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Thread: Variants of mt-DNA haplogroup A in South/Central Asia : Expert opinion required

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    Variants of mt-DNA haplogroup A in South/Central Asia : Expert opinion required

    I recently got tested with Living DNA, which includes y-DNA and mt-DNA SNP testing. Quite surprisingly, my mt-DNA haplogroup came back as A. The variant mentioned is A14 which apparently is found rarely in Altaic Siberia, Kyrgyzstan, Xinjiang but also in Vietnam, Cambodia and Thailand. However, the description given next to the maternal ancestors migration map is describing haplogroup A4, which has very rare presence in Iran, and Tajikistan, but is otherwise more prevalent in Altaic Siberia and Mongolia. I have emailed Living DNA regarding this discrepancy and hopefully they will narrow it down to one of the two variants.
    Screenshot (18)_LI.jpg Screenshot (19)_LI.jpgScreenshot (20)_LI.jpg20200813_235928.png
    I know about my maternal ancestry that my grandmothers' mother was Kashmir, and that might explain some female ancestor who entered Kashmir via Ladakh from Tibet or Xinjiang possibly. Although, my GEDMatch HarrappaWorld scores are not East Asian or Siberian/American shifted so I don't think this could be as a result of some recent influence.

    Another variant of the haplogroup, A2, is a lot more frequent, and is found among Native Americans, which makes me think that it might be more related to Ancestral North Eurasians (ANE) than to Southeast Asians. Nonetheless, I would think that my assigned haplogroup is highly unusual.


    Has anyone here ever come across something like this?
    Last edited by kamil154; 08-16-2020 at 02:51 AM.

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    Also, is there a reason I should doubt the accuracy of this test? I uploaded the raw SNP data to James Lick's mtHap utility tool, and it seems to prefer some variant of haplogroup R which would be a bit more plausible. Howewer, I don't really know much about how to interpret the results or the accuracy so I'm unsure what to take of it. Does anyone here know how to use this tool?

    Here's what the results look like:

    mthap version 0.19b (2015-05-11); haplogroup data version PhyloTree Build 17 (2016-02-18) +mods
    raw data source mtdna.csv (78

    rCRSdiff format was uploaded. Based on the markers found, assuming the following regions were completely sequenced: HVR1 (16001~16569) HVR2 (1~574) CR (575~16000).

    Found 16582 markers at 16582 positions covering 100.0% of mtDNA.


    Markers found (shown as differences to rCRS):

    HVR2: 235G 263G
    CR: 663G 735G 1438G 2706G 4769G 4824G 7028T 11719A 14766T 15326G
    HVR1: 16319A


    Best mtDNA Haplogroup Matches:

    1) R0

    Defining Markers for haplogroup R0:
    HVR2: 263G
    CR: 750G 1438G 2706G 4769G 7028T 8860G 14766T 15326G
    HVR1:

    Marker path from rCRS to haplogroup R0 (plus extra markers):
    H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 235G 663G 735G 4824G 11719A 16319A

    Imperfect Match. Your results contained differences with this haplogroup:
    Matches(7): 263G 1438G 2706G 4769G 7028T 14766T 15326G
    Mismatches(2): 750A 8860A
    Extras(6): 235G 663G 735G 4824G 11719A 16319A


    1) R

    Defining Markers for haplogroup R:
    HVR2: 73G 263G
    CR: 750G 1438G 2706G 4769G 7028T 8860G 11719A 14766T 15326G
    HVR1:

    Marker path from rCRS to haplogroup R (plus extra markers):
    H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 73G 11719A ⇨ R ⇨ 235G 663G 735G 4824G 16319A

    Imperfect Match. Your results contained differences with this haplogroup:
    Matches(8): 263G 1438G 2706G 4769G 7028T 11719A 14766T 15326G
    Mismatches(3): 73A 750A 8860A
    Extras(5): 235G 663G 735G 4824G 16319A


    2) HV

    Defining Markers for haplogroup HV:
    HVR2: 263G
    CR: 750G 1438G 2706G 4769G 7028T 8860G 15326G
    HVR1:

    Marker path from rCRS to haplogroup HV (plus extra markers):
    H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 235G 663G 735G 4824G 11719A 14766T 16319A

