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Thread: Guessing original mtDNA haplogroup when one mutation reverted to ancestral state

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    Question Guessing original mtDNA haplogroup when one mutation reverted to ancestral state

    Hello all,

    First of all excuse me for my lack on knowledge on the field of genetics. I am trying to learn as fast as I can.

    Sometime ago I took a mtDNA Full sequence test with FTDNA and they labeled my kit as H3-T152C!

    I learnt that this meant that the base at position 152 had reverted to its ancestral state. I see that indeed among the HVR2 difference from rCRS I get a "C" at position 152 when the CRS tells it should be a "T"...

    However I read in the forums that this position is sort of "volatile" and it mutates with frequency. I was wondering what stops me for reset this value back to T and if I would get then the "correct" haplogroup of my maternal lineage. Would it be correct?
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    I've never heard of resetting your values, but since we know that ftdna is the leader in Mtdna testing, I might check back there frequently. You might also check the Facebook group about Mtdna. It's run by a friend of mine who works at FamilyTreeDNA and she's very knowledgeable

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    I can't speak to this situation, but I am very dubious of people resetting their own data.

    Jack

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    Quote Originally Posted by C J Wyatt III View Post
    I can't speak to this situation, but I am very dubious of people resetting their own data.

    Jack
    I am not sure if you understood what I asked.

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    What I am asking has nothing to do with FTDNA. They just provided me with my mutations but the algorithm could not place me in any branch below H3 due to that naughty 152 one. My question is, knowing that 152 is a tricky position, if I can run the data on free online predictor with a T in the 152 position instead of a C and 1) get something sensible 2) to which extent I can assume that the "fixed" prediction was indeed the haplogroup of whatever maternal ancestor I had just before the mutation in 152 happened to one of her daughters.

    I'll try anyway.

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    I had a good time confirming all my full mito results from FTDNA although I always stuck to the RSRS version(there's a zip file on this page: http://www.phylotree.org/tree/index.htm). I went to phylotree and downloaded the latest version of the tree and pasted as text into an Excel spreadsheet and placed all my known mutations and differences into the spreadsheet too. Next I did a CTRL+H replacing each mutation with the same value but changing the cell color to green. Once I did that it was pretty easy to look at each level in the tree and see which one was the likely correct one the hide the branches I knew I didn't have.

    This is my step father.
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    I've never proved FTDNA wrong for the 5 kits I've done but there are some mutations that they don't list for instance I'm H3h which is past the C182T to T182C!, C16311T to T16311C! and G15301A to A15301G! mutations so none of them are listed in my mutation list and I like knowing they happened.

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    If I have understood your question right what you are IS H3 but you have a mutation back of (shown as -) 152, so plain H3 would be your HG if you did not have the back mutation. Yes H3 formed many thousands of years ago and some people have say 4 mutations added to that and some have zero. You have one back mutation ie. one mutation if I understand you correctly.
    But 152 is more volatile And is the about second the fastest moving ones. Try Soares et al https://www.sciencedirect.com/scienc...02929709001633 to see it in comparison to other positions in figure 1

    Do you have any exact matches GD=0 and if so you together define a new sub-clade which may be incorporated into the next mtdna phylotree when it is next re-run, if you have all uploaded to genbank (it needs 3 examples). But because it is fast-moving it may be rejected as defining a sub-clade if there is a more stable and clearer option.
    You can can edit your file in a text application and play with what group you get too.
    Out of 64 pre 1800 births 45% Cheshire, 1% Scottish (or Irish), 25% south Derbyshire, 13% Burton on Trent area (where 4 counties within 10 miles), 7% Shropshire, 1% Staffs, 8% Lancs. So far all UK despite what the testing companies say.

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    Quote Originally Posted by Shadogowah View Post
    I am not sure if you understood what I asked.
    Probably not.

    Jack

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    I suppose you could if you were running into problems with getting a proper assignment, but I doubt that is the case. I uploaded my mtdna to https://dna.jameslick.com/mthap/ to get an assignment (I figured 23andme was being overconservative as they sometimes do with y-lines) and despite having a flip at a diagnostic position, the site was still able to figure out what mthg I was.

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    Quote Originally Posted by Judith View Post
    If I have understood your question right what you are IS H3 but you have a mutation back of (shown as -) 152, so plain H3 would be your HG if you did not have the back mutation. Yes H3 formed many thousands of years ago and some people have say 4 mutations added to that and some have zero. You have one back mutation ie. one mutation if I understand you correctly.
    But 152 is more volatile And is the about second the fastest moving ones. Try Soares et al https://www.sciencedirect.com/scienc...02929709001633 to see it in comparison to other positions in figure 1

    Do you have any exact matches GD=0 and if so you together define a new sub-clade which may be incorporated into the next mtdna phylotree when it is next re-run, if you have all uploaded to genbank (it needs 3 examples). But because it is fast-moving it may be rejected as defining a sub-clade if there is a more stable and clearer option.
    You can can edit your file in a text application and play with what group you get too.
    Thanks Judith.

    My understanding was that there are no "pure" H3 modal people anymore because this is very old mutation and everybody that is classified as H3 also have other mutations that define more modern lineages below H3. Only the ancestral mom of all of us was H3 and all her offspring accumulated extra mutations with time. I thought that my classification as H3 had to be interpreted as "the most we can tell" because the back mutation at 152 somehow introduced ambiguity and as far as I know the haplogroup classifications based on the SNP always play safe and do not "predict" based on statistics and assumptions.

    What I understand of what you say is that my identified markers are just modal H3 plus the back mutation and if I ignored the back mutation I would be just plain H3... Is that correct?

    I have indeed 20 matches also classified as H3-T152C! but all them with GD = 3 thus this sort of contradicts what I just interpreted above, doesn't it?
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