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Why no X or Y chromosome for ethnic ancestry results?

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  • Why no X or Y chromosome for ethnic ancestry results?

    I see that some testing companies look at the sex chromosomes as part of their ethnic ancestry tests, and some don't. FTDNA is one of those that don't: "Only your autosomal DNA results from the Family Finder microarray chip are used. The myOrigins tool does not use mitochondrial DNA (mtDNA), X-chromosome DNA, or Y-chromosome DNA results." https://www.familytreedna.com/learn/...l-dna-results/

    Why doesn't MyOrigins look at the sex chromosomes? It's annoying for me, since 23 and Me found Spanish/Portuguese DNA on my X chromosome (and nowhere else), and that must be a real result because FTDNA matched me as distant cousins with two 100% Portuguese siblings. Both of them are X-matches and also match a bit of DNA on chromosome 20 (which I suppose was not an ethnicity-specific bit of DNA, since FTDNA's MyOrigins saw no Spanish/Portuguese in me at all). Their ancestors have lived in Portugal for at least 400-500 years (that's how far they've traced their family tree back genealogically, i.e. on paper not DNA), and the only non-Portuguese name in their whole family tree is one Spaniard centuries ago.

    I mention all that just to say, apparently I actually am part Portuguese, but FTDNA doesn't see it because for whatever reason they don't look at the X or Y when determining ancestry. Are they ever going to start looking at X and Y?

  • #2
    Because Y-DNA is non-recombinant and it does not change for generations as it passes down from father to son, X-chromosomes do undergo some recombinance, however the X-chromosome is not the same as mitochondria (passed from mother to child). Y-DNA and mtDNA having nothing to do with ethnicity. FTDNA MyOrigins does look at X-chromosomes and the other autosomes, same as all the other companies. Why FTDNA did not identify your possible Portuguese is either it was too small to identify and score, and given you say it is small it may just be a coincidental match, either identical by descent, etc or it's just the usual result when each company uses a different source data to determine "ethnicity".

    Also worth mentioning that DNA does not equal ethnicity. Ethnicity is not defined by genetics, there are far more aspects that influence that.

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    • #3
      FTDNA does look at X data for the 23rd chromosome. It just doesn't use mtDNA or Y-DNA because those are different products for FTDNA. Also due to how those two things work, they're more of an ancient ancestry tool than they are a (modern) ethnicity one, unless you go really deep into things.

      At a basic level I'm R1A, but from there, members of R1A could either have Viking ancestors, be descended from a Sunni Tribe in Saudi Arabia, have Ancient Hindu ancestors, or simply have a family tree that hails from Poland as examples.

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      • #4
        Just because a company includes Y and X DNA in their chip or raw data doesn't necessarily mean they are using it for ethnicity. As mentioned, FTDNA does include the X chromosome in their chip/raw data and they use it for DNA matching with other testers, not ethnicity. They do not include Y and mtDNA in their autosomal DNA test at all because they offer separate, designated Y and mtDNA tests where other autosoma DNA companies do not.

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        • #5
          Originally posted by Germanica View Post
          Just because a company includes Y and X DNA in their chip or raw data doesn't necessarily mean they are using it for ethnicity.
          You're right, it doesn't necessarily mean that, but 23 and Me clearly is using it for ethnicity. They found Portuguese ethnicity where FTDNA didn't, and the Portuguese connection is real: it was confirmed by the fact that the FTDNA matching tool found two cousins who are 100% Portuguese.

          Originally posted by bartarl260 View Post
          FTDNA does look at X data for the 23rd chromosome.
          The FTDNA site says that it doesn't: "The myOrigins tool does not use... X-chromosome DNA." https://www.familytreedna.com/learn/...l-dna-results/

          I mean, it does look at the X chromosome for matching purposes (cousins, chromosome browser, etc.), but not for ethnicity purposes (myOrigins). It's a little annoying because there is ethnic info there that might not be picked up, or might be miscounted (percentage too low), if you only look at the other 22 chromosomes. I'm just not seeing why they decided to ignore the X and Y chromosomes when it came to determining ethnicity.



