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  • X-DNA question

    I am new to X-DNA and slowly trying to get my head around how I can use X-matches (on GedMatch) to refine my genealogical research.

    My gr-grandfather was 100% Ashkenazi Jew with his roots in Poland and Russia. The remainder of my ancestry is British. Family Finder, of course, has matched me with hundreds of people with Ashkenazi ancestry, and until now I just assumed that all these matches were related to me on my gr-grandfather's line. A natural assumption, or so I thought.

    A small % of these matches are also match with me on the X chromosome. They all have well documented family trees going back to Russia and Lithuania.

    I recently mapped out my ancestors using the fan chart, and realised that my gr-grandfather did not pass his X chromosome to his son (my grandfather). Therefore, it is not possible for these X-matches to be on my gr-grandfather's side. Am I on the right track here?

    I'm starting to contemplate that I may have another Jewish ancestor somewhere in my family, but on a line other than my gr-grandfather's. Perhaps one of my British ancestors was not as British as I thought?

    Comments?

  • #2
    I wouldn't put too much trust in a smaller than 7cM match on gedmatch on the X chromosome to start with. With that said, do these X matches still come from your grandfather's side?

    Comment


    • #3
      This cuts out some, but I still have a few matches around 7-9 cM.

      Comment


      • #4
        Hi Siroli,
        If you are a male and have an X chromosome match with another male, then the match can be significant even if much less than 7 cM. With two females, the match is usually much less significant unless you have a size that is greater than 6 cM. So sex matters here. You also need to have a segment containing lots of SNPs. Females have two X chromosomes, whereas males have only one, so males are more likely to be identical by descent (IBD) in the smaller segments. Scientists need to do more studies on the X chromosome to determine how much the size matters, so I am basing my recommendations mostly on my observations and what other companies are saying. There simply is not enough information out there. This is new territory. We hope to be able to study the X more as soon as Family Tree DNA has the X matching up and running.

        It actually helps a lot if the same person who matches you on the X also matches other chromosomes because that usually means it is a closer cousin. In my experience, you are much more likely to identify most recent common ancestor(s) (MRCAs) if there are multiple chromosomes involved plus the X. I have seen some amazing success stories here. You can narrow the playing field in many cases.

        Does the spouse of any of these males of Ashkenazim heritage have Jewish heritage as well and would she be in the X pattern line of inheritance?

        Good luck.
        Kathy

        Comment


        • #5
          Yes a small X match male to male can be significant, but taking into account the way X recombination works, I would doubt this occurs that many times. If it did, it would be simply one small segment, not many. That aside, the real issue is that Gedmatch does not distinguish gender when comparing kits and this is why I do not recommend using the Gedmatch X defaults. If one or both kits are female, the risk of IBS is just too high in my opinion. This can be especially evident when looking at the pattern of the match and seeing many small segments on the same match. For example, five matching 3cM X segments is not IBD as X chromosomes do not cross-over that many times and it would certainly be difficult to have that pattern dropped down from generations prior.

          Since Gedmatch uses 200SNPs and 3cM for ALL X comparisons, not just male to male, the female kits being compared increase the chance of IBS by twice since their dual alleles can be composited out of phase by the 1/2 IBD matching comparison. Comparing female to female kits means an even higher chance of IBS. This is why 23andMe doubles the SNPs required for male to female, and doubles it again for female to female X matching on X. Gedmatch does not do this and hence therein lies one issue with its X matching.

          Within Gedmatch, I've taken my own family kits and found IBS segments where my mother matches my son (who did not inherit X from me) and where my mother matches my wife's mother, yet autosomal-wise, they are not even remotely related.

          Until such time the Gedmatch takes into account gender on the X the risk of IBS is too high using 200SNPs and 3cM. I recommend looking deeper at any X match found in Gedmatch and once found, manually using 700 SNPs at 7cM instead for all X comparisons for now.

          Matt.
          Last edited by mkdexter; 27th November 2013, 04:10 PM.

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          • #6
            When I go to the gedmatch X comparison page the default is now 7cM.

