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  • X chromosome ancestry testing: Selecting the right candidate

    I posted this to Rootsweb, but it occurs that some here might also be interested in exploring the information written on the X chromosome.

    After tapping out Y-DNA and mtDNA testing, and learning more or less all (to
    this point) that the information can tell me (until the dating "issue" is
    better resolved), it seems that shifting gears toward autosomal and X
    chromosome testing is the logical alternative.

    After spending a great deal of time documenting Native American ancestors
    the question is whether DNA testing of any sort can assist. Since the paper
    trail is so detailed, why bother? In two words, "cross validation".

    Unfortunately the mtDNA line dead ended before 1900. The YDNA lineage poses
    problems in finding a suitable candidate that can be securely linked to
    either he Hill or Green lines. At some point testing of candidates at
    Tyendinaga, Ontario may be undertaken since in this location all
    individuals of these surnames are presumably descendants (assuming no
    unrecorded adoptions and npes).

    Testing of myself and various relatives with autosomal DNA via DNAPrint and
    DNATribes has provided data for consideration, but the results of testing
    with the former test have provided small percentages of either Native
    American or East Asian. Still, this seems rather non-specfic, and the
    concerns surrounding the validity of the data yields unsatisfactory
    findings. All of this rather pales in comparison with the one milltion to a
    half million markers available via the new chip technology. The question
    is, can this new technology overcome the obstacles noted above?

    Fortunately, in terms of minority ancestry testing, there is good news and
    bad news. The good news is that our family has a wide variety documentary
    sources pertaining to our Six Nations ancestors going back from a birth in
    1747, five generations into the 1600s. The bad news is that for me, that
    means that this ancestor has made a .004% (1/256) contribution to my
    genome. Hence there is unlikely to be more than a "trace" of this
    non-European lineage. There are family members who, due to being the
    youngest child of the youngest child, are 5 generations removed from the NA
    ancestor, whereas I am 8 generations. Hence there would be a 1/64 or 2%
    genomic contribution. There is every possibility that this would be more
    substantial due to the vagaries of recombination at each meiosis, or could
    in fact be zero or undetectible. The Finonacci series to the rescue.

    The X inheritance is like nothing else in genetics. For example, of 128
    ancestors at the 7th generation, only 21 have the opportunity to make any
    sort of contribution. For example, if you are a male, your father made a
    zero contribution since you obtained your Y from him, and your X from your
    mother. The mtDNA ancestor will make a 1/64 contribution at the 7th
    generation and the mother's father's mother's father's mother's father's
    mother will make a 1/8 contribution. By some quirk of fate this woman at
    the top of the fan chart created by Blaine Bettinger:

    http://www.thegeneticgenealogist.com...-x-chromosome/

    is my Native American ancestor. The upshot is that despite my low (under
    the radar) autosomal link to this woman, she made a 1/16 contribution to my
    X genome. What is interesting is that my mother's brothers (one remains)
    have a 1/8 contribution. I always thought that the zig zag back and forth
    between male and female gave me a lesser tie to my ancestor, but the
    opposite is correct.

    Thanks to Anders and the browser at decodeme, we have determined that the
    largest block on my X which matches anyone in the 51 groups of the Human
    Genome Diversity Panel (worldwide) is 364 SNPs (circa 5 Mb haploblock), with
    a perfect match to a Xibo tribesman of Manchuria in northeast China, and the
    only other close match is to a Yakut, and there is a secondary match to a
    Yakut within this block. Manchuria (original home of the Xibo) and Lake
    Baikal (original home of the Yakut) are considered to be the "home" of
    Native Americans before the migration(s) beginning circa 15 KBP.

    All of the high matches (6 or more "high matching" regions) are northern
    East Asian (Xibo, Daur, Miao, She, Tujia), Native American (Pima, Suri),
    West Asian (Hazara, Balochi), and European (Sardinian, Italian, Tuscan).
    The Uyghur individual with 11 "high matching" regions is by far the closest
    match on the X. This is odd, since there is no or low matches to all
    northern Europeans (my primary background) except one person who is Colonial
    American.

