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How to Predict Closeness?

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  • How to Predict Closeness?

    A friend and I happened by chance to find we are in the same MT haplogroup -- N9a3, and have a genetic distance of 1, according to FTDNA. His polymorphisms are identical to mine (we both have T16187C, C16189T, G16230A, C16257a, C16261T, T16278C, C16311T and C16519T in HVR1; and C150T, C152T, C195T, A247G, 315,1C, 522.1A ad 522.1C in HVR2, plus C7810T outside of the HVR regions), I have two additional: 309,1C and T9047Y, -- all based on the RSRS. My review of the literature suggests that 309.1C is somewhat common within N9a3, but that T9047Y is not.

    Any possibility of figuring out how far back our common ancestor is? Neither of us has identified one in our respective trees, although we suspect somewhere in the Polish Pale of Settlement.

  • #2
    Just my opinion - I'd ignore the very common C-insertions at 309 (it's not used in Phylotree, and I believe FTDNA do not count it as Genetic Distance), and I'd consider also to ignore heteroplasmies for matching/age estimation - unless they're proven to be germline (= inherited). If you match someone perfect except of the heteroplasmy, be happy and forget about the Genetic Distance that FTDNA calculate for the heteroplasmy. If you find a perfect match with the same heteroplasmy, be a bit more happy, because it's a bit more of evidence that you could have a common ancestor. For "Y" in fact matches both Allele "C" and "T" perfectly. FTDNA in the contrary chose to judge that you don't match any of them perfectly. It'a just a different perception.

    T9047Y is the notation for heteroplasmy, meaning part of your mtDNA is T9047C (a mutation) and part is T9047T (reference).

    I found only two other sequences in GenBank that have the mutation T9047C, none with the heteroplasmy, so it seems quite rare.

    These are the GenBank sequences: (Haplogroup T2b from, note="ethnicity:Czech; origin_locality:Moravian Wallachia") (from Study about Birt-Hogg-Dubé syndrome - don't be alarmed, as half of the sequences on GenBank are from medical studies. The study is also about autosomal inheritance.)

    The mutation could be either inherited from your mother ("germline"), or developed by you. (See

    Now some of my thoughts on how you could find out wheter it's germline:

    You could test more mtDNA relatives to see if the heteroplasmy will also get detected - not practical because testing will be expensive, as the mutation site is in the Coding Region and you will have to do the "mtFull Sequence".

    Furthermore, FTDNA testing will only report a heteroplasmy if the mutated mtDNA reaches a certain threshold, probably 20% if I remember right (some of the mtDNA FAQ is currently still/again offline ... ).

    The ratio of heteroplasmy can vary a lot from generation to generation, so it means some relatives could be below the threshold and some above it when tested, even if the heteroplasmy is germline. (See So it's not easy to be sure.

    From my own experience: I had a heteroplasmy in the HVR2 detected and checked four more family members with Sanger Sequencing - the curves looked identical, except for the heteroplasmy, that only I had. So I guess it must be my "private mutation". It's also at a site (C195) that is very common to mutate: 15 sequences in GenBank in 15 different Haplogroups have that heteroplasmy...