            As for us males - the nice thing about having one X chromosome (and there are lots of bad things health-wise, but genealogically it is useful to have only one) is that a male-to-male comparison on the X doesn't have to worry about phasing.

            Thus even small segments (3 or 4 cM) are likely from genealogically-scoped common ancestors, albeit probably many centuries back.
            Last edited by S9 H9; 27th November 2013, 09:53 PM.

            Comment


            • #7
              One time I looked at the ancestry of someone who matched me on multiple small X segments at Gedmatch and what I found interesting was that this person had all German ancestry. One of my X chromosomes has a long segment of "French and German" at 23andMe that I am pretty sure I got from my mother intact and she had a German line. I don't put much emphasis on this speculative observation except that I think we need to look more closely at the biogeographical analysis of the X chromosome in more detail in the future. Can we identify "ethnic" segments on the X? I think so and that may be what people are seeing with these multiple small matches. Years ago many genealogists got together and we found some interesting unique segments but we didn't have computer software and the expertise to analyze the data like we have now.
              Kathy

              Comment


              • #8
                Originally posted by Kathy Johnston View Post
                One time I looked at the ancestry of someone who matched me on multiple small X segments at Gedmatch and what I found interesting was that this person had all German ancestry. One of my X chromosomes has a long segment of "French and German" at 23andMe that I am pretty sure I got from my mother intact and she had a German line. I don't put much emphasis on this speculative observation except that I think we need to look more closely at the biogeographical analysis of the X chromosome in more detail in the future. Can we identify "ethnic" segments on the X? I think so and that may be what people are seeing with these multiple small matches. Years ago many genealogists got together and we found some interesting unique segments but we didn't have computer software and the expertise to analyze the data like we have now.
                Kathy
                How much stock can we put in the admixture analyses‎ of the X?

                Comment


                • #9
                  Originally posted by D.Clade View Post
                  How much stock can we put in the admixture analyses‎ of the X?
                  Are we expecting a difference wrt the autosomes?

                  Different companies sell "ancestry" results but with different meanings, so it is difficult to compare them to each other. But 23andMe does a BEAGLE-like phasing on the SNP data as part of the ancestry composition. This would include the X chromosomes for women. This phasing is important for the 23andMe AC because they are trying to map tiny segments of chromosomes, not totaling up SNPs.

                  If what you're looking for as far as admixture of older populations, and you're identifying particular SNPs as "markers", then again I don't see why the X would be fundamentally different than the autosomes. Given the fewer average recombinations/century of the X one might suspect that it might be a path into finding some older ancestry than the autosomes, but the difference isn't that great.

                  A probably much bigger difference (between chromosomes) in creating a defined "ancestry" is that all parts of the different chromosomes are not created equal - some regions seem to be more conserved than others. The HLA region of chr 6 is the classic example. However, I don't know of anyone (company, enthusiast) who is offering "ancestry" analysis on such regions, (unless you want to count the "Neanderthal" and similar identifications.)

                  Comment


                  • #10
                    Originally posted by S9 H9 View Post
                    When I go to the gedmatch X comparison page the default is now 7cM.
                    I still see 3cM and 200SNPs when I run a one-on-one X comparison between two kits. Where did you see 7cM? That would be nice if it did use 7cM but I can't find it where I'm looking. Help! Where did you see 7cM?
                    Last edited by mkdexter; 29th November 2013, 12:54 PM.

                    Comment


                    • #11
                      Please disregard - I found it. In the one-many comparison, gedmatch.com does default to 7cM. In the X, one-on-one comparison, it still defaults to 3cM. Well... that's good to see since you won't know about the 3cM matches unless you do a one-on-one comparison, or manually change the settings in the first place.

                      Matt.

                      Comment


                      • #12
                        Originally posted by S9 H9 View Post
                        Are we expecting a difference wrt the autosomes?

                        Different companies sell "ancestry" results but with different meanings, so it is difficult to compare them to each other. But 23andMe does a BEAGLE-like phasing on the SNP data as part of the ancestry composition. This would include the X chromosomes for women. This phasing is important for the 23andMe AC because they are trying to map tiny segments of chromosomes, not totaling up SNPs.

