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How do we interpret SNPs that show in a 'more' window on the Haplotree & SNPs page

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  • How do we interpret SNPs that show in a 'more' window on the Haplotree & SNPs page

    What I am seeking clarity on is how we should interpret the SNPs that show up in window opened when we click on the 'more' label in our tree as displayed under 'Haplotree & SNPs'.

    Specifically, are the SNPs in the 'more' window to be interpreted as sequentially (in time history) to have occurred before the named SNP on the same line or are they considered later mutations in time ?. Unless we know this we can't construct the actual tree sequence of all SNPs including the ones in the 'more' window.

    Reason I am asking is that I offered to build a complete sequence of SNPs one-by-one in mutation sequence from P310 for various members of the project that I am admin for. e.g. In my own case my branch of Y-DNA is S1194 which shows below P310 and I am listed with a terminal SNP of CTS4528, On the line in the FTDNA SNP tree that lists my haplogroup (in green) if I click 'more' it opens a window in which one other SNP named DF100 shows. So my point here is, did the DF100 SNP mutation come before (in time) the CTS4528 mutation or did it come sequentially (in time) after CTS4528.

    If I assume (and I think this is wrong) that the 'more' box shows a set of SNPs that occurred *after* my terminal haplogroup of CTS4528 then my full sequence in the FTDNA tree would be (starting from P310) ...

    Starting with SNP P310
    CASE 1
    P310=>more(L52=>CTS7650=>P311=>YSC0000082=>)L151=>more(=>L11=>YSC0000191)=>CTS4528=>more(DF100)=>plus my 35 unnamed variants. The total SNP count for me from P310 becomes 1+(4)+1+(2)+1+(1)+35 = total of 45 SNP mutations occurring between P310 and the last (most recent in time) unnamed variant in my Y-Tree from the line with P310.

    or should it be that the SNPs in the 'more' window come first in time before the SNP on the particular line we observe in the FTDNA tree ?:

    Commencing on the line with P310 a sequence of ...
    CASE 2
    more(L52=>CTS7650=>P311=>YSC0000082)=> P310=>more(=>L11=>YSC0000191) =>L151=>S1194=>more(DF100)=>CTS4528=>plus my 35 unnamed variants = 45 SNPs in my tree from P310.

    (The diff between CASE1 & CASE2 is that in CASE2 the more SNPs are placed before the SNP name on the line that the 'more' window shows.

    In a nutshell: on the line in the tree (see grab below) for CTS4528, does the mutation DF100 in the 'more' window come *before* CTS4528 in mutation time history or after CTS4528 in time history sequence ? the answer to this dictates what our detailed SNP tree actually will look like.

    02-grab-2.jpg


    02-grab-1.jpg
    Last edited by dsm; 2nd July 2019, 06:22 PM. Reason: Corrected typo in title

  • #2
    My Understanding,
    "More" shows you the alternate names for that SNP in question, they are not additional SNPs
    Last edited by prairielad; 3rd July 2019, 12:17 AM.

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    • #3
      Thanks for having a go at an answer but if you pick any of them in a 'more' window list as well as the name of the SNP on the line being looked at, and check YBrowse.org you will find they are *not* the same mutation. For example try checking CTS4528 and DF100 they are at completely different locations in the Y-DNA chromosome.

      If you need help finding and using YBrowse, ask & I will provide step-by-step directions.

      Thanks DSM

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      • #4
        They are considered phyloequivalent. That means that any of the names can be used for the same position in the tree at present. In the future some tester may test positive for one and negative for the others and then it will be known which SNP is older and the order of the nodes can be known. ISOGG, FTDNA, and YFull could each pick a different SNP out of the phyloequivalent bunch and in theory if there were 3 SNPs listed end up with each calling that particular node of the Y tree by a different name.

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        • #5
          Originally posted by bhemph View Post
          They are considered phyloequivalent. That means that any of the names can be used for the same position in the tree at present. In the future some tester may test positive for one and negative for the others and then it will be known which SNP is older and the order of the nodes can be known. ISOGG, FTDNA, and YFull could each pick a different SNP out of the phyloequivalent bunch and in theory if there were 3 SNPs listed end up with each calling that particular node of the Y tree by a different name.
          Hi,

          Thanks for your added information. Yes they are phyloequivalents. To explain to other readers, this means that because there is no 'known' branching between the SNPs in question (i.e. in any phyloequivalent cluster), they 'can' be used to name a single phyloequvalent location. *in a tree* ( but not in a chromosome).

          However, my question was not asking about phyloequivalence it was asking which historical sequence the SNPs should be seen in.

          Repeated again, the simplified form of the question was does DF100 come after CTS4528 or before ?. The question was spelled out quite clearly in the original post.

          Thanks

          Doug
          Last edited by dsm; 3rd July 2019, 02:40 AM.

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          • #6
            Based on the feedback above from prarielad & bhemph, I think I have the answer.

            It is :- there isn't a way that phyloequivalent SNPs can be date sequenced.

            This is because, up and until a new branch emerges that comes from one of the SNPs in the phyloequivalet cluster there is no way of knowing which SNP mutated before another in that cluster so their sequence in a phyloequivalent cluster is merely take your pick and thus irrelevant.

            We actually have a good example in the P310 tree in that at one time L151 was not at a branch in the tree and was just one of the SNPs in a phyloequvalent cluster until about (IIRC) 5 or so years ago when an L151 find (can't recall if it was an ancient DNA find or a DNA test) showed up that split the cluster and L151 is just in front of the SNP triggering the split. i.e. after L151 is a new branch that leads (interestingly enough) to S1194 (including DF100 & CTS4528).
            So it may very well be that the discovery of DF100 and/or CTS4528 and/or S1194, triggered the split in the tree that follows L151.

            In the below grab, L151 is shown between two 'more' windows (one on the P310 line & the other on the L151 line) but some years ago L151 was just another phyloequivalent SNP in the 'more' window off P310. The other SNPs that today show in the 'more' window of L151 in the grab below, were also included in the older P310 'more' window.

            When the branch off L151 was found, the phyloequivalent cluster for P310 got split as shown and using standard dating techniques, L151 could finally be dated and thus placed in correct mutation aging sequence in the tree (between P310 and S1194.


            Also, I believe that this issue of being able to date sequence the mutations in our unnamed variants hits the same challenge. i.e. we can't date sequence them until they 1st get named (when someone else shows the same mutation) and then that particular newly named SNP is moved into a position in the tree and out of unnamed variants.



            02-grab-3.jpg
            Last edited by dsm; 3rd July 2019, 07:41 PM.

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            • #7
              Someone in my project recently split a block. FTDNA hasn't changed the tree yet, but when I click on this member's Haplotree and SNPs, the "more" shows one SNP in green for Tested Positive and two in blue for Downstream.

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              • #8
                Yes, a rare occurance but is sure to happen more as more peoples unnamed variants get matched to new testers.

                D

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