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Haplogroup N - exact match for India

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  • akaara
    Guest replied
    Originally posted by Kaiser
    akaara: Would you like to volunteer more info, like your ancestral place or origin and population group (W Eurasian, South Asian, Native American etc)? Phylogeography helps, particularly when DNA results are inconclusive (though I believe you will go for further HVR-2 testing as well).

    vraatyah: Thanks for certifying me as a population geneticist!
    I was told I have Native American ancestry but the DNA tests did not support this, though it would have been back 4 generatoins or so. I wonder if they got the Indian from North America confused with Indians from India?

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  • akaara
    Guest replied
    thanks for the insight. I neglected to mention that she also told me it was N and also N* whatever that means. Anyplace I can look online for this information on N* and W?

    I don't think my family background would be of much help. Supposedly my mito has changed very little at least from my mother's mother's mother's line. The person who did my results said it was unusual that I had so few mutations, like it's an old/ancient lineage... but if that's the case, why can't they break it down further?

    I know it was the second number 16286T which was the uncommon part.

    Thanks so much for the help.. it's fascinating stuff!
    Last edited by ; 3 November 2006, 06:35 AM.

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  • Kaiser
    replied
    akaara: Would you like to volunteer more info, like your ancestral place or origin and population group (W Eurasian, South Asian, Native American etc)? Phylogeography helps, particularly when DNA results are inconclusive (though I believe you will go for further HVR-2 testing as well).

    vraatyah: Thanks for certifying me as a population geneticist!
    Last edited by Kaiser; 3 November 2006, 05:14 AM.

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  • vraatyah
    replied
    Kayser: absolutely correct conclusion. It's a "minor" branch of W that lacks the usual 16292 and has 16286 instead.

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  • Kaiser
    replied
    Cacio: The following link points to a case similar to akaara's:

    http://archiver.rootsweb.com/th/read...-10/1097539824

    In this case HVR-1 values are 16093C, 16223T, 16286T, 16519C. HVR-2 testing was also carried out which helped single out the lineage ie, 'W', according to Bennet Greenspan. In akaara's case, HVR-1 alone may not be enough to crack the haplogroup conclusively but it does hint at a 'W' lineage.

    Any comments?

    PS: mtDNA Haplogroup 'W' has a 17.5% distribution in Sindh Province of Pakistan. Frontier (NWFP) Province shows 'W' at 4.5% .
    Last edited by Kaiser; 2 November 2006, 11:09 PM.

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  • cacio
    replied
    akaara:

    you do seem to have a strange situation - but more because you have very few mutations relative to CRS. Are these your only mutations?

    Two quick thoughts. 16223T means that you could be everything but R, because R has a different value. R comprises the vast majority of European lineages (and a good number of Indian too). This of course leaves a huge number of possibilities. After that, you don't seem to have any mutation indicative of a haplogroup.

    I briefly looked at the Palanichamy paper indicated by Kaiser, and at ysearch.org. One place where 16286T pops up is W. W is a subgroup of N2 which is itself a subgroup of N. Indeed, ysearch has two observations who have 16223 and 16286 (plus in addition 16519). One is listed as W, one as N* (which could be a W, simply, they didn't have enough information to discriminate). 16519 mutates often; moreover, many companies test only until 16365 or so. So presumably one should not give too much weight to the lack of 16519.

    So a working hypothesis could be W. W is present in India, especially in Pakistan. It is also present from India throughout central asia to northern and central Europe, so it is a pretty dispersed haplogroup.

    But that's only a working hypothesis. 16223T is also consistent with all the big M haplogroup, of which India is full. As said, HVR2 may give more information. And hopefully someone else may have better suggestions, vraatyah for instance?

    cacio

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  • akaara
    Guest replied
    She didn't think it could be broken down into a specific haplogroup.

    But she did say my 16286T is the part that is unusual and they did find a match in India to my own. So I guess until more research is done in India, it'll be difficult to delve into deeper.

    The only thing I know is I have a match with someone in India and that my 286 is what makes my mito uncommon.

    16223 and 16286 or 16223T and 16286T

    and she told me that it most likely comes from India because it is a rare sequence in Europe.

    Does that make sense? So basically it doesn't tell me anything except I have an old pair of genes.

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  • cacio
    replied
    akaara:

    good, so when you get your mutation numbers, one can check.

    The mtdna is composed by around 16600 letters. HVR1 is approximately the last 600, from 16000 on. So as you see it is a relatively small fraction of the mtdna (although it is usually the most informative). HVR2 is from 1 to 600 approximately, so that's 600 more letters, and this would give some more information. Sometimes even that is not enough to predict accurately the haplogroup, but that certainly will help.

    As you say, India is a very big and diverse country, there are many more lineages than in Europe, and many of them have not been studied well in the literature. Papers are always finding new results about India.

    cacio

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  • akaara
    Guest replied
    finally got ahold of them on the phone! They told me that my mtDNA is extremely rare and unusual. The person who actually did my test is going to call me back and we're going to discuss possibly doing an HVR-2 and she is going to tell me those 16223T and 16286T... I think that's how you do that... not sure though.

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  • akaara
    Guest replied
    I re-read it and they did use the HVR-1.. I am wondering if maybe different companies use different naming methods?

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  • cacio
    replied
    Akaara:

    which company did you test with?

    Usually companies test HVR1. When they send you your results, they tell you your haplogroup (N in your case) as well as a string of numbers or mutations that look something like this:

    16189C 16223C etc.

    What I meant is that you can check these numbers against those of the paper. These numbers should be contained either in the email that they sent, or on your page on the company's webiste.

    For instance, in the case of FTDNA, that would appear under mtdna results on the personal page.

    cacio

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  • lgmayka
    replied
    Originally posted by akaara
    I don't have a CD so I'd have to scan it or something...
    Which testing company did you use?

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  • akaara
    Guest replied
    Originally posted by cacio
    akaara:

    if you post your mutations here or on mitosearch.org, may be one can check against that paper to see where in the bit N tree they fit.

    cacio
    I don't have a CD so I'd have to scan it or something...

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  • akaara
    Guest replied
    They didn't tell me much except the various areas N comes from and that my sequences matched those exactly as found in India. So what does that mean? They never said anything about HVR-1 & HVR-2 testing... but I would think that this was tested if they can conclude that it was India? I really don't know and they are not returning my phone calls or emails.

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  • Kaiser
    replied
    Phylogeny of Mitochondrial DNA Macrohaplogroup N in India, Based on Complete Sequencing: Implications for the Peopling of South Asia, Palanichamy et al, 2004.

    mtDNA Macrohaplogroup N and Macrohaplogroup R are sister lineages that harbour a diverse subset of over 75 mtDNA sequences (studied till 2004).

    Macrohaplogroup N includes West Eurasian N1, N2 and X; South Asian: N5; East Asian: A, N9; Oceania: O, S.

    Macrohaplogroup R includes West Eurasian: R1, R2, JT, pre-HV and U; South Asian: R5, R6, R7, R8, R30, R31; East Asian:R9, R11, B; Oceania: P.

    akaara: Did you test for HVR-1 only? If so, your mtDNA sequence may not provide enough data for for further resolution. HVR-2 test might help. Additionally, some companies test other coding regions (at no extra cost) if no resolution is forthcoming from HVR-1 & HVR-2 testing. You need to get back to the company. For the moment, the information that you can derive from your Macrohaplogroup N classification is just this: You are descended from a woman who lived in Africa some tens of thousands of years ago!!

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