                        If what you're looking for as far as admixture of older populations, and you're identifying particular SNPs as "markers", then again I don't see why the X would be fundamentally different than the autosomes. Given the fewer average recombinations/century of the X one might suspect that it might be a path into finding some older ancestry than the autosomes, but the difference isn't that great.

                        A probably much bigger difference (between chromosomes) in creating a defined "ancestry" is that all parts of the different chromosomes are not created equal - some regions seem to be more conserved than others. The HLA region of chr 6 is the classic example. However, I don't know of anyone (company, enthusiast) who is offering "ancestry" analysis on such regions, (unless you want to count the "Neanderthal" and similar identifications.)
                        Thank you for that excellent answer. Is BEAGLE-like phasing less useful or the same with a guy's single X chromosome?
                        This would include the X chromosomes for women.

                        Comment


                        • #13
                          Originally posted by mkdexter View Post
                          I still see 3cM and 200SNPs when I run a one-on-one X comparison between two kits. Where did you see 7cM? That would be nice if it did use 7cM but I can't find it where I'm looking. Help! Where did you see 7cM?
                          When you run a "One-to-many DNA comparison" the default in both the autosome and X boxes is 7cM. This is what I was referring to.

                          If you run a "X 'One-to-one'" comparison the boxes are blank but you can put in 7cM or whatever. In my opinion one ought not to start here, though, but rather in the One-to-many comparison, and pick people to compare to out of that match list (which as I noted already is defaulting to 7cM threshold for both X and autosomes.)

                          Comment


                          • #14
                            A recent match on 23andMe has a double X match with me of 23cM and 29cM blocks.

                            I am feeling that those numbers are particularly high and significant, certainly well above the 7cM block suggested minimum. Overly optimistic I know 29cM is pretty high for me on the atChromosomes.

                            I have read where X-DNA inheritance varies wildly from the mathematical probabilities. Is that more so than atDNA? or is it just because we are looking at one chromosome only and anything can happen in a smaller sample size?

                            On the other hand, there are no other block matches on any other Chromosome Is it unusual to have such large blocks on the X and get goose eggs on the others?

                            My match has many gaps in her family history so not a lot of help there. I have suggested to her to upload to either GedMatch or FamilyFinder or both to see additional matches and blocks between 7 and 10 cM

                            Comment


                            • #15
                              Originally posted by D.Clade View Post
                              Thank you for that excellent answer. Is BEAGLE-like phasing less useful or the same with a guy's single X chromosome?
                              Not sure what you are asking.

                              As us males only have one X chromosome we don't need any type of phasing algorithm for male to male comparisons on the X chromosome.

                              Since females have two X, comparing a male's X to a females X chromosomes will still benefit from having the female's SNP file phased.

                              If you use gedmatch.com, a male will notice on the one-to-many comparison that he gets a "0" in "X-DNA" column for a great majority of his male matches, while his non-zero value in that column will usually be female matches. This ought to be revealing.

                              In my One-to-Many matching at gedmatch.com, only 4 of my matches in the X-DNA column is with males, while I have nearly 30 with females. This is on a very long list of 669 autosomal matches.

                              A female running a One-to-Many match will match many other females in the X-DNA column, and fewer male matches.

                              This is the problem of using non-phased SNPs below about 7cM - there are just too many similar small segments of DNA floating around in the population from which we all spring.

                              On the other hand, when a male-to-male does match on the X we know there is not a phasing issue. For example, with one of the four males (on gedmatch) on which I share X segments the sharing total is two segments - one of 3.5cM (549 SNPs) and 3.0 cM (518 SNPs). We really do share these segments (albeit there are a couple of no-calls in those strings.) His mother and my mother really do share common ancestors in some historical frame, though even then we can't be sure if those 3.5cM and 3.0cM segments are not random recombinations of even older population-wide tiny fragments.

                              The bottom line in all of this is if you want to avoid chasing after ghost ancestors then you'll want to up the threshold for "sharing" to even higher than 7cM, say up to 10cM. Yes, you'll be losing a few real cousins, but you'll drop many falsely-close but extremely distant "cousins".

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