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Thread: What is ZZ11 and what do we do with it?

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    Quote Originally Posted by Mikewww View Post
    I really do not know the answer but is the location really prone to back mutation or is the issue that some testing systems (maybe all today) have a hard time sequencing the DYZ19 region?
    Back-mutation certainly occurred in the line leading to the R-Y18894 clade (tested 396C and 392C).

    Back-mutation certainly occurred in YF05239 (tested 197C), which is directly under R-L2.

    Back-mutation certainly occurred in YF04510 (tested 340C), which belongs to R-FGC14124*.

    Thus, 4 customer examples just from the members of YFull's U152 and DF27 groups.
    Last edited by lgmayka; 04-20-2016 at 09:23 PM.

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    I don't exactly disagree with lgmayka's perception that ZZ11 is a bit chimerical. But I think that characteristic is hardly limited to ZZ11, among all SNPs -- and not a reason to ignore something that altered the phylogeny, at a time and place several thousand years (and miles) from where we currently stand. It's highly useful, if present. We may continue to disagree about its proper use; or the horrible consequences either of failing to test for it, or testing and getting the wrong answer; or the threat of wasting a few hundred dollars here and there.

    Anyway, last night I went through the exercise of checking all the results so far in the P312 project for the P312 SNP Pack -- the only test that purports actually to look for ZZ11. I had previously done this in the DF27 project, where we had ZZ11* (no call or heterozygous call) for 11/14 DF27 guys, and 1/1 U152 guy who should not have been in that project anyhow. In my enthusiasm, I mistook that for a good result, assuming that they all should (at best) show heterozygosity. Having looked at the P312 guys, my enthusiasm has waned. I think the test isn't targeting accurately enough to get a credible read. Perhaps those asterisks were about evenly divided between no-calls and mixed calls. Anyway, with a couple dozen more tests (only a few of whom were DF27 or U152), everyone who got any call at ZZ11 got the asterisk -- 17 out of the 25 I hadn't already examined in the DF27 project. The other 8 had no result reported for ZZ11.

    Of the four new U152 guys, both who were L2+ had the ZZ11*, and both who were PF6658+ had no result. Does that mean anything, really? I kind of doubt it. A case might be made that the little-tested Z29645>S27900 is consistently ZZ11*; and maybe even that DF99 is. But, does that mean anything? I doubt it.

    I think we just need a better test than the P312 chip offers at present; or more enriched data for that problematic region, before betting the farm on its validity OR throwing out the baby with the bath water. And I sort of wish Alex would join this discussion.

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    Quote Originally Posted by lgmayka View Post
    Back-mutation certainly occurred in the line leading to the R-Y18894 clade (tested 396C and 392C).

    Back-mutation certainly occurred in YF05239 (tested 197C), which is directly under R-L2.

    Back-mutation certainly occurred in YF04510 (tested 340C), which belongs to R-FGC14124*.

    Thus, 4 customer examples just from the members of YFull's U152 and DF27 groups.
    How do you know certainly that these are back mutations versus bad (ambiguous) reads that are not just reflective of a testing technology or interpretation method that struggles with this portion of the DYZ19 region?
    Last edited by TigerMW; 04-22-2016 at 04:40 PM.

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    Quote Originally Posted by Mikewww View Post
    How do you know certainly that these are back mutations versus bad (ambiguous) reads that are not just reflective of a testing technology or interpretation method that struggles with this portion of the DYZ19 region?
    The reads were not ambiguous. I already cited them: 396C, 392C, 197C, and 340C.

    Yes, one could claim that the Big Y somehow always reads this location wrong. But that makes the location rather worthless anyway, at least for the near future.

    Yes, one could claim that ZZ11 is not where we think it is. But then where or what is it? If no one can define it unambiguously, it is rather worthless for scientific purposes.
    Last edited by lgmayka; 04-22-2016 at 05:27 PM.

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    Quote Originally Posted by razyn View Post
    We may continue to disagree about its proper use; or the horrible consequences either of failing to test for it, or testing and getting the wrong answer; or the threat of wasting a few hundred dollars here and there.
    The examples of back-mutation I cited are not "wrong" answers. The reflect the reality of a finicky location that apparently often back-mutates (probably due to copy-over from elsewhere).

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    Quote Originally Posted by lgmayka View Post
    The examples of back-mutation I cited are not "wrong" answers. The reflect the reality of a finicky location that apparently often back-mutates (probably due to copy-over from elsewhere).
    I wasn't talking about your four examples; I believe in back mutations, or return to a status quo ante. I was talking about the results from the three dozen tests with the P312 SNP pack, the only ones to my knowledge that have actually purported to look for it.

    Also, Alex lists several places to look for evidence of it, not just one. I suspect this SNP pack only looks at one; and for that matter I'm pretty sure the YFull data you cite is only looking at one.

    Also, if it's a real event with phylogenetic consequences, it probably has several equivalents -- some or one of which may be easier to test reliably (and may be more stable, over four or five millennia).

    So, hold off on the hyperbolic phrases like "worthless for scientific purposes," please. Scientific purposes include continuing to look for the branching points; if the ZZ11 event is indeed a major one, for the early Bronze Age peopling of central and western Europe, we need to find ways to look for it. And if actually looking for it proves that it's not such a branching point, I'll shut up. That hasn't really happened, yet.

