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Thread: drought of ancient DNA papers on prehistoric Europe/SW Asia

  1. #941
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    Quote Originally Posted by rms2 View Post
    I could have missed some, but I did a quick count of the British Kurgan Bell Beaker y-dna results. I counted 15 L21 out of 21 total, or about 71%.
    Beaker-era/Bronze Age DF19 just HAS to show up somewhere, some day...

    Circumstantial evidence says they are hiding in a box bordering from Poland>Norway>Ireland>France

    The center of that target points to Germany, Low Countries and East coast of Britain - already some of the oldest, most researched Beaker sites. Yet the oldest DF19 is still from late Roman York.
    R1b>M269>L23>L51>L11>P312>DF19>DF88>FGC11833 >S4281>S4268>Z17112>BY44243

    Ancestors: Francis Cooke (M223/I2a2a) b1583; Hester Mahieu (Cooke) (J1c2 mtDNA) b.1584; Richard Warren (E-M35) b1578; Elizabeth Walker (Warren) (H1j mtDNA) b1583;
    John Mead (I2a1/P37.2) b1634; Rev. Joseph Hull (I1, L1301+ L1302-) b1595; Benjamin Harrington (M223/I2a2a-Y5729) b1618; Joshua Griffith (L21>DF13) b1593;
    John Wing (U106) b1584; Thomas Gunn (DF19) b1605; Hermann Wilhelm (DF19) b1635

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  3. #942
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    Quote Originally Posted by Dewsloth View Post
    Beaker-era/Bronze Age DF19 just HAS to show up somewhere, some day...

    Circumstantial evidence says they are hiding in a box bordering from Poland>Norway>Ireland>France

    The center of that target points to Germany, Low Countries and East coast of Britain - already some of the oldest, most researched Beaker sites. Yet the oldest DF19 is still from late Roman York.
    Unless I am mistaken, I think we still have no ancient y-dna from Kurgan Bell Beaker's Northern Province. Maybe that's where DF19, DF99, and U106 were hiding.

    Beaker Northern Province.jpg

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  5. #943
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    I want more (really, any) papers by academicians who aren't wearing blinders that lead them -- rather than make an erroneous call due to possible deamination -- to throw out C>T or G>A results. If the mutation they should be looking for is one (such as U152) for which that is the defining mutation, they damn well ought to pay attention, before they throw it out. Is the sample otherwise P312*? ZZ11+? (Or whatever -- U152 isn't the only example.) It's one thing to err on the side of caution; but it's something else to err by project design.

    I'm the grandson of a harness manufacturer, and I have some ~90-year-old catalogs from his company. There may be six or eight pages illustrating the different blinder designs one might order, normally as bridle attachments. They were very useful for a team, in traffic. The driver wants them not to be distracted, e.g. by a tin lizzie, or a really cute mare. But if your job is to look for something a bit off the beaten path, you really should not put them on before your journey begins.

    P1016678.jpg
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    Last edited by razyn; 01-03-2020 at 08:59 PM.

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  7. #944
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    What's the solution to that problem?

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    Apart from savage and repeated floggings at the gratings, I'm a bit stuck for remedial treatment of this particular condition.
    It affects archaeology even more virulently than palaeogenetic inquiries.

    In UK, at least three of the "leading lights" are self-described "marxists". Leading to dead-ends of reasoning, and what #1 son nailed as "Ha! Whig history, then?", when I was attempting to describe the archaeological impasse over the Hogmanay cocktails.
    Not any sort of Marx that I ever read. That's the odd thing.

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  11. #946
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    Quote Originally Posted by razyn View Post
    I want more (really, any) papers by academicians who aren't wearing blinders that lead them -- rather than make an erroneous call due to possible deamination -- to throw out C>T or G>A results. If the mutation they should be looking for is one (such as U152) for which that is the defining mutation, they damn well ought to pay attention, before they throw it out. Is the sample otherwise P312*? ZZ11+? (Or whatever -- U152 isn't the only example.) It's one thing to err on the side of caution; but it's something else to err by project design.

    I'm the grandson of a harness manufacturer, and I have some ~90-year-old catalogs from his company. There may be six or eight pages illustrating the different blinder designs one might order, normally as bridle attachments. They were very useful for a team, in traffic. The driver wants them not to be distracted, e.g. by a tin lizzie, or a really cute mare. But if your job is to look for something a bit off the beaten path, you really should not put them on before your journey begins.

