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Thread: DF27 aDNA Discussion Thread

  1. #51
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    Here is a table of the calls of P312, DF27, Z195, Z225, U152, L2, L20, and L21 of 61 of the R1b specimens with Steppe autosomal DNA from Olalde et al. 2019. This table is only meant to highlight the difficulty of getting a call for an SNP that is included in a test of ancient specimens. All of those SNPs were included in the testing of all of these individuals. This is to make readers aware that no mention of certain SNPs in the academic literature can be due to no-call or due to a result of it being considered unreliable since it is possible to be due to deamination. Other downstream SNPs are irrelevent for this point.

    D means derived, A means ancestral and - means no-call.

    Code:
    ID P312 DF27 Z195 Z225 U152 L2 L20 L21
    I0257 - - - - - - - -
    I12648 - - - - - - - -
    I3484 - - - - - - - -
    I3866 - - - - - - - -
    I0261 - - - - - - - -
    I3775 - - - - - - - -
    I10940 - A - - - - - -
    I12877 - - - - - - - -
    I3486 - - - - - - - -
    I7687 - - - - - - - -
    I8344 - - - - - - - -
    VAD002 - - - - - - - -
    I12641 - - - - - - - -
    I12809 - - - - - - - -
    I12855 - - - - - - - -
    I3488 - - - - - - - -
    I6472 - - - - - A - -
    I8343 - - - - - - A A
    pir001.SG - - - - - - - -
    I3238 - - - - - - - -
    I12032 - - - A - - - -
    I7691 - - - - - - - -
    EHU001 - - - A - - - -
    I12561 - - - - - - - -
    I2472 - - - - - - - -
    I3487 - - - - - - - -
    I3496 - - - A - - - -
    I6588 - - - - - - - -
    I7423 - - - - - - A -
    I7672 - - - - - - - -
    I7675 - - - - - - - -
    I3323 - - - A - - - -
    I1836 - - - - - - - -
    I1840 - - - A - A A A
    I8570 - - - A - A A -
    I4559 - - - - - - - A
    VAD005 - - - - - A - A
    VAD004 - - - A - - - A
    I10895 A - - A - - - A
    I12410 D - - A - A A A
    I12640 D - - - - - - -
    I3576 D - - A - A A A
    I3582 D - - A - - A -
    I5665 D - - A - - - -
    I6618 D - - - - - A -
    I8341 D - - - - - - -
    EHU002 D - - A - - A A
    I3494 D - - A - A A -
    I4563 D - - A - - A -
    I6470 D - A A A A A -
    I2470 D - - - - - - A
    I3324 D - - - - - A A
    I3585 D - - A - A A A
    I6539 D - - - - - - A
    I3756 D - - A - A A A
    I12209 D D - A - A A A
    esp005.SG D D - A A - D A
    I3997 D - D A A A A A
    VAD001 D - - D - A A A
    I3809 D - - - - - - -
    I6492 - - - - - - - D

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  3. #52
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    Quote Originally Posted by ArmandoR1b View Post
    Umm, if the DNA is damaged there is a no-call. Same thing. So if Razyn were alluding to a no-call at DF27, which he wasn't, then it would be in essence the same thing that I am talking about. MikeWWW was talking about DF27 and ZZ12 not being picked up. So, in essence, MikeWWW and I are talking about the same thing which is important SNPs that would identify a specimen as DF27+ not being identified as such due to no-calls.

    Z195 also gets a no-call in most of the specimens of the Olalde et al. 2018 and 2019 studies. I gave you the reason for the no-call but you somehow believe it is irrelevant when it is actually extremely important. When a no-call exists for an SNP that is included in a test of ancient DNA is mostly due to damaged DNA.

    I looked at 61 of the Iberian specimens that were positive for L51, or equivalent, or downstream SNPs. These all have steppe autosomal DNA also. Here's the important part, only 2, out of 61, have a call for Z195 even though they were all tested for Z195.

    Since we are in agreement that if Z195 was called then we could conclude that we found about 40% of the DF27 positive specimens but 96.7% of the specimens don't have a call for Z195. That's a 96.7% no-call rate of Z195 for those specimens.

    Want to guess what the no-call rate is for DF27? It is 58/61 which is 95%. So the no-call rate for Z195 was actually worse than DF27.

    39 out of 61 of those specimens have a no-call for Z225. That is almost a 64% no-call rate for Z225.

    39 out of 61 of those specimens have a no-call for P312. That is almost a 64% no-call rate for P312.

    You have stated, "It seems that there isn’t a problem calling Z225 or Z195" and that is why I am pointing out that some of the studies do have a problem calling Z225 or Z195.

    I'll also mention here that EHU002 from El Hundido, Monasterio de Rodilla, Burgos, Castilla y León dated to 2562–2306 cal BCE is positive for P312 but does not have a read for DF27 or Z195 meaning we have no idea if it is negative or positive for DF27 or Z195. With all of the DF27 found in Bronze Age Iberia there is no reason to think this specimen would be negative for DF27 if it had a read on DF27.

