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Thread: Positive for both R1a-M420 and R1b-M343

  1. #1
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    Positive for both R1a-M420 and R1b-M343

    Has anyone come across this before?
    Any suggestions for how it is likely to have arisen?

  2. #2
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    If there is no explanation offered for this test result, I will have to assume that the conventionally-accepted strict division between R1a and R1b populations is an artificial one.
    The M420 result has a rare genotype that appears to be shared with only one other individual that I know about (who is confirmed R1a1a1).
    Unless both of the tests showing this were wrong, the only explanation that makes sense to me is that the M343 (R1b) mutation has arisen independently in at least two populations, one of which was R1* and the other of which was R1a1a1.
    If there is any other reasonable explanation, I would be interested to hear of it.

  3. #3
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    Quote Originally Posted by epp View Post
    If there is no explanation offered for this test result, I will have to assume that the conventionally-accepted strict division between R1a and R1b populations is an artificial one.
    The M420 result has a rare genotype that appears to be shared with only one other individual that I know about (who is confirmed R1a1a1).
    Unless both of the tests showing this were wrong, the only explanation that makes sense to me is that the M343 (R1b) mutation has arisen independently in at least two populations, one of which was R1* and the other of which was R1a1a1.
    If there is any other reasonable explanation, I would be interested to hear of it.
    You would receive answer by giving some details :

    What company tested you ?
    Did you have positive test for any other R1a or R1b marker(s) ?

    In the Morley y-haplogroup y-tree http://ytree.morleydna.com/Experimen...ny20140207.pdf

    There is no special appendix, only some no-calls or back-mutations.

    R1a M420/L146/PF6229 [213/215]

    R1b M343/PF6242 [3919/4014]

    Coverage statistics [x=y] y is the number of kits supposedly downstream of this SNP, and x is the number of these kits that are positive for the SNP. Some non-positive results could in fact be no-calls or back-mutations.
    If this SNP is situated on a branch untouched by Geno 2.0 testing then the figure (which would be 0=0) is omitted. It is also omitted for SNPs that were not Geno-tested and have no positive-testing downstream kits.
    Last edited by palamede; 03-02-2014 at 07:38 PM.

  4. #4
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    Welcome to Anthrogenica, epp.

    The only two possibilities I can think of is a lab error was made somewhere. Depending on who you've tested with, requesting a repeat run can be done. When I was uncertain of my mtDNA designation, I contacted FTDNA, who promptly organised a repeat much to my satisfaction.

    If these results are correct, then, our understanding of R1's phylogeny will face an upheaval.

  5. #5
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    Thanks for this, guys.
    The sample was double-tested, but the testing company is now in the process of checking it.
    I can't identify this company, as in return for the raw data, I promised confidentiality.
    I wasn't tested for subclades of R1a or R1b, but am checking the markers on the Morley tree.
    Given what you say, I suppose that if between 1 and 2.5.% of these SNPs back-mutate, it is theoretically possible that the established R1b tree arose out of a R1a* individual with a M420 back-mutation or that the established R1a tree arose out of a R1b* individual with a M343 back mutation. Possibly, then, there could be a few R1a/R1b positives around whose ancestors were less successful in reproducing?

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    Yet, the suprising situation is that this company sent you results that were obviously conflicting. Not a very good start....

  7. #7
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    My results have now been re-checked and confirmed - AA for M343 and AA for M420. Perhaps this is not conflicting after all?
    According to the Morley tree, 1 in every 42 people defined as R1b are not M343+, presumably as a result of one or more back-mutations.
    What if the MRCA of confirmed R1a were such an individual (of R1b* descent but back-mutated to M343-)?
    This would not be exceptional, as all R1 individuals alive today are already thought to descend from a tiny population that managed to survive the last ice age.

  8. #8
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    Quote Originally Posted by epp View Post
    My results have now been re-checked and confirmed - AA for M343 and AA for M420. Perhaps this is not conflicting after all?
    Any locus can back-mutate. To find out which one did, it is useful to test SNPs which are branch-line equivalents if they exist, such as M513 to M420.

    However, the more likely explanation is that you are referencing the opposite strand than the one being reported against. If the reference/variant alleles are A vs. C or G vs. T, there seldom is a problem. However if the reference/variant alleles are A vs. T or C vs. G, ambiguity and confusion often arise if it isn't made clear which strand is being tested. (A and T are complementary, as are C and G).

    Since M343 is a C to A mutation, I suspect that your M343 positive call is correct. (The opposite strand would mutate G to T).

    However since M420 is a T to A mutation, the opposite strand would report an A to T mutation. One must confirm which allele other M420+ samples are reporting vs. the allele that other M420- samples are reporting, using the same test product.

  9. #9
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    Quote Originally Posted by VinceT View Post
    Any locus can back-mutate. To find out which one did, it is useful to test SNPs which are branch-line equivalents if they exist, such as M513 to M420.

    However, the more likely explanation is that you are referencing the opposite strand than the one being reported against. If the reference/variant alleles are A vs. C or G vs. T, there seldom is a problem. However if the reference/variant alleles are A vs. T or C vs. G, ambiguity and confusion often arise if it isn't made clear which strand is being tested. (A and T are complementary, as are C and G).

    Since M343 is a C to A mutation, I suspect that your M343 positive call is correct. (The opposite strand would mutate G to T).

    However since M420 is a T to A mutation, the opposite strand would report an A to T mutation. One must confirm which allele other M420+ samples are reporting vs. the allele that other M420- samples are reporting, using the same test product.
    Thanks for this information.

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