    P1016678.jpg
    I think the bigger issue has been with the selected coverage of 1240k positions as opposed to whole genome sequencing. The 1240k misses both U152 and DF27. I was told a while back that the 1240k would be expanded to include many more Y-DNA SNPs and I see in the Sicily pre-print that most of the samples are labeled as "1240k, mtDNA+3000SNPs". Hopefully it will include them.
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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  13. #947
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    Quote Originally Posted by rms2 View Post
    What's the solution to that problem?
    I think he’s suggesting removing the blinders.

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    Quote Originally Posted by Webb View Post
    I think he’s suggesting removing the blinders.
    What does that mean? Assuming that no C>T or G>A result is ever the product of deamination?

    I'm no geneticist, but how does one really get around such a problem as things currently stand?

    I guess what Rich R suggested above is the answer, but it doesn't fix the problem with past 1240k results.

  15. #949
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    I am indeed suggesting removing them, or really, not starting with them attached. I can see using them more like clip-on sunglasses, rather than assuming that Xlocus, C-T is a real, possibly new, mutation. But this is 2020, and we already know what to look for, if we have a BAM file. Some of what-to-look-for (as we know from sequencing hundreds, or thousands, of living guys) is in fact C-T, or G-A. And it (e.g. U152+) is patently ancient; so it should (and we know from a handful of BAM files that it does) appear in that form, anciently. But if it does, willy-nilly, they are throwing it out. That is a protocol, but clearly an unscientific one. More like antiscientific.

    I raised this objection once before, but can't find it. I think it was in discussing the Mittnik et al paper; anyway a very recent (2019) one, in which the co-authors specifically stated that those calls were excluded because they might be the artifacts of deamination. And some heavy artillery types, maybe Wing Genealogist and/or lgmayka, argued in favor of doing so. It was someone whose work I respect, but I beg to differ with whoever it was.

    There is another set of blinders associated with "heterozygosity." DF27, to state one important example, reads one way forward and another way reverse (strand that is being observed, at a given location on a given pass). On a one-pass chip observation, that's rarely if ever getting called a SNP.

    I know that impoverished grad students can't afford NextGen sequencing to be sure of their calls. But I can, and I do, wish there were more pressure on non-impoverished aDNA labs in places like Cambridge (either one), Jena, Copenhagen and Leicester to spend what it takes to get it right. We know, and care, where it's phylogenetically important to look. Do they?

    I got the impression from the following article that there is something that can be done in the sample preparation phase; but I don't fully understand this language, and am too old to learn it. Just as part of the conversation, though: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3685887/

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    Quote Originally Posted by razyn View Post
    I am indeed suggesting removing them, or really, not starting with them attached. I can see using them more like clip-on sunglasses, rather than assuming that Xlocus, C-T is a real, possibly new, mutation. But this is 2020, and we already know what to look for, if we have a BAM file. Some of what-to-look-for (as we know from sequencing hundreds, or thousands, of living guys) is in fact C-T, or G-A. And it (e.g. U152+) is patently ancient; so it should (and we know from a handful of BAM files that it does) appear in that form, anciently. But if it does, willy-nilly, they are throwing it out. That is a protocol, but clearly an unscientific one. More like antiscientific.

    I raised this objection once before, but can't find it. I think it was in discussing the Mittnik et al paper; anyway a very recent (2019) one, in which the co-authors specifically stated that those calls were excluded because they might be the artifacts of deamination. And some heavy artillery types, maybe Wing Genealogist and/or lgmayka, argued in favor of doing so. It was someone whose work I respect, but I beg to differ with whoever it was.

    There is another set of blinders associated with "heterozygosity." DF27, to state one important example, reads one way forward and another way reverse (strand that is being observed, at a given location on a given pass). On a one-pass chip observation, that's rarely if ever getting called a SNP.

    I know that impoverished grad students can't afford NextGen sequencing to be sure of their calls. But I can, and I do, wish there were more pressure on non-impoverished aDNA labs in places like Cambridge (either one), Jena, Copenhagen and Leicester to spend what it takes to get it right. We know, and care, where it's phylogenetically important to look. Do they?

    I got the impression from the following article that there is something that can be done in the sample preparation phase; but I don't fully understand this language, and am too old to learn it. Just as part of the conversation, though: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3685887/
    C->T does get called for L2 in the 1240k panel. DF27 and U152 have no coverage.
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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