    Razyn was talking about authors of the academic studies throwing out C>T and G>A results a priori. I0806 from Quedlinburg and I12209 dated 1368–1211 BCE from La Requejada, San Román de Hornija, Valladolid, Castilla y León are two perfect examples of that. They are both derived for DF27 which is a G>A mutation and because of that they are not considered DF27+ in the academic world.

    No one. Not a single person was talking about subclades under DF27 that aren't being tested for.

    I think you have, or had, a flawed understanding of what no-calls are and why they exist if included in a test. DF27, Z195, and Z225 are included in all of the 1240K testing of the ancient specimens. Otherwise there would never be a call for those positions. There is also a spreadsheet, that I linked to earlier, that mentions them being included in the 1240K test.
    You seem to not understand Razyn's lamentation in post #10. While I am not in his head, I can guess as to his meaning of the post by his use of certain terms, "Because derived calls for those mutations could be false positives, caused by deamination. And if they could be, the default assumption (per their sometimes-stated criteria, a pre-existing condition) is that they are false positives. No-call is less likely to get you denied tenure than wrong-call. But this set of blinders helps to make the back story for several important haplogroups, including "brothers" DF27 and U152, a slow plot to develop. Especially in peer-reviewed academic literature, which is pretty slow at the best of times."
    I bolded the parts where he is questioning the inability to make a call versus the unwillingness to make a call. In all of my posts, I was pointing out that if Z195 and Z229/Z225 are included in the 1240K scan, then if the dna is not damaged, a call should be made for these two, at least. I also acknowledged that there is possibly a substantial amount of DF27 that is not Z195 and Z229/Z225 that is possibly being missed. If the dna is damaged, then it is damaged. But there are a number of samples that are left at P312* by academics, that are later called by members of this forum.
    On your follow up post, you have sample I3324 listed as derived for P312, however, R. Rocca called this sample as Z195, and Kolgeh called it as Z209 or P312.
    Sample I3582 you have listed as derived for P312 and ancestral for Z225, however, R. Rocca called this sample as Z216 and Kolgeh called it as Z278.
    There are a number of other samples listed as derived, yet R. Rocca and Kolgeh made calls for.
    This is a quote from you, "They are both derived for DF27 which is a G>A mutation and because of that they are not considered DF27+ in the academic world". This is what Razyn is lamenting, not considered DF27 in the academic world. So again, unable to make a call and unwilling to make a call.
    And finally, I think you have, or had a flawed understanding of how to read people's posts. You actually don't read them. You rush to challenge them, assuming they are arguing with you, such as, No one. Not a single person was talking about subclades under DF27 that aren't being tested for. This forum is open to anyone, to post anything, within reason. I posted this as a discussion point for the possibility of some of DF27 being called as P312, due to no calls or downstream positions not being included in the 1240K scan.

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  5. #53
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    I also made a tasteless allusion to the luck of the Irish, by which I only meant that L21 (very abundantly present among the male Irish) is luckier than U152 or DF27 (more abundantly present elsewhere). And for that matter, it's luckier than many other SNPs, both higher and lower on the tree. It gets calls.

    Anyway, RRocca and Webb and ArmandoR1b are all among the good guys. I may occasionally argue with any of you about some detail, but I pay attention to what any of you have to say.

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  7. #54
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    So i have the lucky irish number, cool.

    One question (i know this might be not the place to do it), if i am CTS8221/Z2542-, but not tested in DF13/S521/CTS241, do that makes me already negative for DF13?

  8. #55
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    Quote Originally Posted by razyn View Post
    I also made a tasteless allusion to the luck of the Irish, by which I only meant that L21 (very abundantly present among the male Irish) is luckier than U152 or DF27 (more abundantly present elsewhere). And for that matter, it's luckier than many other SNPs, both higher and lower on the tree. It gets calls.

    Anyway, RRocca and Webb and ArmandoR1b are all among the good guys. I may occasionally argue with any of you about some detail, but I pay attention to what any of you have to say.
    I came into this hopeful I'd be L21, but I suppose DF27 is the second best option..
    DF27, you're my silver medal

    And a big thanks to you, Webb, Armando, and RRocca for doing all the work while I just show up make a stupid comment and head back to autosomal.

    One day I'll test my Y DNA fully to be of use.. one day
    Last edited by sktibo; 10-23-2020 at 05:34 AM.

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  10. #56
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    Quote Originally Posted by sktibo View Post
    I came into this hopeful I'd be L21, but I suppose DF27 is the second best option..
    DF27, you're my silver medal

    And a big thanks to you, Webb, Armando, and RRocca for doing all the work while I just show up make a stupid comment and head back to autosomal.

    One day I'll test my Y DNA fully to be of use.. one day
    Even the canadian primer minister is R-DF27.