    Now the decision, to test my uncle, or not, since decodeme offers "more" in
    relation to anything concerning the X chromosome (and the browser is
    excellent). How much more information would this provide. As an "RP"
    (retired person) I can no longer test anyone "just because".

    Perhaps those of you considering what the X can or cannot tell you about
    your ancestry might want to fill in the fan charts and see whose DNA is
    likely to be represented on this chromosome. Recall though that, as Ander's
    (Norwegian ancestry) match to a Mongol and Pima shows, interpretation is not
    necessarily straightforward. At this point, being as objective as possible,
    my Xibo and Yakut matches may be interesting distractors - only time will
    tell. At some point individual European ancestors may be identified or
    recognized by their signature on the X - I don't see this as in any way a
    pipe dream - just something that awaits further developments.

  • #2
    DKF,

    Thanks for the links to the inheritance graphics. On the graphic for males, I was struck by the consistent reading on the direct female line. That would make X testing a good adjunct to mtDNA results, to further prove relatedness between identical or near matches on mtDNA.

    I wish I could afford one of the genome scans but I frittered away my testing dollars on family autosomal and X STR's from DNAF/FTDNA. Sigh. Perhaps the New Year will bring more disposable income and refined offerings from the scanners.

    Comment


    • #3
      Originally posted by tomcat
      DKF,

      Thanks for the links to the inheritance graphics. On the graphic for males, I was struck by the consistent reading on the direct female line. That would make X testing a good adjunct to mtDNA results, to further prove relatedness between identical or near matches on mtDNA.

      I wish I could afford one of the genome scans but I frittered away my testing dollars on family autosomal and X STR's from DNAF/FTDNA. Sigh. Perhaps the New Year will bring more disposable income and refined offerings from the scanners.
      Yes Tomcat you and Al and Blaine and a few others I can think of would be "perfect" candidates for this sort of testing. The latter two have tested with either decodeme or 23andme and so we just have to get a few things sorted around in order to assist everyone to find their various block matches from the Human Diversity Panel. I honestly believe that this is the approach that will tell us for example the migrational history of the Mohawk people back into Asia. If my results are duplicated in others with the same ancestry then we are going to be on a more solid footing. Exciting times ahead.

      Hope you can find a way to get tested, I certainly do not regret a penny spent with decodeme and 23andme. I would have to think twice now. There is a downside to being retired - the word "budget" actually takes on a personal meaning. I expect I will have to go cap in hand to family members to ask for a "contribution" in order to get my uncle tested. I have never done that before - I lost track a long time ago of the number of people for whom I had "taken care of" the testing for everything imaginable.

      David.

      Comment


      • #4
        I have a close FGS match who has one extra mutation but we have an ancestral spot of our mtDNA ancestors of near Bantry Bay in Cork c. 1837-41.. we match on the Coding region exactly..His sisters and my sister and I share many many markers on our X profiles..
        however we do NOT share the X haploblock at DXS 10074-10075-10079 nor do we share the mini block at DXS 10066-67-68.

        I DO however share one of my X blocks with one person and the other one with another person.. he is currently testing another relative as am I..we have shared know names

        They are minimal in expense at FTDNA and are a good starting point and Thomas Krahn has that interactive database at DNA-FP..there are currently 518 users with datasets displayed there..(Which is free)

        If everyone who could not currently afford 23and me who has tested and has a sample at FTDA tested those markers it would be only about $50-60 with a free interactive database that has e-mails attached..

        But maybe I do not understand the relevance of the whole genome study?
        Many of us have done most of it in bits and pieces..
        FGS, Y lines for every ancestor we can find..X and at markers for siblings...
        I only have the one sister but I did my son who shares one block of course..
        Tom has done a PACK of siblings..bless him..

        all are welcome

        Comment


        • #5
          Originally posted by Kathleen Carrow
          I DO however share one of my X blocks with one person and the other one with another person.. he is currently testing another relative as am I..we have shared know names

          They are minimal in expense at FTDNA and are a good starting point and Thomas Krahn has that interactive database at DNA-FP..there are currently 518 users with datasets displayed there..(Which is free)

          Since I posted that I went and looked and I now have 2 more matches on those blocks.. and I e-mailed them.
          I plan to be much more focused on finding matches with testing I have done already..saving my $$ to test more male relatives..
          __________________

          Comment


          • #6
            This thread caught my attention

            I am awaiting FGS. After that I, yet another RP, will have come close to exhausting my play money. However, I could always afford $60-70 a pop.