    Imperfect Match. Your results contained differences with this haplogroup:
    Matches(6): 263G 1438G 2706G 4769G 7028T 15326G
    Mismatches(2): 750A 8860A
    Extras(7): 235G 663G 735G 4824G 11719A 14766T 16319A


    3) P

    Defining Markers for haplogroup P:
    HVR2: 73G 263G
    CR: 750G 1438G 2706G 4769G 7028T 8860G 11719A 14766T 15326G 15607G
    HVR1:

    Marker path from rCRS to haplogroup P (plus extra markers):
    H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 73G 11719A ⇨ R ⇨ 15607G ⇨ P ⇨ 235G 663G 735G 4824G 16319A

    Imperfect Match. Your results contained differences with this haplogroup:
    Matches(8): 263G 1438G 2706G 4769G 7028T 11719A 14766T 15326G
    Mismatches(4): 73A 750A 8860A 15607A
    Extras(5): 235G 663G 735G 4824G 16319A


    3) R30

    Defining Markers for haplogroup R30:
    HVR2: 73G 263G
    CR: 750G 1438G 2706G 4769G 7028T 8584A 8860G 11719A 14766T 15326G
    HVR1:

    Marker path from rCRS to haplogroup R30 (plus extra markers):
    H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 73G 11719A ⇨ R ⇨ 8584A ⇨ R30 ⇨ 235G 663G 735G 4824G 16319A

    Imperfect Match. Your results contained differences with this haplogroup:
    Matches(8): 263G 1438G 2706G 4769G 7028T 11719A 14766T 15326G
    Mismatches(4): 73A 750A 8584G 8860A
    Extras(5): 235G 663G 735G 4824G 16319A


    3) R(T16189C)

    Defining Markers for haplogroup R(T16189C):
    HVR2: 73G 263G
    CR: 750G 1438G 2706G 4769G 7028T 8860G 11719A 14766T 15326G
    HVR1: 16189C

    Marker path from rCRS to haplogroup R(T16189C) (plus extra markers):
    H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 73G 11719A ⇨ R ⇨ 16189C ⇨ R(T16189C) ⇨ 235G 663G 735G 4824G 16319A

    Imperfect Match. Your results contained differences with this haplogroup:
    Matches(8): 263G 1438G 2706G 4769G 7028T 11719A 14766T 15326G
    Mismatches(4): 73A 750A 8860A 16189T
    Extras(5): 235G 663G 735G 4824G 16319A


    3) R31

    Defining Markers for haplogroup R31:
    HVR2: 73G 263G
    CR: 750G 1438G 2706G 4769G 7028T 8860G 11719A 14766T 15326G 15884A
    HVR1: (16362C)

    Marker path from rCRS to haplogroup R31 (plus extra markers):
    H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 73G 11719A ⇨ R ⇨ 15884A (16362C) ⇨ R31 ⇨ 235G 663G 735G 4824G 16319A

    Imperfect Match. Your results contained differences with this haplogroup:
    Matches(8): 263G 1438G 2706G 4769G 7028T 11719A 14766T 15326G
    Mismatches(4): 73A 750A 8860A 15884G (16362T)
    Extras(5): 235G 663G 735G 4824G 16319A


    3) R2'JT

    Defining Markers for haplogroup R2'JT:
    HVR2: 73G 263G
    CR: 750G 1438G 2706G 4216C 4769G 7028T 8860G 11719A 14766T 15326G
    HVR1:

    Marker path from rCRS to haplogroup R2'JT (plus extra markers):
    H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 73G 11719A ⇨ R ⇨ 4216C ⇨ R2'JT ⇨ 235G 663G 735G 4824G 16319A

    Imperfect Match. Your results contained differences with this haplogroup:
    Matches(8): 263G 1438G 2706G 4769G 7028T 11719A 14766T 15326G
    Mismatches(4): 73A 750A 4216T 8860A
    Extras(5): 235G 663G 735G 4824G 16319A


    3) R7

    Defining Markers for haplogroup R7:
    HVR2: 73G 263G
    CR: 750G 1438G 2706G 4769G 7028T 8860G 11719A 13105G 14766T 15326G
    HVR1: 16319A 16362C

    Marker path from rCRS to haplogroup R7 (plus extra markers):
    H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 73G 11719A ⇨ R ⇨ 13105G 16319A 16362C ⇨ R7 ⇨ 235G 663G 735G 4824G

    Imperfect Match. Your results contained differences with this haplogroup:
    Matches(9): 263G 1438G 2706G 4769G 7028T 11719A 14766T 15326G 16319A
    Mismatches(5): 73A 750A 8860A 13105A 16362T
    Extras(4): 235G 663G 735G 4824G
    Last edited by kamil154; 08-16-2020 at 02:45 AM.

