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Thread: Interesting structure under DF17 being revealed by Big Y

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    Interesting structure under DF17 being revealed by Big Y

    With five of the DF17 results in for Big Y there is some interesting groupings forming. Below DF17 are two groups: 8849102=G and 15786167. Below 8849102 is 14953259. Below 14953259 is S1041.

    I also noticed that there may be some STR correlations for some of these new clades:

    DF27>Z195>Z274>DF17>"8849102*"
    Burness----CDYb=39

    DF27>Z195>Z274>DF17>"8849102">"14953259*"
    Menge------CDYb=39

    DF27>Z195>Z274>DF17>"8849102">"14953259">S1041
    Durkin------CDYb=39, DYS389i=14
    Mulvihill----CDYb=39, DYS389i=14

    DF27>Z195>Z274>DF17>"15786167"
    Hart ----DYS464c = 16
    Tran ----DYS464c = 16
    Last edited by breckenheimer; 04-21-2014 at 01:41 AM.
    R1b-P312-DF7+ DF17+ CTS7768+ FGC14124+
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    Earliest known Y ancestor: Hesse, Germany 1705

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    We also have several reported DF17 in the BritainsDNA group of 2000 results provided by Dr. Jim Wilson a couple of weeks ago. I've also seen two Italians reported (maybe YFull?).
    Going thru the BritainsDNA data, I could only identify one sample that is S1041 (sample 628). If we could get position info on the SNPs reported, we could add another 7 folks to our DF17 chart. Competitive fears probably rule that out.

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    Dr. Wilson released the Chromo2 position info shortly after the 2000 results. We've been mining it for new SNP tests.

    https://www.dropbox.com/s/46ubi9qntb...positions.xlsx
    Last edited by razyn; 04-24-2014 at 04:59 PM.

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    I can't find any correspondence between those positions and the BigY. They may use a different reference.

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    Quote Originally Posted by breckenheimer View Post
    With five of the DF17 results in for Big Y there is some interesting groupings forming. Below DF17 are two groups: 8849102=G and 15786167. Below 8849102 is 14953259. Below 14953259 is S1041.

    I also noticed that there may be some STR correlations for some of these new clades:

    DF27>Z195>Z274>DF17>"8849102*"
    Burness----CDYb=39

    DF27>Z195>Z274>DF17>"8849102">"14953259*"
    Menge------CDYb=39

    DF27>Z195>Z274>DF17>"8849102">"14953259">S1041
    Durkin------CDYb=39, DYS389i=14
    Mulvihill----CDYb=39, DYS389i=14

    DF27>Z195>Z274>DF17>"15786167"
    Hart ----DYS464c = 16
    Tran ----DYS464c = 16
    I want to refresh this thread, toward the goal of reorganizing the R1b-DF27 project a bit to reflect growing knowledge (not necessarily MY knowledge, but whoever has it, it's growing) about the positioning of DF17. I think it's going to require at least a nod in the direction of Z274. The DF27 project was set up without a category for Z274, because nobody was getting Sanger-sequenced test results for it; but now that FTDNA has that new haplotree, at least one kit (N67378) in DF27 is now displaying Z274 as "terminal."

    Trying to sort it with the little plus and minus signs in SNP results (known to, and displayed by, the FTDNA computer) is making me a little crazy. I suspect that the most productive sources are going to be the Big Y comparisons posted to the Yahoo group's files (mainly by David Carlisle), and the Chromo2 results for 2000 cases released last Feb. by Jim Wilson. Some of you DF17 guys may be using a structure based on other analyses [including YFull, Chris Morley's experimental tree (last made public in Feb. 2014, though his ClarifYDNA service is still working on that if you have membership and access), ISOGG, older diagrams like Thomas Krahn's Draft Tree or the ones Rich Rocca did in 2011]. They don't agree with each other; and I don't think they agree with the data we can now see in the two sources I just called productive. But to make our project's grouping sequence hierarchical and productive, somebody needs to go crosseyed studying the various (and often conflicting) sources better than I have done. I'm not sure it's all reliable (i.e. some chip or other test may just be calling one of these SNPs inconsistently: Z274, Z196 or DF17). Does the issue have to do with no-calls at DF17 being listed as DF17- some of the time? And if so, is Z274 even phylogenetically relevant?