            I am anticipating more mysteries await me when my FGS returns. My mother was born on an island. Her family's roots are allegedly nearly 400 years old on that island. But the paper trail is virtually zip. A fair number of members of the purported families of my mother, my grandmother, and my great grandmother have taken various levels of dna testing, y and mt. I don't know about X.

            I don't anticipate any Native American ancestry, although there is a theoretical possibility because of the alleged presence of Native American ancestry in a family that may be related from the island (who were Sarawak).

            Assuming that there is no Native American ancestry, would X testing provide any information that I might be able to use to unravel the tightly interwoven threads of my mother's ancestry despite the absence of a paper trail before 1825? If so, I did not see where that option was available to me through FT DNA except in relation to Native American ancestry. Is there an option at FT DNA? I do not mean to denigrate anyone else, but FT DNA has gained a certain level of trust and respect from me that is not easily won.

            Comment


            • #7
              Originally posted by Deirwha
              I am awaiting FGS. After that I, yet another RP, will have come close to exhausting my play money. However, I could always afford $60-70 a pop.

              I am anticipating more mysteries await me when my FGS returns. My mother was born on an island. Her family's roots are allegedly nearly 400 years old on that island. But the paper trail is virtually zip. A fair number of members of the purported families of my mother, my grandmother, and my great grandmother have taken various levels of dna testing, y and mt. I don't know about X.

              I don't anticipate any Native American ancestry, although there is a theoretical possibility because of the alleged presence of Native American ancestry in a family that may be related from the island (who were Sarawak).

              Assuming that there is no Native American ancestry, would X testing provide any information that I might be able to use to unravel the tightly interwoven threads of my mother's ancestry despite the absence of a paper trail before 1825? If so, I did not see where that option was available to me through FT DNA except in relation to Native American ancestry. Is there an option at FT DNA? I do not mean to denigrate anyone else, but FT DNA has gained a certain level of trust and respect from me that is not easily won.
              That was what I was attempting to say in my post..
              The X markers are available at Family Tree DNA..with a fee of $9.50 to "prepare" this sample the X haploblocks at FTDNA such as the 3 marker at DXS 10074-10075-10079 and the 4 markers at DXS 10066-67-68-69 is less than $60..

              You can then put the results at Thomas Krahn's database at DNA -Fingerprint.. here : http://www.dna-fingerprint.com

              If you match someone it is interactive and you can then email them..if you have a match fine..if not you are not out many hundreds of more $$..

              Right now between my sister and I we have 3 blocks..2 from mother( separate ones) and one from Dad..Since they are X markers you know where you inherit them from..

              if enough people did that it would be very helpful..
              I currently have 2 matches on one haploblock and 5 matches on the other..the 3rd haploblock is the one that would have come from Dad and that one of course there are no matches on..since I do not know who my Father's father was that one is very important..

              But that does not mean I would have necessarily had a match at 23andMe or elsewhere..

              Comment


              • #8
                Thank you

                Would you recommend those same blocks for me (or are there alternatives?)

                Comment


                • #9
                  Originally posted by Deirwha
                  Would you recommend those same blocks for me (or are there alternatives?)
                  Thomas K. had said this:
                  "Once we have a useful number of participants in our database, this will
                  be without a doubt a helpful tool to explore heritage in a mixed
                  male-female-male-female etc. line. So even if I don't want to make too
                  much advertising on this list for my own company, I would strongly
                  recommend to just test those three linked markers from the Szibor paper
                  (DXS10074 / DXS10075 / DXS10079) for as many people as possible. I also
                  recommend to connect our X haplotype observations with the male Y
                  haplogroups, because if the paternal line comes from one region of the
                  world, it is most likely, that the female partner will also come from
                  the same geographical region. This would allow us to establish the X
                  haplogroup map more quickly and the erroreous designations will soon be
                  averaged out if the sample number increases."

                  and there is an earlier thread here on the markers..
                  "Testing DYX 10074-10075 and 10079" or something like that..he also told me the "Other " Haploblock was a lesser one ..
                  if I find the quote from him on that one I will post that also..
                  Kath

                  Comment


                  • #10
                    Thanks

                    I copied down those test numbers.

