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Could an X-match be an Y-match?

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  • Could an X-match be an Y-match?

    Hi, I have two small X-matches very far out on the X-chromosome at 152647871 to 154570039 base pairs. The total length of the X-chromosome being 156040895 makes these matches appear very close to the end. I was reading in Bryan Sykes book 'Adam's Curse' that there are regions at the ends of the Y-chromosome which are recombining and exchanging genes with the X-chromosome. My question is: could this X-match be a match from a region of my Y-chromosome which is matching with a region on an X-chromosome? If not, why not?

  • #2
    X-chromosome and Y-chromosome are different chromosomes. They have nothing common, I think. But one person can have same dna segments with another person in both of X-chromosome and Y-chromosome with another person.

    I borrow this book from library: Adam's Curse: A Future Without Men. Thank you giving a tip to interesting reading.
    Last edited by ifiru; 3rd January 2018, 05:05 AM.

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    • #3
      First consideration for an "X match" is its size. If the matching segment is small (say, 10 cM or less), it's unlikely to be genealogically useful in any way, based on the collective experience of a lot of people who have posted here. Second, it is usually not worth spending time on any X match, unless there is also a strong autosomal match.

      There is indeed a small piece of X that is homologous to a small piece of Y, probably necessary so that the X and Y will pair up and then reliably disjoin from each other during male meiosis. However, I'm not sure of the length of this region in cM (that's the metric that we care about most for genealogy, not the number of base pairs), nor whether there are enough SNP's that are sampled within this region to allow the matching algorithm to function correctly. Some facts would be useful here.

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      • #4
        The PAR (Pseudoautosomal regions)of X are not tested by FTDNA
        The PAR regions are areas where the X and Y can recombine with one another (swap sections). These are located at the beginning and end of the X and Y chromosomes.

        Build 36 positions
        PAR 1 - positions 1 to 2709520
        PAR 2 - positions 154584238 to 154913754

        FTDNA only test positions between 2710157** and 154551755 on the X chromosome, they do not test the PAR regions
        **They test one X chromosome PAR1 Region SNP, Position 1370495

        FTDNA and Gedmatch chromosomes browsers use Build 36 Positions, Gedmatch Genesis uses build 37 Positions.

        Build 37 Positions
        PAR 1 - positions 60,001 to 2,699,520
        PAR 2 - positions 154,931,044 to 155,260,560

        Build 38 Positions
        PAR 1 - Positions 10,001 to 2,781,479
        PAR 2 - Positions 155,701,383 to 156,030,895

        If tested with a company which tests the PAR regions (Ancestry and 23andme) and Gedmatch shows matching in these regions, the match could be on your X chromosome and may be from an ancestors Y chromosome. your maternal Grandfathers Y, maternal Grandmothers Fathers Y, ect.

        Or it may be on your Y chromosome. Brothers with same father should show at least half base pair matching along these sections. Full base pair when also sharing same X from mother.(Gedmatch chromosomes browser with Graphic)
        Last edited by prairielad; 3rd January 2018, 12:24 PM.

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        • #5
          Does anyone have the lengths of the 2 PAR regions on the X chromosome in centiMorgans?

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          • #6
            Originally posted by John McCoy View Post
            Does anyone have the lengths of the 2 PAR regions on the X chromosome in centiMorgans?
            The following utility gives 0, so I am not sure if it is registerable...less then 1cM???

            http://compgen.rutgers.edu/map_interpolator.shtml

            EDIT
            Correction, it does not give 0, but gives N/A for one position therefore can not subtract the two to get cM size, although position "1" would not have a cM length, so PAR1 is about 6cM
            Attached Files
            Last edited by prairielad; 3rd January 2018, 02:25 PM.

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            • #7
              Here is an example of how to use the Interpolator
              Attached Files

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              • #8
                Using Build 36 positions, Interpolator gives under 1cM for PAR2
                Attached Files
                Last edited by prairielad; 3rd January 2018, 02:31 PM.

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                • #9
                  So the PAR regions are indeed quite short in terms of the human genetic recombination map -- short enough that I don't think they are likely to be significant sources of error in interpreting strong X matches. The risk would be, that in a strong X match (matching segment length greater than 10 cM AND with a strong autosomal match implying second cousins or closer), one might infer a maternal connection where the actual relationship is through a PAR region match on the Y chromosome. If the matching segment lengths are long enough, this risk should be extremely small.

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                  • #10
                    One thing nobody ever seems to mention is the fact that part of the X chromosome recombines with the Y Chromosome.

                    So it is in fact possible for you to inherit part of your X chromosome from your mother's father's father. Your mother's father's X partially recombined with his Y, so one of your mother's X's contains a portion of her father's Y, and then her two X's recombine and you likely get some of that passed onto you.

                    The same holds true for your father. Part of his X and Y recombined, so if you are male, you received part of the X he got from his mother in your Y chromosome, and of course the rest of the Y from him, but even his Y was a combination of his father's X and Y. If you are female, you still receive part of the Y that your father got from his father.

                    Moral of the story is, the X match doesn't filter out the part of the X that recombines with the Y, so it is not a very accurate indicator of anything.

                    Oh, and here's a video that shows how the X/Y recombination is different than the other chromosomes! https://www.biointeractive.org/class...n-y-chromosome

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