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Thread: DF27 aDNA Discussion Thread

  1. #21
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    Quote Originally Posted by Webb View Post
    I think I was incorrect. FTDNA has this snp on their tree with a Canadian and German but doing a little more digging, I believe this sample clusters somewhere with the Colombian and Scot under R-PH92.
    According to the post by Roberta at https://dna-explained.com/2020/09/18...-updates-here/ they are R-Y75899 and are below R-Y31431 which is a brother clade to R-PH92.

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  3. #22
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    Quote Originally Posted by R.Rocca View Post
    It's not that. Most ancient DNA samples are purposely not whole genome tested, but rather are targeted around certain areas to get the most DNA comparison against other samples for autosomal PCRs etc. The positions where DF27 and U152 are located are not called. Some of the earlier studies did call those areas, but that is not longer the case with the newer ones.
    Well, this is not the first time we've had this conversation. And I take your point, in post #950 here: https://anthrogenica.com/showthread....l=1#post635249 If they are testing with a 1240K array, and those loci are not on the test, their failure to find DF27 and U152 is not because of their fear of deamination at loci they aren't seeing.

    On the other hand, if academics tell us they are throwing out C>T and G>A results a priori, I think we should believe them. This was stated in the Mittnik et al paper about the Lech Valley. That was when I started objecting. https://anthrogenica.com/showthread....l=1#post609549.

    And I don't think I was mistaken, because even if DF27 and U152 loci were on an array they used, they would have tossed a single-call example. (They would accept two out of three; but most of those aDNA samples aren't yielding three calls at a locus.) This is what they said, quoted from the Mittnik et al paper by Wing Genealogist in post #6 of that same thread:

    SI 4 – Y-chromosomal haplogroup assignment
    Assignment for Y-chromosomal haplogroups was performed following the nomenclature of the
    International Society of Genetic Genealogy (ISOGG) version 11.110 (retrieved 21 April 2016,
    http://www.isogg.org). Haplogroup defining SNPs that were covered in any of the 53 males are
    listed in table S8. Calls on C-to-T [like U152+] or G-to-A [like DF27+] SNPs were only considered
    reliable when more than 50% of calls showed the allele (table S8).
    So the other problem besides leaving those loci off the chip test (your explanation) was not believing their eyes when they used NextGen sequencing and the locus was covered (my complaint -- admittedly relevant for only a minority of the aDNA results we are now seeing).

    Parenthetically, a couple of years ago Armando and I brought I0806 Quedlinburg guy to the attention of IŮigo Olalde, on a 23andMe chat. And IIRC he corresponded further with Armando. Somewhere (I can't find it) he mentioned that they wouldn't accept a single call for a G to A mutation, because of the probability of its just being damage. But you (Rocca) had also seen a ZZ11+ call for that sample.

    Anyway -- in the race to discover (via aDNA) and explain the peopling of western Europe, DF27 starts with his left foot wearing a lead shoe (disregard potential deamination damage), and his right foot wearing a concrete block (leave it off the test). Ready, set, GO!!! L21 wins, with U152 a distant second, on the back of his speedy grandson L2! DF27 not in the race. Who would have thought it. Luck of the Irish.
    Last edited by razyn; 09-27-2020 at 05:31 PM.

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  5. #23
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    Quote Originally Posted by razyn View Post
    Parenthetically, a couple of years ago Armando and I brought I0806 Quedlinburg guy to the attention of IŮigo Olalde, on a 23andMe chat. And IIRC he corresponded further with Armando. Somewhere (I can't find it) he mentioned that they wouldn't accept a single call for a G to A mutation, because of the probability of its just being damage. But you (Rocca) had also seen a ZZ11+ call for that sample.

    Anyway -- in the race to discover (via aDNA) and explain the peopling of western Europe, DF27 starts with his left foot wearing a lead shoe (disregard potential deamination damage), and his right foot wearing a concrete block (leave it off the test). Ready, set, GO!!! L21 wins, with U152 a distant second, on the back of his speedy grandson L2! DF27 not in the race. Who would have thought it. Luck of the Irish.
    You remember correctly. Olalde, out of the blue, responded to a post of mine about the origin of DF27. That is when I brought up DF27 in I0806 Quedlinburg and I even gave him a link to Anthrogenica, most likely to this post, and I also pointed out,in similar words, that the lack of a read of DF27 in ancient specimens doesn't allow for a proper hypothesis of the origin of DF27 in Europe. Unfortunately he didn't respond to that last point. My hope is that someday high resolution NGS or WGS testing is done on all of the R1b-M343 specimens and if possible they use petrous bone.

