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

  1. #11
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    Quote Originally Posted by Osiris View Post
    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.
    Attachment 22087

    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.
    I am not sure if I understood all but you are telling me that indeed in some cases the back mutation is not an obstacle to actually build the branch below once you find enough samples who match other SNPs and in my case I am placed in some sort of substitutes box waiting because I have no closer matches to identify a new branch, isn't it?
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  3. #12
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    H3-T152C!

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    Quote Originally Posted by Kale View Post
    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.
    Hello Kale. Do you mean that the predictor gave you the same result you already had?
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    H3-T152C!

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    Well, for any of you who could be curious about it, the predictor with my results indeed places H3-T152C! as the most suitable candidate. It considers several "children" below H3 as imperfect matches.

    However it also suggests H22 and H24 as suitable candidates too.
    Last edited by Shadogowah; 03-14-2018 at 02:05 PM.
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    H3-T152C!

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    The altered file with the mutation 152 reverted to T indeed predicts again H3 but now with the same amount of confidence also suggests H20 and H24 so I think my initial idea was right and the problem is that the back mutation introduces uncertainty about which haplogroup I could belong, either an undiscovered branch of H3 or one below H20, H22 or H24.
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    Quote Originally Posted by Shadogowah View Post
    Hello Kale. Do you mean that the predictor gave you the same result you already had?
    It basically said yes, that assignment was correct, here is why (showing positive, negative, and no-call markers). As it turns out, 23andme just didn't test very deep, so all markers diagnostic for subclades were untested.

    Quote Originally Posted by Shadogowah View Post
    The altered file with the mutation 152 reverted to T indeed predicts again H3 but now with the same amount of confidence also suggests H20 and H24 so I think my initial idea was right and the problem is that the back mutation introduces uncertainty about which haplogroup I could belong, either an undiscovered branch of H3 or one below H20, H22 or H24.
    I have a similar thing going on with my Y, kind of frustrating. Positive for the hugely common branch...
    R1b1a1a2a1a2b1 (L2), but absolutely nothing downstream. On the other hand, I'm also positive for...
    R1b1a1a2a1a2b3b (S47), but 23andme doesn't test for...
    R1b1a1a2a1a2b3, or anything downstream of S47.
    So either I'm an uncommon basal lineage of the common branch R-L2*, or a regular member of the uncommon branch R-S47
    One of them has to be wrong, unless of course, I have two daddys O_o
    Last edited by Kale; 03-14-2018 at 06:46 PM.

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    Quote Originally Posted by Shadogowah View Post
    I am not sure if I understood all but you are telling me that indeed in some cases the back mutation is not an obstacle to actually build the branch below once you find enough samples who match other SNPs and in my case I am placed in some sort of substitutes box waiting because I have no closer matches to identify a new branch, isn't it?
    Correct, back mutations are common. The MTDNA tree is not that complicated and it's fairly easy to make your own review of your data on the tree. I personally found it worthwhile because I could see all the back mutations that affected my line.

    But I agree with the others that you are almost certainly H3-T152C! and that eventually you'd find other people under that node with mutations that match yours and will form a new branch someday. Depending on what your extra mutations are of course.

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  11. #17
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    [QUOTE=Shadogowah;363771

    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?[/QUOTE]

    I understand a little better now! There is a HUGE range in mutation rate which dominates our instinctive understanding of the mutations. The 50% likelihood of a mutation (average) is one per 40 generations i.e. about 1000 years, but some people have many and some have few. The value comes from https://www.ncbi.nlm.nih.gov/pmc/art...3/#!po=18.0556

    As a non-member I cannot access the H3 data in the ftdna project but you can join and investigate. My personal H4 example is I am H4a1a1a (6000 years old) but I have 5 extra mutations 3 of which count and 2 fast moving which will never be defining in the tree but 3 that will eventually form further sub-clades and letters, hence I have more than 100 GD=3 matches.
    The key to your question is what HG are all of your GD=3 matches. If they are H3 then you are too and you have 3 further mutations which eventually will be sub-clades. But if they are all different HGs then you could be too. The 152 will probably not be used to make a new sub clade at all.

    The mtdna tree is formed by an algorithm which is maximum likelihood based and works on the huge amounts of data for number of people and mutations so for any individual there will be a slight range of outcomes.
    Ftdna and James Lick both use version 17 of the tree but neither can give you a clade if it has not been defined yet.
    So all in all I completely agree with your approach of editing your 152 back and revisiting the prediction.
    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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    Thanks Judith. All my 20 matches are also labeled as H3-T152C! and looks like a total heterogeneous bunch from the expected Iberians to British, Swiss and even Scandinavians.
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