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    Quote Originally Posted by Mikewww View Post
    We don't have a location for ZZ11_2 documented in YBrowse. Can ZZ11_2's position-anc-der be derived or predicted?
    There is at least a ZZ11_2 and suspect there may be a ZZ11_3 as well. There is a large portion of DYZ19 that has not been mapped. That region is still sequenced by BigY and FGC tests, and the reads from those regions simply get mapped to regions of the reference sequence that most closely resemble them. Judging what I can from the BAM files available to me, it looks as though reads from 2 or 3 different regions of the Y chromosome are being aligned to the region around 22286799. Only 1 of those regions has the ZZ11 mutation. Until a more complete reference sequence for DYZ19 becomes available, it isn't possible to assign positions to a ZZ11_2 or a ZZ11_3.

    Quote Originally Posted by Mikewww View Post
    Most testing institutions don't really like this kind of SNP. It is a risky SNP, no doubt. If I thought I was ZZ11* (DF27- U152-) it would be especially risky or if I thought was P312* the same would be the case. It might have been wiped out.
    There would be no concern of being ZZ11*, but being P312* would definitely be a concern. We should try to estimate some sort of back mutation rate for this SNP. That would allow us to better quantify our concerns. Ideally, most of our P312 branches would have other branches as well, which formed early on. The odds of recLOH on all the branches would be fairly low. Just a single P312* guy is a real problem.

    Quote Originally Posted by Mikewww View Post
    Given all of that, I don't know that ZZ11 does much terms of making formal, conservative trees but that does not eliminate its importance in the phylogeny. It pretty much proves DF27 and U152 are more closely related to each other than to L21, DF19, DF99 or L238, right?

    I don't think ZZ11 should be included in a SNP testing approach based on traversing the tree, but I could be wrong.
    If we do believe the mutation exists and we can confidently place it on the tree then it should be on the tree even if not all the downstream branches are going to remain positive for it. I think those should be the only conditions.

    When it comes to determining if someone belongs to the R-ZZ11 branch it makes far more sense to test for mutations that are thought to be more stable that are known to be downstream of ZZ11. There is no need to confuse the issue of what branching and mutations happened throughout history with what mutations we can reliably expect to find today.
    Quote Originally Posted by Mikewww View Post
    SNP Packs are not tree traversing, they "all in one" fell swoops. I don't know if FTDNA would accept ZZ11 but we could try to get it in something. The likely places would be the R1b-M343 Backbone or the R1b-P312 Packs. What do you think of trying to get this placed in a pack?
    If it can be tested reliably, then it should be included. If it can't, don't include it. Back mutations are good mutations too, but they do require FTDNA to up their game when it comes to interpreting the results.

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    Quote Originally Posted by lgmayka View Post
    The reads were not ambiguous. I already cited them: 396C, 392C, 197C, and 340C.

    Yes, one could claim that the Big Y somehow always reads this location wrong. But that makes the location rather worthless anyway, at least for the near future.

    Yes, one could claim that ZZ11 is not where we think it is. But then where or what is it? If no one can define it unambiguously, it is rather worthless for scientific purposes.
    Let me just use the words "in error". It is possible that the system, maybe any testing system, would have trouble with this particular part of the Y chromosome.

    I'm distinguishing between a truly unstable mutation and a difficult/technically infeasible mutation to read (today!)

    If so, then I agree with Razyn, we don't want to throw the baby out with the bath water. Let's save our knowledge of this mutation for a day when testing systems can handle it. Perhaps more importantly, we can be very confident the U152 and DF27 are brothers where as L21, DF19, DF99 and L238 are their cousins. The tree of paternal lineages is what it is regardless of our current abilities to deal with the complexities of the Y chromosome.

    Our tree description needs enhancements. There are some branches that are real but aren't feasible to test for reliably today. Call it a phantom SNP or whatever, it's still a real branch. Razyn, take note again. I do care about the real phylogeny, not just a constructed model based on simple notions.
    Last edited by TigerMW; 04-22-2016 at 06:50 PM.

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    Quote Originally Posted by Mikewww View Post
    Can you put some kind of probability or range around the words "very prone"? That's hard to use in decision-making.
    I agree with Mike, it would be great if these issues could be quantified more. Unfortunately it is hard to do. Right now, on my Big Tree, I have 649 ZZ11 men. In my database of results, I see 319 positive results. It shows up maybe 10% of the time in 1000 genomes VCF files, half the time in BigY VCF files and never in FGC interpretation files. I have BAM files for about 15% of the BigY/FGC men on my tree so I could check many of those. That would still leave many unknown.

    YFull would probably be a better option, even though there are fewer men. I may yet do that.

    Quote Originally Posted by lgmayka View Post
    Back-mutation certainly occurred in the line leading to the R-Y18894 clade (tested 396C and 392C).

    Back-mutation certainly occurred in YF05239 (tested 197C), which is directly under R-L2.

    Back-mutation certainly occurred in YF04510 (tested 340C), which belongs to R-FGC14124*.

    Thus, 4 customer examples just from the members of YFull's U152 and DF27 groups.
    Are these the only 3 branches with back mutations in the YFull data? How many DF27 and U152 men are there? I can take a look and count as well.

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    Quote Originally Posted by Mikewww View Post
    How do you know certainly that these are back mutations versus bad (ambiguous) reads that are not just reflective of a testing technology or interpretation method that struggles with this portion of the DYZ19 region?
    I trust these numbers. BigY tests have great coverage in the region around 22286799, and that position is also the best place for ZZ11+ reads to align. The reads with the ZZ11 mutation are generally about 1/3 to 1/2 of them. If they were there, they'd show up.

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