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  7. #24
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    It's not hard to believe df27 is hard to read since even in our fresh samples, many here have just an inferred positive for df27. i.e me after a m343 pack and a BigY.
    Let' say you find another snp contemporary to, or close enough to df27, would that be a big deal to change ?

  8. #25
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    Quote Originally Posted by Ric View Post
    It's not hard to believe df27 is hard to read since even in our fresh samples, many here have just an inferred positive for df27. i.e me after a m343 pack and a BigY.
    Let' say you find another snp contemporary to, or close enough to df27, would that be a big deal to change ?
    We've known ever since Thomas Krahn created the individual SNP test for DF27 that it was hard to read. See https://www.worldfamilies.net/forum/...?topic=10485.0 The issue is that ever since Rocca et al. 2012 geneticists should have known to find a way to be sure that DF27 would be captured with their testing even if they have to use two different tests on the same specimen which is what seemed to happen with I0806 from Quedlinburg and esp005 from Valdiosera et al. 2018 and subsequently Olalde et al. 2019. The testing you got at FTDNA is different from what is done by geneticists on ancient specimens. The Big Y testing at least captures so many variants that it is easy to find existing, and new mutations that were previously unknown, downstream from DF27 wheres the 1240k testing, and similar, by geneticists on ancient specimens, only captures specific regions and therefore a huge number of positions on the Y chromosome is missed and therefore what would be inferred as DF27 due to downstream markers is labeled as P312 or upstream if the DNA damaged so badly that even P312 doesn't have a read.

    There is no contemporary to DF27. All mutations downstream from DF27 are descendants of DF27 and therefore younger. It is many of these downstream markers that are not captured by the testing performed by geneticists on ancient specimens. I've pointed the problem of a lack of a read on DF27 and downstream markers in a lot of posts, in this forum and others, prior to this thread.
    Last edited by ArmandoR1b; 09-27-2020 at 08:50 PM.

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  10. #26
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    United States of America United Kingdom Germany Ireland Scotland Wales
    It seems that there isn’t a problem calling Z225 or Z195, at least by a number of people who have gone through the bam files when they become available. I would assume, then that these two markers are on the 1240k testing, however, there is still a lot of DF27 that isn’t either of these clades.

  11. #27
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    VK335 is also at YFull. I just found it by going to the YFull DF27 page and searching for VK. It was probably there already when I made the first table.

    Sample Coverage YFull v8.08.00 link YFull formed Country MajorDivision MinorDivision Age Finer_age 14C Cal. Date (1 sigma) SampleType
    VK166 4.498 https://bit.ly/3353vNp 2800 ybp UK Oxford, England St_Johnís_College_Oxford Viking 880-1000 CE Petrous
    VK87 3.021 https://bit.ly/3j6ZfCG 4500 ybp Denmark Jutland Hesselbjerg Viking 850-900 CE Tooth
    VK403 1.49 https://bit.ly/36aI2EA 3500 ybp Sweden Skara Varnhem Viking 10-12th centuries CE Petrous
    VK329 1.195 https://bit.ly/3mSXlb2 3100 ybp Denmark Jutland Ribe Viking 9-11th centuries CE 711-864 CE Petrous
    VK335 1.058 https://bit.ly/2FWGtQh 4400 ybp Sweden Oland Oland Viking 9-11th centuries CE Petrous
    VK261 1.049 https://bit.ly/2EBvvPf 4500 ybp UK Dorset, England Ridgeway_Hill_Mass_Grave_Dorset Viking 10-11th centuries CE 970-1025 CE Petrous
    VK147 0.822 UK Oxford, England St_Johnís_College_Oxford Viking 880-1000 CE Petrous
    VK365 0.764 Denmark Langeland BogÝvej Viking 10th century CE Tooth

  12. #28
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    Quote Originally Posted by Webb View Post
    It seems that there isn’t a problem calling Z225 or Z195, at least by a number of people who have gone through the bam files when they become available. I would assume, then that these two markers are on the 1240k testing, however, there is still a lot of DF27 that isn’t either of these clades.
    If the DNA isn't damaged at the position that Z195 is found at then Z195 will have a call. If it is damaged then we have to rely on other markers. The majority of the VK samples have a coverage greater than 0.5 and a very large number were done on the petrous bone. VK261, VK329, VK403 and VK87 are positive for markers downstream of Z195. I'll check to see if all of them have a read on Z195 but they probably do since they have a coverage of greater than 1.0 and most of them had testing done on the petrous bone. That isn't the case with all studies of ancient specimens!

