern part with it being highest along the border of Spain. That is an area that hasn't always been divided as it is now.

    One of the reasons that I am creating a table of the Olalde et al. 2019 study specimens that lack of calls of DF27, Z195, and Z225 is because the lack of those calls means that many of those specimens would have easily shown to be positive for DF27 if there had been a call for DF27 and/or Z195.

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  17. #39
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    Quote Originally Posted by ArmandoR1b View Post
    The high DF27 percentages in Spain and France is definitely not due to a group such as the Visigoths. That is a group that arrived in Spain in the Roman period. DF27 was already in Spain thousands of years prior to them and any group that could be defined as Germanic. The hot spot of DF27 in France is in the southern part with it being highest along the border of Spain. That is an area that hasn't always been divided as it is now.

    One of the reasons that I am creating a table of the Olalde et al. 2019 study specimens that lack of calls of DF27, Z195, and Z225 is because the lack of those calls means that many of those specimens would have easily shown to be positive for DF27 if there had been a call for DF27 and/or Z195.
    The only issue is that the two Sicilian Bell Beakers were called as Z195 by Reich's lab. To me this suggests that Z195 or an equivalent is captured in the 1240K test?

  18. #40
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    Quote Originally Posted by Webb View Post
    The only issue is that the two Sicilian Bell Beakers were called as Z195 by Reich's lab. To me this suggests that Z195 or an equivalent is captured in the 1240K test?
    If the DNA is decayed then there is nothing to capture. Therefore it makes no difference if an SNP is included in a test. Which means we have no idea if an SNP is negative or positive since there is no result when the DNA is decayed.

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