    A couple of weekends ago I met Mike Durkin at the I4GG conference in Maryland. We got to discuss DF17 very casually, in my case from fuzzy memory rather than firm knowledge or conviction; and btw we had lunch with Thomas Krahn, but there was sort of a dense fog of input rolling in from a wide variety of sources -- most of it unrelated to DF17. I think we have enough DF17 cases, with potential subclades, that we need to get you guys sorted right. And not incidentally, color-coded more like your closer neighbors in the Z195/Z196 vicinity. Whoever we turn out to be.

    Talk amongst yourselves.
    Last edited by razyn; 09-01-2014 at 12:10 PM.

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    Quote Originally Posted by razyn View Post
    I want to refresh this thread, toward the goal of reorganizing the R1b-DF27 project a bit to reflect growing knowledge (not necessarily MY knowledge, but whoever has it, it's growing) about the positioning of DF17. I think it's going to require at least a nod in the direction of Z274. The DF27 project was set up without a category for Z274, because nobody was getting Sanger-sequenced test results for it; but now that FTDNA has that new haplotree, at least one kit (N67378) in DF27 is now displaying Z274 as "terminal."

    Trying to sort it with the little plus and minus signs in SNP results (known to, and displayed by, the FTDNA computer) is making me a little crazy. I suspect that the most productive sources are going to be the Big Y comparisons posted to the Yahoo group's files (mainly by David Carlisle), and the Chromo2 results for 2000 cases released last Feb. by Jim Wilson. Some of you DF17 guys may be using a structure based on other analyses [including YFull, Chris Morley's experimental tree (last made public in Feb. 2014, though his ClarifYDNA service is still working on that if you have membership and access), ISOGG, older diagrams like Thomas Krahn's Draft Tree or the ones Rich Rocca did in 2011]. They don't agree with each other; and I don't think they agree with the data we can now see in the two sources I just called productive. But to make our project's grouping sequence hierarchical and productive, somebody needs to go crosseyed studying the various (and often conflicting) sources better than I have done. I'm not sure it's all reliable (i.e. some chip or other test may just be calling one of these SNPs inconsistently: Z274, Z196 or DF17). Does the issue have to do with no-calls at DF17 being listed as DF17- some of the time? And if so, is Z274 even phylogenetically relevant?

    A couple of weekends ago I met Mike Durkin at the I4GG conference in Maryland. We got to discuss DF17 very casually, in my case from fuzzy memory rather than firm knowledge or conviction; and btw we had lunch with Thomas Krahn, but there was sort of a dense fog of input rolling in from a wide variety of sources -- most of it unrelated to DF17. I think we have enough DF17 cases, with potential subclades, that we need to get you guys sorted right. And not incidentally, color-coded more like your closer neighbors in the Z195/Z196 vicinity. Whoever we turn out to be.

    Talk amongst yourselves.
    Dick, on the Semargl site, every DF17 Geno 2.0 results displays Z274 as a positive snp for all the testers. Likewise, all of the North/South cluster testers also show it as a positive snp. I think it highly unlikely these are false. However, the key would be to try and figure out how far down from Z195 it is and how far up from Z220 and DF17 it is.
    Last edited by Webb; 09-01-2014 at 12:47 PM.

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    The positioning of Z295 and S21184 is not irrelevant to this discussion, either. And I don't think the Semargl site is very close, on that. One of several reasons I've mostly been looking elsewhere, of late. But the general idea is to try to get us on the same page, whoever may have the better data or algorithms to play with.