    Something else that is very important is that Z195 is only 40%-60% of all DF27. So even when Z195 is captured and testing isn't done well enough then all of the samples that should be DF27+ but are Z195- aren't recognized as DF27+ unless positive for a downstream marker which can easily be missing or ignored due to be a possible false positive due to deamination.

    The Olalde et al. 2018 study had a lot of samples that had no read on Z195. The coverage isn't noted in the supplementary table. I created a table with extra columns from that study and posted it in another thread quite some time ago but I'll post it here again so you can see which R-M269 specimens did not get a read on Z195. Look for the columns labeled Negative and No Coverage.


    Code:
    ID Colloquial ID Y haplogroup-ISOGG version 11.110 (21 April 2016) SNP or equivalent Derived SNP and 2016 Haplogroup Negative No Coverage SNPs in autosomes Label Grouping for Beaker-associated individuals
    I4890 feature 545 R1b1a1a2a1a L151 L151/PF6542=R1b1a1a2a1a P312, DF27, Z195, L21, U152 37,650 Beaker Central Europe BK_Czech_CZE
    I7288 RDVS_59/80-I1 R1b1a1a2 M269 CTS11468/PF6520=R1b1a1a2 P312, DF27, Z195, L21, U152 91,114 Beaker Central Europe BK_Czech_CZE
    I5024 RISE566, F0521, A01168, gr. 14 R1b1a1a2a1a L151 L151/PF6542=R1b1a1a2a1a P312, DF27, Z195, L21, U152 92,728 Beaker Central Europe BK_Czech_CZE
    I1381 2-Grave487 R1b1a1a2a1a L151 L151/PF6542=R1b1a1a2a1a U106, L21 P312, DF27, Z195, U152 690,979 Beaker Central Europe BK_France_Mon
    I1382 3-Grave515 R1b1a1a2a1a2 P312 P312=R1b1a1a2a1a2 L21 DF27, Z195, U152 607,837 Beaker Central Europe BK_France_Mon
    I1390 11-Grave68 R1b1a1a2a1a2 P312 P312=R1b1a1a2a1a2 DF27, Z195, L21, U152 449,568 Beaker Central Europe BK_France_HAR
    I1389 10-Grave69 R1b1a1a2a1a2 P312 P312=R1b1a1a2a1a2 DF27, Z195, L21, U152 97,913 Beaker Central Europe
    I3599 Grave 13 R1b1a1a2a1a2 P312 P312=R1b1a1a2a1a2 DF27, Z195, L21, U152 36,524 Beaker Central Europe
    I3588 Grave 2 R1b1a1a2a1a L151 P310/PF6546/S129=R1b1a1a2a1a U106, L21 P312, DF27, Z195, U152 419,937 Beaker Central Europe BK_Germany_BAV
    I4132 RISE560, F0187, grave 3 R1b1a1a2a1a2 P312 P312=R1b1a1a2a1a2 DF27, Z195, L21, U152 271,486 Beaker Central Europe
    I5661 RISE926 R1b1a1a2 M269 PF6543/S1159/YSC0000191=R1b1a1a2a1a DF27, Z195, L21, U152 90,529 Beaker Central Europe BK_Germany_BAV
    I5663 RISE929 R1b M343 M343=R1b P297, M269, L23, L51, L52, L151, DF27, Z195, L21, U152 23,224 Beaker Central Europe BK_Germany_BAV
    I5657 RISE921 R1b1a1a2 M269 PF6509=R1b1a1a2 L23, L51, L52, L151, DF27, Z195, L21, U152 61,081 Beaker Central Europe
    I5660 RISE925 R1b1a1a2 M269 two R1b1a1a2 SNPs L23, L51, L52, L151, DF27, Z195, L21, U152 58,395 Beaker Central Europe
    I3604 Obj. 278, grave 9 R1b1a L754 CTS10349/FGC42/PF6492=R1b1a1a2 L23, L51, L52, L151, DF27, Z195, L21, U152 30,589 Beaker Central Europe BK_Germany_BAV
    I3607 Obj. 335, grave 7 R1b1a1a P297 CTS5577/PF6464=R1b1a1a M269,L23, L51, L52, L151, DF27, Z195, L21, U152 10,064 Beaker Central Europe BK_Germany_BAV
    I5021 RISE563, F0234, obj. 8, grave 3 R1b1a1a2 M269 four R1b1a1a2 SNPs L23, L51, L52, L151, DF27, Z195, L21, U152 97,061 Beaker Central Europe BK_Germany_BAV
    I5022 RISE564, F0241, obj. 25, grave 6 R1b1a1a2 M269 two R1b1a1a2 SNPs L23, L51, L52, L151, DF27, Z195, L21, U152 65,655 Beaker Central Europe BK_Germany_BAV
    I0805 QLB26 R1b1a1a2 M269 two R1b1a1a2 SNPs L23, L51, L52, L151, DF27, Z195, L21, U152 225,361 Beaker Central Europe BK_Germany_SAN
    I1530 ROT1 R1b1a1a2 M269 CTS623/PF6419=R1b1a1a2 L23, L51, L52, L151, DF27, Z195, L21, U152 32,225 Beaker Central Europe
    I6534 HB0030 R1b1a1a2 M269 two R1b1a1a2 SNPs L23, L51, L52, L151, DF27, Z195, L21, U152 72,026 Beaker Central Europe BK_Poland_POL
    I4251 RISE1122, grave 7 R1b1a1a2 M269 five R1b1a1a2 SNPs L23, L51, L52, L151, DF27, Z195, L21, U152 80,714 Beaker Central Europe BK_Poland_Sam
    I5755 BB_01_MXI R1b1a1a2 M269 four R1b1a1a2 SNPs L23, L51, L52, L151, DF27, Z195, L21, U152 119,998 Beaker Central Europe BK_Switzerland_Sio
    I5757 BB_18_MXI R1b1a1a2a1a L151 L151=R1b1a1a2a1a P312, DF27, Z195, L21, U152 74,999 Beaker Central Europe BK_Switzerland_Sio
    I2478 T1 ind b Us 9 R1b1a1a2a1a2 P312 P312=R1b1a1a2a1a2 Z195, L21 DF27,U152 622,069 Beaker Northern Italy BK_Italy_Gui3
    I1388 9-Grave1 R1b1a1a2a1a L151 L151=R1b1a1a2a1a U106 P312, DF27, Z195, L21, U152 375,748 Beaker Southern France BK_France_Mar
    I4068 skeleton 228-M3 R1b1a1a2a1a2 P312 P312=R1b1a1a2a1a2 L21 DF27, Z195, U152 469,691 Beaker The Netherlands BK_Netherlands_Tui
    I4069 skeleton 229-M4 R1b1a1a2a1a2 P312 P312=R1b1a1a2a1a2 L21 DF27, Z195, U152 721,500 Beaker The Netherlands BK_Netherlands_Tui
    I5748 skeleton 575 (Jan) M22 R1b1a1a2a1a2 P312 P312=R1b1a1a2a1a2 L21 DF27, Z195, U152 636,009 Beaker The Netherlands BK_Netherlands_Tui
    I5750 skeleton 230 Extra-M8 R1b1a1a2a1a2 P312 P312=R1b1a1a2a1a2 Z195 DF27, L21, U152 641,693 Beaker The Netherlands BK_Netherlands_Tui
    I7202 Grave 94 R1b1a1a2a1a2 P312 P312=R1b1a1a2a1a2 L21 DF27, Z195, U152 548,005 Czech_EBA
    I6537 HB0049 R1b1a1a2a1a L151 P310=R1b1a1a2a1a U106, L21 P312, DF27, Z195, U152 533,101 Poland_BA
    Last edited by ArmandoR1b; 09-27-2020 at 09:22 PM.

