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Thread: Reliability of the X chromosome as IBD, as opposed to IBS

  1. #1
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    Reliability of the X chromosome as IBD, as opposed to IBS

    Given the nature of the X chromosome, is there a minimum cM size for it to be considered real, i.e., IBD, as opposed to a very distant match or even IBS. For example, would you consider a match of 5cM between two women to be from a common ancestor, and if so would this match be within the genealogical time frame considered by most to be real?

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    This is a good question, because many people will set this threshold at Gedmatch and may waste lots of time.

    Because females have two Xs and males have one, there's no way to know which X a particular SNP is matching on for a female. Therefore it is wise to set different minimums for

    male : male (lowest threshold, perhaps about 7.5 cM)
    male : female (medium threshold, perhaps about 9 cM minimum)
    female : female (greatest threshold because the most possibility of randomly matched SNPs from either side exists, perhaps 11 cM or over)

    In addition when comparing two females who may be closely related, it's useful to look at double inheritance, as in the dark blue in my post here:

    http://www.anthrogenica.com/showthre...ll=1#post14083

    (Note that my numbers are illustrative -- different thresholds may be more accurate, but the point is that a 12 cM match male : male is much better to pursue than one of the same length that is female : female.)
     

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    Thanks AJL. So, if I share a match with a female on one segment, at over 11cM, and my mother's only match with this woman is about 6.67cM on the X chromosome, then her match is likely a false positive? In addition, my mother shares IBS matches with this woman's nationality. How about this one? I share a match with another woman on one segment at 8.82cM. My mother's only match with this woman is on the X chromosome at 6.64cM. In this particular case, I share other matches with this woman's nationality through my father, but my mother has no known ancestry with this nationality. Moreover, I share another match with a man who also shares cM with this woman, but my mother does not share with this man, so her chromosome match with the woman is an isolated case.

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    You're most welcome!

    Quote Originally Posted by leonardo View Post
    I share a match with another woman on one segment at 8.82cM. My mother's only match with this woman is on the X chromosome at 6.64cM.
    Yes, this is exactly why you have to be careful.

    In any of these cases, the maximum true length of matching should conservatively be taken as the shorter of the two segments: provided they overlap.

    It is possible in the above case that your mother might have inherited a larger segment in common with the match and just didn't pass it on to you, because she only gave you one of her Xs, but in general I would not spend too much time trying to pursue matches of this length because they are unlikely to be productive. (I have several X matches of about 12 cM that all seem to originate in the 17th century or so.)
     

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    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

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  8. #5
    Hi,
    I am new to exploring X inheritance. From what was said and I hope I am understanding correctly, that many small CM's on the X, even if they together total over 11 CM, if they are all smaller than 11 CM, do not count them?

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    If you are comparing to another female, you could consider the possibility that a single match of 11 cM is valid, provided there is also a decent-length autosomal match. However, a number of smaller matches totalling 11 cM can be ignored.
     

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    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

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  11. #7
    Thanks! I was looking at 20 CM in total the largest segment 13. No autosomal though. A match?

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    That sounds like a plausible match though I would not say it is certain if it is female : female. It would help if there were a known male relative to compare.
     

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    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

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  14. #9
    Thanks! That helps my understanding of X matches.

  15. #10
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    Quote Originally Posted by AJL View Post
    In any of these cases, the maximum true length of matching should conservatively be taken as the shorter of the two segments: provided they overlap.

    It is possible in the above case that your mother might have inherited a larger segment in common with the match and just didn't pass it on to you, because she only gave you one of her Xs, but in general I would not spend too much time trying to pursue matches of this length because they are unlikely to be productive. (I have several X matches of about 12 cM that all seem to originate in the 17th century or so.)
    Something here does not make sense. Leonardo wrote "... I share a match with a female on one segment, at over 11cM, and my mother's only match with this woman is about 6.67cM on the X chromosome".

    While we might normally judge the "authenticity" of a child's match by the parent's, in this case that would be incorrect. Leonardo has only a single X chromosome, all of which he inherited from his mother. Therefore, he simply cannot match anyone -- male or female -- for more cM than his mother does (or at more SNPs).

    I can only conclude that this is actually a false negative for his mother. She must match the other woman everywhere her son does. It would appear that the matching algorithm is simply discounting some of that matching -- wrongly, in this case -- because both parties are women.

    The bottom line is that in this case, he should judge the quality of his mother's match by his own, and not the other way around.

    EDIT: If my mother had been able to test, I could probably show you examples of X chromosome matches that appear for me that probably would not appear for my mother. This is because I have male-male and male-female matches that probably wouldn't meet the threshold for a female-female match.

    In fact, I can give you an example very close to home. I share three segments on the X chromosome with my youngest sister. And since I only have a single X chromosome, which my daughter inherited from me, my sister and my daughter should match in exactly the same places that my sister and I do.

    They do not. First, my sister and my daughter only share two segments. The second segment my sister and I share is only 6.82 cM in length and contains 846 SNPs. This not only fails to meet the female-female threshold for length, it doesn't contain enough SNPs, either. My sister and my daughter obviously actually do match here, but the algorithm doesn't allow the match to be shown.

    The second interesting thing about their matching is that the two segments the two of them do share are both slightly longer than the ones I share, and contain a few more SNPs. The "missing" segment reflects a false negative produced by the algorithm itself; while the extra matching reflects the fact that my sister also has a paternal X chromosome and my daughter also has a maternal one.
    Last edited by geebee; 05-30-2017 at 09:53 AM.
    The short explanation of my ancestry is German-British-Catalan, but it actually includes smaller amounts of French, Irish, Swiss, Choctaw and probably Cherokee. My avatar picture is of my father, his father, and his father's father. The baby in the picture is my eldest brother.

    GB

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