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Thread: Big Y results for N-P189.2 show 326 novel variants

  1. #1
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    Big Y results for N-P189.2 show 326 novel variants

    Big Y results for an N-P189.2 man arrived last Thursday. He has 326 novel variants. Can anyone beat that?

    Note, though, that a second N-P189.2 man also ordered the Big Y. His results have not yet arrived. He will presumably share at least some "novel variants" with the first man.
    Last edited by lgmayka; 03-06-2014 at 12:49 AM.

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    I have posted this in another thread, but this subforum and thread is the more appropriate place.

    Two men in the N-P189.2 clade have received Big Y results. Although the BAM files have not yet been evaluated by YFull, Chris Morley ran the VCF/BED files through his program. He found that, not counting SNPs at the level of N or above, and not counting "unresolved" SNPs:
    - They share 153 SNPs distinctive to their clade, almost all not previously named
    - They average 69 (64 vs. 74) private SNPs, almost all not previously named.

    If we apply Michał's rule-of-thumb for VCF results (180 years per SNP), the two men in this exclusively European clade
    - Diverged from the rest of N about 40,000 years ago
    - Diverged from each other about 12,400 years ago.

    Please note that N-P189.2 tests negative for Page56, but positive for M231. FTDNA's new haplotree shows this correctly, apparently because they used one or more N-P189.2 examples from Geno 2.0. (In my own project, at least one N-P189.2 transferred Geno results; and the All Stories page of Genographic lists two Croatian N-M231 which are almost certainly N-P189.2.)

  4. #3
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    Rio de Janeiro Colonial
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    J1a1 FGC6064+ M365+
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    H1ao1

    Suebi Kingdom Portugal 1143 Portugal 1485 Portugal Order of Christ Brazilian Empire Brazil
    That can be an Eastern Asian Y DNA N probably brought to Eastern Europe via the Huns ? Let's wait if more cases of that same lineage can be found in places from Eastern Central Asia and China.

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    One member of N-P189.2 has had his Big Y results analyzed by YFull. YFull found the following "private" SNPs (i.e., not shared by anyone in YFull's database):

    94 best-quality
    70 acceptable-quality
    23 ambiguous
    2 low-quality

    If we use Michał's rule of thumb for YFull results (150 years per best/acceptable SNP), this yields an estimate of 24,600 years since the P189.2 clade branched off from the rest of N.

    The number of SNPs found by FTDNA but rejected by YFull is very large. This man's Big Y Matches page lists 272 Shared Novel Variants (shared with the other Big Y N-P189.2, who has not yet submitted his BAM file to YFull).

    Note that these results are very new--YFull's official haplotree does not yet reflect this.
    Last edited by lgmayka; 07-21-2014 at 08:13 PM.

  6. #5
    Is the 94+70 figure for SNPs alone, or for SNPs and INDELs?

    How many of the 94+70 "private" markers found by YFull were not found by my gratis analyses (with half-week turnaround)? Will you allow me to name all of the ones I found in at the start of April?

    Note that my algorithm does not presuppose unreliability because of a mutation's position; it uses phylogenetic behaviour to judge the suitability of a candidate mutation. If -- as more data is acquired and the entire dataset is algorithmically reassessed -- a mutation turns out to act unreliably, it will end up getting excluded from the analysis.

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    94+70 is for SNPs alone.

    I don't have the list of 164 SNPs myself, so I don't know whether YFull found any that you did not find. I am more surprised by the fact that YFull apparently discarded such a large number.
    Big Y Results page in FTDNA account: 371 Novel Variants
    Big Y Matches page in FTDNA account: 272 Shared Novel Variants (shared with another N-P189 man)
    ClarifYDNA: 155 shared SNPs, and an average of 64 private SNPs
    YFull: 164 private SNPs (other N-P189 man has presumably not submitted his BAM file)

    It is possible that YFull is exercising "an abundance of caution" because N-P189 is such an academia-shattering discovery. Academics will likely attack both YFull and FTDNA for including N-P189 on their respective published haplotrees. (An academic attacked ISOGG for that reason last year.) FTDNA, of course, has much more evidence at its disposal.
    Last edited by lgmayka; 07-22-2014 at 11:28 PM.