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  14. #29
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    By the way, if anyone wants to see which SNPs are included in the 1240k SNP test see the thread at https://anthrogenica.com/showthread....1-1240K-Y-SNPs
    Last edited by ArmandoR1b; 09-27-2020 at 09:41 PM.

  15. #30
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    Quote Originally Posted by Webb View Post
    It seems that there isn’t a problem calling Z225 or Z195, at least by a number of people who have gone through the bam files when they become available. I would assume, then that these two markers are on the 1240k testing, however, there is still a lot of DF27 that isn’t either of these clades.
    Quote Originally Posted by ArmandoR1b View Post
    If the DNA isn't damaged at the position that Z195 is found at then Z195 will have a call. If it is damaged then we have to rely on other markers. The majority of the VK samples have a coverage greater than 0.5 and a very large number were done on the petrous bone. VK261, VK329, VK403 and VK87 are positive for markers downstream of Z195. I'll check to see if all of them have a read on Z195 but they probably do since they have a coverage of greater than 1.0 and most of them had testing done on the petrous bone. That isn't the case with all studies of ancient specimens!
    I found time to analyze VK261 and VK329. Neither of them have a read for Z225 or Z195 and therefore their placement on the Y-DNA tree is based on downstream SNPs from Z195 since they are both inferred positive for Z195. So even with these specimens with decent coverage with DNA from the petrous bone have a problem with both Z225 and Z195.

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