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    Here is the MTree https://www.yfull.com/mtree/A14/ with a wide spread from Vietnam to Russia.

    If you do WGS, you could upload to YFull and get perhaps better resolution.

    Mine was just M30 from 23andme Genotyping, but M30g after the sequencing. Plus, the tree gets periodically updated.

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    Quote Originally Posted by poi View Post
    Here is the MTree https://www.yfull.com/mtree/A14/ with a wide spread from Vietnam to Russia.

    If you do WGS, you could upload to YFull and get perhaps better resolution.

    Mine was just M30 from 23andme Genotyping, but M30g after the sequencing. Plus, the tree gets periodically updated.
    I was already considering uploading to Y-full, but the Living DNA raw file is in .cvs format, whereas y-full requires .FASTA or .BAM, and I'm not sure if there's a way around that.

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    Quote Originally Posted by poi View Post
    Here is the MTree https://www.yfull.com/mtree/A14/ with a wide spread from Vietnam to Russia.

    If you do WGS, you could upload to YFull and get perhaps better resolution.

    Mine was just M30 from 23andme Genotyping, but M30g after the sequencing. Plus, the tree gets periodically updated.
    So I just read up about this. Apparently Living DNA is chip-based genotyping not WGS. What difference does that make? Their mt-DNA test does offer 4000+ SNP's (comparable to 23andme), so shouldn't that be enough resolution?
    Last edited by kamil154; 08-16-2020 at 03:24 AM.

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    Quote Originally Posted by kamil154 View Post
    So I just read up about this. Apparently Living DNA is chip-based genotyping not WGS. What difference does that make? Their mt-DNA test does offer 4000+ SNP's (comparable to 23andme), so shouldn't that be enough resolution?
    Genotyping (living dna, 23andme, ancestry, ftdna etc) have only selected SNPs coverage, so just a few thousand MtDNA SNPs. There are plenty more so that is where sequencing is the best. You get everything and the resolution is much finer(assuming YFull and other tools can do it). It doesn’t matter when it comes to autosomal analysis but unilineals benefit quite a bit from having WGS. If you want to drill deeper, WGS is the ultimate for Y and MtDNA genetics.

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    I have a 23andMe UP Pashtun DNA relatives match with A4 as his mtDNA.

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    Quote Originally Posted by subzero85 View Post
    I have a 23andMe UP Pashtun DNA relatives match with A4 as his mtDNA.
    I think A14 (A-a1a) might well be a subclade of A4 (denoted by A-a1 on YFull) from what I can gather. My maternal great-grandfather was in fact a UP Pashtun from Kaimganj/Farukkhabad whose family migrated from Afghanistan in the mid 1800's. Hovever my Mt-DNA should be coming from my maternal grandmother's female ancestors, and her background is half Kashmiri/Punjabi.
    Last edited by kamil154; 08-16-2020 at 05:14 AM.

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    So if we take A-a1 on YFull to be A4 (as I suspect), both my sub-clade A14 and also A21 seem to derive from it, and I see several Indian flags matched Y-Full for A21. Wikipedia claims that A13 and A14 are present in "Xinjiang and Ladakh" and A21 is present in "Tibet and Jammu & Kashmir" so I guess there ought to be some link to the Kashmir region.

    I would appreciate if anyone can confirm if A4 and A-a1 are indeed interchangeable.

    https://www.yfull.com/mtree/A-a1/
    https://en.wikipedia.org/wiki/Haplogroup_A_(mtDNA)
    Last edited by kamil154; 08-16-2020 at 05:16 AM.

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    I am a carrier of mtdna A11-a* while Khanabadoshi is a carrier of mtdna A8. They're common in Tibetans and Turkic/Siberian populations respectively (Khana is 1/4th Uzbek).

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