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Thread: L1 Haplogroup

  1. #1
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    L1 Haplogroup

    I've just gotten my aunt's DNA results back from Ancestry, and Wegene has predicted her mtdna haplogroup as L1. It seems very unlikely, and so I was looking at the raw data and I discovered a few things. For one thing, she isn't haplogroup H or U, although none of the defining SNPs for N were tested, but I did find two SNPs with mutations that aren't found in Europe, they are almost entirely African. Here are the SNPs:

    rs28357671 (C;C)
    rs28357676 (A;A)

    According to SNPedia and grch37, 100% of Europeans are (T;T) and (G;G) for those SNPs.

    Are there any other defining SNPs I can check in my aunt's raw data? There are many missing because Ancestry has changed their testing recently, but I would like to be able to confirm haplogroups or rule them out.

    I know that N is a huge overarching haplogroup that is the parent of most subclades in Europe, so are there any SNPs I can check that being negative will absolutely rule out N as an option?

    Thanks!
    DNA Tribes
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    92.1% European, 3.2% South Asian, 2.9% North African & Middle Eastern, 0.9% Siberian, 0.6% Amerindian, 0.2% Sub-Saharan African

    My mother
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  2. #2
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    An update on this, using Phylotree I've managed to work out the following:

    L1 Markers:

    T14178C - Positive
    G14560A - Positive

    L2'3'4'5'6 Markers:

    A10688G - Negative
    G13105A - Negative
    T13506C - Negative
    T8468C - Negative
    T3594C - Negative (L3'4 specific)
    A1018G - Negative (L3 specific)
    T10115C - Negative (L2 specific)
    A7972G - Negative (L5 specific)

    So it looks like she might be L1. I've ordered an mtDNA test to make sure, because there are a lot of markers missing. However, she is negative on every single non-L1 marker tested, including being absolutely negative for HV, and some markers for J, T, U, B, R, and N.

    If it's true that my dad and aunt are L1, it doesn't make sense. It's a Sub-Saharan African haplogroup, and I've traced my dad's maternal line back to 1720 in a small town in the east of Scotland. Neither myself nor my aunt get African in our DNA results either, and considering it would have to be relatively recent, it makes even less sense. I have an Indian ancestor born around 1780, and both me and my aunt show consistent South Asian results (she actually gets 5% South Asian on K13).

    Can anyone help me with this? I'm very confused!
    DNA Tribes
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    92.1% European, 3.2% South Asian, 2.9% North African & Middle Eastern, 0.9% Siberian, 0.6% Amerindian, 0.2% Sub-Saharan African

    My mother
    95% European, 2.9% North African & Middle Eastern, 2.1% Amerindian

  3. #3
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    Quote Originally Posted by Ais View Post
    An update on this, using Phylotree I've managed to work out the following:

    L1 Markers:

    T14178C - Positive
    G14560A - Positive

    L2'3'4'5'6 Markers:

    A10688G - Negative
    G13105A - Negative
    T13506C - Negative
    T8468C - Negative
    T3594C - Negative (L3'4 specific)
    A1018G - Negative (L3 specific)
    T10115C - Negative (L2 specific)
    A7972G - Negative (L5 specific)

    So it looks like she might be L1. I've ordered an mtDNA test to make sure, because there are a lot of markers missing. However, she is negative on every single non-L1 marker tested, including being absolutely negative for HV, and some markers for J, T, U, B, R, and N.

    If it's true that my dad and aunt are L1, it doesn't make sense. It's a Sub-Saharan African haplogroup, and I've traced my dad's maternal line back to 1720 in a small town in the east of Scotland. Neither myself nor my aunt get African in our DNA results either, and considering it would have to be relatively recent, it makes even less sense. I have an Indian ancestor born around 1780, and both me and my aunt show consistent South Asian results (she actually gets 5% South Asian on K13).

    Can anyone help me with this? I'm very confused!
    This might be relevant? It's about Indian Siddhi's, mostly brought to India by the Portuguese, although i think there were some sub-Saharan Africans brought to parts of India & Pakistan during the period when the Islamic world was spreading into the subcontinent. I've only read the abstract so far though. Another article mentioned that they were mainly Gujarat & Karnataka, although the ones in Karnataka mostly had L0 and L2a?:

    https://www.sciencedirect.com/scienc...02929711002230

    Edit: Looking at it again, the author estimates the admixture between the two only occured around 200 years ago, so unless it was an exception, i would guess it was much older?
    Last edited by Anglecynn; 08-11-2018 at 10:42 AM.
    Y-DNA: I1* (Ware, Hertfordshire)
    MT-DNA: U5a1b4 (Boughton Aluph, Kent)
    Father's MT-DNA: J1c8 (Wolverhampton, Staffordshire)
    Grandfather's MT-DNA: H1b (Littlehampton, Sussex)

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     Ais (08-11-2018)

  5. #4
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    Quote Originally Posted by Anglecynn View Post
    This might be relevant? It's about Indian Siddhi's, mostly brought to India by the Portuguese, although i think there were some sub-Saharan Africans brought to parts of India & Pakistan during the period when the Islamic world was spreading into the subcontinent. I've only read the abstract so far though. Another article mentioned that they were mainly Gujarat & Karnataka, although the ones in Karnataka mostly had L0 and L2a?:

    https://www.sciencedirect.com/scienc...02929711002230

    Edit: Looking at it again, the author estimates the admixture between the two only occured around 200 years ago, so unless it was an exception, i would guess it was much older?
    Thanks for the link!