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  9. #7
    Quote Originally Posted by lgmayka View Post
    It is possible that YFull is exercising "an abundance of caution" because N-P189 is such an academia-shattering discovery. Academics will likely attack both YFull and FTDNA for including N-P189 on their respective published haplotrees.
    It is more likely your wild imagination. A single SNP does very little in terms of inflating the age estimate of divergence. Actually it is more the lack of SNPs(not the presence of a single or multiple SNPs) associated with the other main line that may potentially cause a problem for the East Asian origin of N.(but overall even that is highly unlikely given the abundance of other arguments in support of that theory not to mention other yet to be verified N*s and NO*s in East Asia and the general location of O's)

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    YFull has released a new haplotree for N, now based on 3 Big Y BAM files from N-P189.2 as well as the ancient sample of Hungarian N-Y6503. Here is how the SNP counts stand. I have included a translation into elapsed time, presuming the usual equivalence for Big Y BAM files analyzed by YFull (140-150 years per SNP):

    The two Balkan N-P189.2 men diverged 420-450 years ago.
    The Balkan men diverged from the Dutch N-P189.2 man 3600-3900 years ago.
    N-P189.2 diverged from the ancient Hungarian N-Y6503 sample 8800-9400 years ago.
    N-Y6503 diverged from the rest of N (N-Z7462 or N-L735) 23100-24700 years ago.
    Last edited by lgmayka; 12-03-2014 at 04:16 PM.

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    Quote Originally Posted by lgmayka View Post
    YFull has released a new haplotree for N, now based on 3 Big Y BAM files from N-P189.2 as well as the ancient sample of Hungarian N-Y6503. Here is how the SNP counts stand. I have included a translation into elapsed time, presuming the usual equivalence for Big Y BAM files analyzed by YFull (140-150 years per SNP):

    The two Balkan N-P189.2 men diverged 420-450 years ago.
    The Balkan men diverged from the Dutch N-P189.2 man 3600-3900 years ago.
    N-P189.2 diverged from the ancient Hungarian N-Y6503 sample 8800-9400 years ago.
    N-Y6503 diverged from the rest of N (N-Z7462 or N-L735) 23100-24700 years ago.
    So essentially these modern Europeans have a common ancestor going back ~3700 years.
    If the 1000bc Hungarian is a migrant from Central Asia, which is not implausible in light of IR1's G2a1 mtDNA, does this not weigh on the side on these modern Europeans also having an eastern origin going back a just a few thousand years?
    http://www.nature.com/ncomms/2014/14...COMMS-20141028
    A third genomic shift occurs around the turn of the first millennium BC. The single Iron Age genome, sampled from the pre-Scythian Mezőcsát Culture (Iron Age (IR1), 830–980 cal BC), shows a distinct shift towards Eastern Eurasian genotypes, specifically in the direction of several Caucasus population samples within the reference data set. This result, supported by mtDNA and Y-chromosome haplogroups (N and G2a1, respectively, both with Asian affinities) suggests genomic influences from the East. This is supported by the archaeological record which indicates increased technological and typological affinities with Steppe cultures at this time, including the importation of horse riding, carts, chariots and metallurgical techniques26.

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    Quote Originally Posted by parasar View Post
    So essentially these modern Europeans have a common ancestor going back ~3700 years.
    If the 1000bc Hungarian is a migrant from Central Asia, which is not implausible in light of IR1's G2a1 mtDNA, does this not weigh on the side on these modern Europeans also having an eastern origin going back a just a few thousand years?
    When you write "eastern origin," I assume you mean Central Asia--e.g., autosomally ANE. The TMRCA of 9000 years seems to fit an ANE migration into Eastern Europe.

    Your hypothesis that the 2900-year-old Hungarian is a recent migrant from Central Asia has no factual basis (and is in fact contradicted by autosomal DNA results). His yDNA haplogroup N-Y6503 is found only in Europe, and his mtDNA haplogroup G2a is found in Russia as well. There may be some confusion between G2a and G2a1. G2a1 is now defined by T14200C, but was formerly defined by a mutation at 16227. If the authors were using the old definition, they would call it as G2a1 instead of simple G2a (which GenBank shows as Russian).

    EDIT: IR1 does have the 14200C mutation.

    According to this Wikipedia table, G2a is commonly found among Kazakhs and Uyghurs, and in Kyrgyzstan, Buryatia, Tibet, Nepal, and Mongolia. It could thus be considered Central Asian or Old East Asian (as opposed to Modern East Asian, the progeny of agricultural expansion).
    Last edited by lgmayka; 12-03-2014 at 07:09 PM.

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