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    This is what we do know. Z274 can not be equivalent to Z195 as none of the L165 or SRY2627 guys have it. It can not be equivalent to DF17 as the north/south guys have Z274 but not DF17 and vice versa. So the next question is this, is DF17 north/south cluster. How old is DF17? When do DF17 and say Z209/Z210/Z220 share a common ancestor? Where is Mark Jost when you need him?

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    Quote Originally Posted by Webb View Post
    So the next question is this, is DF17 north/south cluster.
    No, that cluster was described originally on the basis of three unusual STR marker values (not SNPs) -- and DF17 guys typically have none of the three. They were DYS437=14, DYS448=18, and GATAH4=10. All of the groupings under Z220 have those, at least modally -- except my little L484+ grouplet, or subcladie of CTS4065. And that's because we have a back-mutation on GATAH4, to the ancestral 11. Several M153s also have a back-mutation there, but not enough to shift the group's modal.

    Where is Mark Jost when you need him?
    Maybe in Ireland? I haven't seen him in the vicinity of DF27 for about a year, anyhow. That's about when he and Mike Www got all excited over Big Y, etc. news for L21 and its subclades -- chacun à son goût. One of these days, I hope to broaden his horizons; but it would be better to do it after we actually know something, rather than just conversationally. So, we are testing a lot, a process that consumes some money and lots of time. Stonehenge wasn't built in a day.

    But knowing something does not, technically, require recognition -- by ISOGG, or the FTDNA haplotree, or really anything. Those are goals, not prerequisites. Mainly it requires testing, and competent analysis of the test results. We're working in that patch, or sincerely trying to.
    Last edited by razyn; 09-02-2014 at 12:16 PM.

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    Quote Originally Posted by razyn View Post
    The DF27 project was set up without a category for Z274, because nobody was getting Sanger-sequenced test results for it; but now that FTDNA has that new haplotree, at least one kit (N67378) in DF27 is now displaying Z274 as "terminal."
    Just a footnote about Z274. [It currently looks to me as if it should be on our trees under Z196, above the divide between DF17 and Z220, and mutually exclusive with the whole L176.2 branch. If someone knows for a fact that this isn't right, please post here.] I have a little documentation of why Z274 was not being Sanger sequenced (and therefore we had no results for it visible in our projects for a couple of years after its discovery). Inclusion of Z274 on the Geno2 chip array in the fall of 2012 made it visible -- after results from that test started showing it -- in a little string of other Z-SNPs whose positions we understood better.

    Anyway, I had asked the FTDNA Help Desk about the status of several such SNPs in Feb. 2012, and received this reply March 2, 2012:

    Hi Richard,

    I've asked the lab for another update on the specific SNPs that you were interested in and this is the information I was provided:

    Z274 is almost impossible to design primers for because it's in a highly repetitive region so this will not be available any time soon.
    Z294 is also tricky, must be designed manually, and will not be available soon.
    Z209, Z214 and Z278 are still being tested but should be ready within the next few weeks.

    I hope this helps!
    Well, it did, in that my order for the newly available Z209 was placed the same day -- March 2, 2012. And Z220 five days later; and Z216 March 27. I guess it might be worthwhile to paste in my Feb. 18, 2012 query (following up on my earlier request of Oct. 13, 2011), to which the above was the Help Desk response:

    I'd like to know if there is any hope of an available SNP test for Z294, or indeed any of the 25 new SNPs under Z196. There was chatter on DNA-Forums at the end of June [2011] to the effect that the subclades of Z196 could be tested sometime in July. I keep looking at your Advanced Orders menu of SNPs, a few times a week, and there still aren't any. There is a particularly large group of clients whose asterisk could be removed by discovery of a SNP encompassing the "North/South Cluster" of R-P312, identified from STR off-modals by Ken Nordtvedt several years ago.
    I concluded that Feb. followup by citing the DNA-Forums thread on which we had been discussing our Z196 test results and issues. I've deleted that part of my Help Desk message -- because DNA-Forums shut down a couple of years ago, and links to its old messages don't work.

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