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L2a mtDNA results...Hit a brick wall..sort of confused.

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  • L2a mtDNA results...Hit a brick wall..sort of confused.

    Greetings all..

    I had my sample tested in the Genographic project a few years ago. Since then I have done an upgrade for HVR1 & HVR2 on FTDNA.
    My results are as follows;

    HVR1; 16223T 16278T 16286T 16294T 16309G 16390A 16519C
    HVR2; 73G 146C 152C 195C 207A 263G 315.1C

    Before I had my HVR2 ran, In the top three matching countries I had 36 matches of recent ancestral origins from Mozambique (8.6%), 2 from Sao-Tome/Principe (1.6%) and 2 from Angola (1.2%). I had matched persons from 14 different countries (8 African 4 European and 2 Middle east)

    I had my HVR2 ran and I match no one.

    My questions are;

    Does the HVR2 results invalidate the the matches I have with those I matched in HVR1?

    Is the HVR1 sequence the more stable of the two and therefore does not matter?

    I looked through sites pertaining to ethnic affiliations with my sequence and have suffered even more information overload and confusion. I want to get a better picture of ethnic affiliation with my sequences. Where else should I be looking?

    Thanks in advance for any assistance.

  • #2
    HVR1 (and HVR1/2) matches don't imply anything recent. The common ancestor can be many thousand years in the past (as a rule of thumb, there is one HVR1 mutation every 20,000 years!). So your matches were more a broad indication of possible ancient origin. You belong to a very common haplogroup in Africa, especially in West Africa, and your specific HVR1 motif seems to be quite common too, there are several observations also in Salas's paper on African mtdna (The Making of the African mtDNA Landscape). Salas suggests that most L2a in America is of West African origin, with perhaps a little of South-Eastern origin.

    Therefore, HVR2 mismatches don't really disqualify anything - the information was quite general to start with. Sometimes, certain HVR2 mutations could indicate a more specific subgroup. But this is rare, usually subgroups are defined by more stable coding region mutations.

    Should you find a HVR1+HVR2 match, of course, that would be informative.

    (also, locations 309 and 315 in HVR2 mutate frequently, so you should ignore them - if this is the difference, you should consider that a HVR2 match as well).

    You should also note that much fewer people have tested HVR2, as you can see for instance if you look on

    HVR1 is more variable than HVR2, in general, and thus contains more information. That's why it is tested first. But, as you've seen, mutations happen in HVR2 as well.

    As said, L2a is widespread in Africa. Potentially, to distinguish various groups, one could look at the whole mtdna sequence, including coding region. However, as far as I know, there isn't yet a database of full mtdna sequences from Africa, so, even if you were to do the FGS test, you probably wouldn't be able to say much yet. Perhaps, in the future, as more data is gathered, people will have a better view of mtdna distribution in Africa.