                    Comment


                    • #11
                      Originally posted by DKF View Post
                      ...
                      Hope you can find a way to get tested, I certainly do not regret a penny spent with decodeme and 23andme...
                      Is one lab preferrable to the other? Is DeCode sinking with the Icelandic economy? I know DeCode runs more SNP's. Is one service easier to use? What is DeCode's coverage of X compared to 23etMoi?

                      Comment


                      • #12
                        Originally posted by Kathleen Carrow View Post
                        I have a close FGS match who has one extra mutation but we have an ancestral spot of our mtDNA ancestors of near Bantry Bay in Cork c. 1837-41.. we match on the Coding region exactly..His sisters and my sister and I share many many markers on our X profiles..
                        however we do NOT share the X haploblock at DXS 10074-10075-10079 nor do we share the mini block at DXS 10066-67-68.

                        I DO however share one of my X blocks with one person and the other one with another person.. he is currently testing another relative as am I..we have shared know names

                        They are minimal in expense at FTDNA and are a good starting point and Thomas Krahn has that interactive database at DNA-FP..there are currently 518 users with datasets displayed there..(Which is free)

                        If everyone who could not currently afford 23and me who has tested and has a sample at FTDA tested those markers it would be only about $50-60 with a free interactive database that has e-mails attached..

                        But maybe I do not understand the relevance of the whole genome study?
                        Many of us have done most of it in bits and pieces..
                        FGS, Y lines for every ancestor we can find..X and at markers for siblings...
                        I only have the one sister but I did my son who shares one block of course..
                        Tom has done a PACK of siblings..bless him..

                        all are welcome
                        Here is a link to the original paper where these markers are analyzed:

                        http://www.excli.de/vol6/Hering06-07proof.pdf

                        Guess I better test these too. I know what my SNPs are in this region of the X. It would be interesting to also have the STRs from this area with high linkage disquilibrium (in other words the region is unlikely to be split by recombination) - although there is variability in this region so I will check on the level of cM/Mb in the specific area (the lower the better) and can be more specific in a later post.

                        Comment


                        • #13
                          Originally posted by tomcat View Post
                          Is one lab preferrable to the other? Is DeCode sinking with the Icelandic economy? I know DeCode runs more SNP's. Is one service easier to use? What is DeCode's coverage of X compared to 23etMoi?
                          Each has their advantages and disadvantages. The price factor is clearly in favor of 23andme, but to date they don't have a browser like that of decodeme to compare degree of matching between members of various population groups (for example).

                          I think I will wait a bit and see if the latter brings down their price or the former develops more sophistocated tools to interpret the results. The Ancestry Painting is good, but mostly for novices happy with a "general idea" about things.

                          Comment


                          • #14
                            Originally posted by DKF View Post
                            ...Guess I better test these too. I know what my SNPs are in this region of the X. It would be interesting to also have the STRs from this area with high linkage disquilibrium (in other words the region is unlikely to be split by recombination) - although there is variability in this region so I will check on the level of cM/Mb in the specific area (the lower the better) and can be more specific in a later post.
                            Was just thinking the same. The haploblock STR's could yield higher resolution. Although they are in an LD block they are not constrained from adding or dropping repeats. But you need a match on the block as defined by SNP's in order to make any sense of the STR repeat motifs.

                            Comment


                            • #15
                              Originally posted by tomcat View Post
                              Was just thinking the same. The haploblock STR's could yield higher resolution. Although they are in an LD block they are not constrained from adding or dropping repeats. But you need a match on the block as defined by SNP's in order to make any sense of the STR repeat motifs.

                              I don't understand..I have the Block with STRs? or do I have SNPS??
                              DXS10074 = 8-15
                              DXS10075 = 16-18
                              DXS10079 = 16-18

                              so my blocks are 8-18-18 AND 15-16-16 one form Dad and one from Mom but WHERE are my SNPS?
                              Is that something I should have?

                              Comment

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