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          • #6
            My observation is, of the current four main consumer DNA genetic genealogy testing companies (23andMe, Ancestry, FTDNA and MyHeritage), only 23andMe presents their Ancestry Composition results also as "Ancestry Composition Chromosome Painting." 23andMe explains how they determine customers' Ancestry Composition, and specifically (in Step 5) how they summarize and display the results in the Chromosome Painting at https://www.23andme.com/ancestry-composition-guide/.

            The page you found in the FTDNA Learning Center, about FTDNA not using the X chromosome for myOrigins, was something new to me. I would have thought they'd use the X, too, but you learn something new every day! We can hope that FTDNA and at least MyHeritage may also add something similar to Ancestry Composition Chromosome Painting to their tools in the future (Ancestry's DNA results do not include a chromosome browser, and because of that I don't know if they would be inclined to show their ethnicity estimates in a Chromosome Painting).

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            • #7
              spruithean' s post says it all: until you examine an entire genome and come to hypotheses based on certain associations with conditions arising from specific chromosomes, suggesting a medical condition found in a statistically large group, there is no such thing as "ethnicity" that can be determined by DTC DNA tests, it is simply a (very successful) marketing ploy that has caused upset or elation among some samplers.

              I find it particularly despicable that the very narrow range of identifiers suggesting Native American Indian ancestry have been exploited, considering that so many tribes have never associated their cultures with anyone's "line" except the matrilineal one, and adoptions of entire language groups through conquest or assimilation makes such distinctions meaningless.

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              • #8
                Originally posted by KCH View Post

                You're right, it doesn't necessarily mean that, but 23 and Me clearly is using it for ethnicity. They found Portuguese ethnicity where FTDNA didn't, and the Portuguese connection is real: it was confirmed by the fact that the FTDNA matching tool found two cousins who are 100% Portuguese.
                Is the Portuguese ancestry that 23andMe found actually, and solely reported on the X chromosome? The Chromosome Painter should tell you whether it is or not. Lots of things can contribute to why one company might pick up on an ethnicity that another does not, not necessarily because of the X chromosome. And having 2 DNA matches with 100% Portuguese ancestry doesn't necessarily mean you have Portuguese ancestry - how much DNA do you share with them and on what chromosome? Below a certain threshold, they could very well not be identical by descent. I have a few distant DNA matches who are 100% Swedish and I have no known Swedish ancestry - I consider them likely identical by state.

                Particularly matches who only match you on the X chromosome and not on any autosomal chromosome - since there is less recombination on the X chromosome, you can share significant DNA with someone on the X yet not be identical by descent. This is why I'm not too keen on companies who report X-only matches - it can be very misleading.

                The FTDNA site says that it doesn't: "The myOrigins tool does not use... X-chromosome DNA." https://www.familytreedna.com/learn/...l-dna-results/

                I mean, it does look at the X chromosome for matching purposes (cousins, chromosome browser, etc.), but not for ethnicity purposes (myOrigins). It's a little annoying because there is ethnic info there that might not be picked up, or might be miscounted (percentage too low), if you only look at the other 22 chromosomes. I'm just not seeing why they decided to ignore the X and Y chromosomes when it came to determining ethnicity.
                23andMe does use X for ethnicity, but not Y.

                Y is a completely different type of DNA from autosomal and simply doesn't really work for percentage based ethnicity reports the way autosomal does (ie, there's no recombination). That's why it's not used for ethnicity, even at 23andMe. It's not really possible.

                X is like autosomal in some ways, but not in others, which is probably why some companies may use it for ethnicity and others don't. The X does recombine like autosomal DNA does, so it can be used for ethnicity, but like I said above, there's less recombination than autosomal DNA, meaning longer matching segments with the ethnicity reference panel could be identical by state, not by descent - so the ethnicity found on the X could be misleading in some cases. Perhaps that's why not everyone uses X for ethnicity.

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