    It might have made sense that it was connected to my Indian ancestry, but it's on a different line. I've managed to trace the maternal line back to 1720, and it's all Scotland. I think there must be a mistake somewhere, it's so unlikely that L1 would exist in Scotland, but I've checked and double checked, and all of the markers are negative for everything except L1.
    DNA Tribes
    Me
    92.1% European, 3.2% South Asian, 2.9% North African & Middle Eastern, 0.9% Siberian, 0.6% Amerindian, 0.2% Sub-Saharan African

    My mother
    95% European, 2.9% North African & Middle Eastern, 2.1% Amerindian

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     Anglecynn (08-11-2018)

  7. #5
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    It's fascinating -- could be something like someone moving back to Scotland from the colonies with a mixed wife and then daughters with L1, but I would find it hard to accept without something more definitive. I'd probably try to talk her (or another relative on that mtDNA line) into one of the tests that do mtDNA, although I know that means more money.

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  9. #6
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    Quote Originally Posted by Ais View Post
    Thanks for the link!

    It might have made sense that it was connected to my Indian ancestry, but it's on a different line. I've managed to trace the maternal line back to 1720, and it's all Scotland. I think there must be a mistake somewhere, it's so unlikely that L1 would exist in Scotland, but I've checked and double checked, and all of the markers are negative for everything except L1.
    Ahh well can rule that out then! Could be. I remember there was a family in Yorkshire with the A (y-DNA) haplogroup - i think they speculated it could date back to the Roman period, as they had no sub-saharan ancestry either?

    L is not uncommon among Berbers, too. There is some evidence for small numbers of North Africans ending up in the Isles since the Roman period - so that's an option.

    Or alternatively i think a number of west Africans came the Britain during the early modern era - many ended up as servants to the rich of the time, even in the 16th century.
    Y-DNA: I1* (Ware, Hertfordshire)
    MT-DNA: U5a1b4 (Boughton Aluph, Kent)
    Father's MT-DNA: J1c8 (Wolverhampton, Staffordshire)
    Grandfather's MT-DNA: H1b (Littlehampton, Sussex)

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  11. #7
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    Quote Originally Posted by msmarjoribanks View Post
    It's fascinating -- could be something like someone moving back to Scotland from the colonies with a mixed wife and then daughters with L1, but I would find it hard to accept without something more definitive. I'd probably try to talk her (or another relative on that mtDNA line) into one of the tests that do mtDNA, although I know that means more money.
    I've ordered the mtDNA test, and I'm going to ask my aunt to take it. I'm very curious as to what it'll show up! I might have made a mistake when looking at the markers, or Ancestry could have made a mistake, but while that could be true for one or two markers, it seems unlikely to be true for all of them.
    DNA Tribes
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    92.1% European, 3.2% South Asian, 2.9% North African & Middle Eastern, 0.9% Siberian, 0.6% Amerindian, 0.2% Sub-Saharan African

    My mother
    95% European, 2.9% North African & Middle Eastern, 2.1% Amerindian

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  13. #8
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    Quote Originally Posted by Anglecynn View Post
    Ahh well can rule that out then! Could be. I remember there was a family in Yorkshire with the A (y-DNA) haplogroup - i think they speculated it could date back to the Roman period, as they had no sub-saharan ancestry either?

    L is not uncommon among Berbers, too. There is some evidence for small numbers of North Africans ending up in the Isles since the Roman period - so that's an option.

    Or alternatively i think a number of west Africans came the Britain during the early modern era - many ended up as servants to the rich of the time, even in the 16th century.
    Very strange! I'm hoping that the mtDNA test will show whether it's L1b or L1c. While L1b is found primarily in West Africa, it has also been found in low levels in Morocco (4-5%), whereas L1c isn't found outside of West and Central Africa, and peaks among the Pygmy peoples. I imagine, if it is indeed L1, then it's likely to be L1b. I appreciate the ideas about where it could come from as well, as I've been scratching my head wondering how on earth it could be possible when the haplogroup isn't found in Britain at all!
    DNA Tribes
    Me
    92.1% European, 3.2% South Asian, 2.9% North African & Middle Eastern, 0.9% Siberian, 0.6% Amerindian, 0.2% Sub-Saharan African

    My mother
    95% European, 2.9% North African & Middle Eastern, 2.1% Amerindian

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     Anglecynn (08-11-2018)

  15. #9
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    There are some subclades of L haplogroups that may have exited Africa between several hundred to many thousands of years ago, and you might turn out to be in one of those subclades. Did you order the mtDNA full sequence test? That will give you a much more specific results that should be helpful in solving the puzzle.

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  17. #10
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    I just got the results back from my aunt's MTDNA test - she's L1b! She has no matches at all, but I suppose that's not surprising since not that many people take MTDNA tests.
    DNA Tribes
    Me
    92.1% European, 3.2% South Asian, 2.9% North African & Middle Eastern, 0.9% Siberian, 0.6% Amerindian, 0.2% Sub-Saharan African

    My mother
    95% European, 2.9% North African & Middle Eastern, 2.1% Amerindian

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