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  12. #57
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    Quote Originally Posted by alejandromb92 View Post
    Even the canadian primer minister is R-DF27.
    Ahhh man, seriously...

    Can I trade for U152

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  14. #58
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    Interestingly enough there was a study done on the Basque region and surrounding areas linking haplotypes to Roman era tribes. While we all wouldn’t be surprised by the high numbers of DF27, L21 was as high as 21% in the Basque region of Spain but quickly dropped off further west. I’ll look for the study and post a link. I found the link:

    https://www.researchgate.net/publica...erited_Markers
    Last edited by Webb; 10-24-2020 at 11:32 PM.

  15. #59
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    Quote Originally Posted by Webb View Post
    You seem to not understand Razyn's lamentation in post #10. While I am not in his head, I can guess as to his meaning of the post by his use of certain terms, "Because derived calls for those mutations could be false positives, caused by deamination. And if they could be, the default assumption (per their sometimes-stated criteria, a pre-existing condition) is that they are false positives. No-call is less likely to get you denied tenure than wrong-call. But this set of blinders helps to make the back story for several important haplogroups, including "brothers" DF27 and U152, a slow plot to develop. Especially in peer-reviewed academic literature, which is pretty slow at the best of times."
    I bolded the parts where he is questioning the inability to make a call versus the unwillingness to make a call.
    He did mention no-calls there but the, rightfully made, complaint was really about some mutations that really should be taken into consideration as derived are considered false positives just because they possibly are due to deamination. He isn't really complaining that DF27 and others are getting no-calls.

    Quote Originally Posted by Webb View Post
    In all of my posts, I was pointing out that if Z195 and Z229/Z225 are included in the 1240K scan, then if the dna is not damaged, a call should be made for these two, at least.
    My point is that the DNA is damaged at the positions for Z195 and Z229/Z225 very often. That means Z195 being called is a rare occurrence. It happened way too often with the Iberian samples.

    Quote Originally Posted by Webb View Post
    I also acknowledged that there is possibly a substantial amount of DF27 that is not Z195 and Z229/Z225 that is possibly being missed. If the dna is damaged, then it is damaged. But there are a number of samples that are left at P312* by academics, that are later called by members of this forum.
    Yes, but I wasn't commenting on the non-Z195 and non-Z225 misses.


    Quote Originally Posted by Webb View Post
    On your follow up post, you have sample I3324 listed as derived for P312, however, R. Rocca called this sample as Z195, and Kolgeh called it as Z209 or P312.
    Sample I3582 you have listed as derived for P312 and ancestral for Z225, however, R. Rocca called this sample as Z216 and Kolgeh called it as Z278.
    There are a number of other samples listed as derived, yet R. Rocca and Kolgeh made calls for.
    Yes, I3324 and I3582 are derived for P312 that is expected for any specimen that is also derived for downstream SNPs. Derived means positive. I also stated Other downstream SNPs are irrelevent for this point. The point was the frequency of the calls for P312, DF27, Z195, Z225, U152, L2, L20, and L21. R. Rocca saw a downstream derived call for both I3324 and I3582. There is no-call for Z195 for I3324. The downstream derived call is for S450 which also shows up in my analysis. But like I said it is irrelevant for the high no-call rate of Z195.

    Quote Originally Posted by Webb View Post
    This is a quote from you, "They are both derived for DF27 which is a G>A mutation and because of that they are not considered DF27+ in the academic world". This is what Razyn is lamenting, not considered DF27 in the academic world.
    That is exactly why I said Razyn was talking about authors of the academic studies throwing out C>T and G>A results a priori. Those are calls not being accepted as derived when upstream SNPs are derived and 'brother" clades are ancestral. The data shows there is a derived call but they don't want to accept it.

    Quote Originally Posted by Webb View Post
    So again, unable to make a call and unwilling to make a call.
    No, it is only about unwilling to accept a call. It is not about "unable to make a call" or "unwilling to make a call". When a call is mentioned we are talking about there being data in the raw DNA. A call is not a synonym for a decision as you seem to allude to in the beginning of the post and the end of the post.
    Last edited by ArmandoR1b; 10-25-2020 at 05:24 AM.

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  17. #60
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    Quote Originally Posted by Webb View Post
    Interestingly enough there was a study done on the Basque region and surrounding areas linking haplotypes to Roman era tribes. While we all wouldn’t be surprised by the high numbers of DF27, L21 was as high as 21% in the Basque region of Spain but quickly dropped off further west. I’ll look for the study and post a link. I found the link:

    https://www.researchgate.net/publica...erited_Markers
    By experience i think the spanish region with more frecuency of L21 is Galicia, also according this study by Joe Flood (The phylogenealogy of R-L21: four and a half millennia of expansion and redistribution)



    I have saw on FB a lot of galicians and some other iberians with L21, but never a basque, there may be some with L21, but a 1/5 of them is a high % in my opinion.
    Last edited by alejandromb92; 10-25-2020 at 09:58 AM.

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