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Thread: Balanovsky 2016: new SNP R1b-GG400 in Eastern Europeans and West Asians

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    Balanovsky 2016: new SNP R1b-GG400 in Eastern Europeans and West Asians

    Oleg Balanovsky's paper to be read at ASHG 2016 in October looks like it could be helpful:

    Y-chromosomal sequencing and screening reveal both stability and migrations in North Eurasian populations.

    Y-chromosomal markers exhibit the highest interpopulation diversity in the genome and thus form one of the most informative tools for tracing population history. However, their information value depends on discovering SNPs which subdivide haplogroups with broad geographic distribution into branches revealing fine population structure. Progress in such discoveries has recently moved from a slow linear phase to a rapid exponential phase due to NGS.

    We applied this approach to the Y-chromosomal pool of North Eurasian populations and concentrated on haplogroups C, G1, G2, N1b, N1c, and R1b. We sequenced 181 Y-chromosomes (capturing 11 Mb from each sample), developed the NGSConv software for calling Y-chromosomal SNPs, and identified roughly 2,500 SNPs, most of which were new. Then we constructed phylogenetic trees and dated dozens of their branches using our estimates of the mutation rate. The last – but not the least – step included screening branch-defining SNPs in the entire Biobank of indigenous North Eurasian populations (led by prof. Elena Balanovska), which includes 26,000 samples from 260 populations. This screening resulted in frequency distribution maps of 29 branches of haplogroups R1b and C, thus increasing the phylogenetic resolution by an order of magnitude compared to the two initial haplogroups.

    For haplogroup R1b, we identified a previously unstudied “eastern” branch, R1b-GG400, found in East Europeans and West Asians and forming a brother clade to the “western” branch R1b-L51 found in West Europeans. The ancient samples from the Yamnaya archaeological culture are located on this eastern branch, showing that the paternal descendants of the Yamnaya population – in contrast to the published autosomal findings - still live in the Pontic steppe and were not an important source of paternal lineages in present-day West Europeans.
    https://ep70.eventpilot.us/web/page....6&id=160121213

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    The SNP GG400 is not on Y-Full, but I'm guessing there will be an equivalent. Any ideas?

    My notes say that CTS1078/Z2103, Z2105 is found notably in Armenians and also found in Greece, Poland, Lithuania, Ukraine, Slovakia, Hungary, Croatia, and Russia and is Polish Project L23EE Type. Same haplotype as L23EE type occurs in Pakistan and India. And Ossetian R1b looks to be Z2105.

    Or could GG400 be a subclade?
    Last edited by Jean M; 09-09-2016 at 12:17 PM.

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    Quote Originally Posted by Jean M
    Polish Project L23EE Type.
    R1b-L23 EE Type = L23>Z2103>Y5587

    Is this new GG400 equivalent to Y5587 ?
    Last edited by Tomenable; 09-09-2016 at 12:45 PM.

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    No it can't be because it must be L23>GG400 if it is a brother clade to L51.

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    If it's a brother clade of L51, it's more something like Z2103 than its subclades.

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    Quote Originally Posted by ffoucart View Post
    If it's a brother clade of L51, it's more something like Z2103 than its subclades.
    Yes.

    Apart from L23>Z2103>Y5587 there is also quite a lot of basal or unresolved L23* (xZ2103) in Poland.

    So maybe some of this L23* will now be assigned to a new clade L23>GG400.

    And maybe Yamnaya L23(xZ2103) was also GG400+.

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    Quote Originally Posted by Tomenable View Post
    Yes.

    Apart from L23>Z2103>Y5587 there is also quite a lot of basal or unresolved L23* (xZ2103) in Poland.

    So maybe some of this L23* will now be assigned to a new clade L23>GG400.

    And maybe Yamnaya L23(xZ2103) was also GG400+.
    There is also a southern European / WA clade, which is M269 x L23 (= PF 7558), ie parallel to L23
    Last edited by Gravetto-Danubian; 09-09-2016 at 01:00 PM.

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    From their description, "new SNP" GG400 is either phylogenetically equivalent to Z2103 or a renaming of one of the known SNPs at the R1b-Z2103 level. Get the position numbers and we'll know.
    For haplogroup R1b, we identified a previously unstudied “eastern” branch, R1b-GG400, found in East Europeans and West Asians and forming a brother clade to the “western” branch R1b-L51 found in West Europeans. The ancient samples from the Yamnaya archaeological culture are located on this eastern branch, showing that the paternal descendants of the Yamnaya population – in contrast to the published autosomal findings - still live in the Pontic steppe and were not an important source of paternal lineages in present-day West Europeans.
    Here is the link to the current R1b Basal Subclades Phylogenetic Trees. https://www.familytreedna.com/groups.../about/results
    I'm rather surprised by the "previously unstudied" comment. "Little studied" would be true.
    YFull R1b-M269>L23>Z2103>Z2106>Z2108>Y14512>Y20971>Y22199, ISOGG R1b1a1a2a2c1b Y14416, FTDNA R-M64

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    Quote Originally Posted by Joe B View Post
    I'm rather surprised by the "previously unstudied" comment. "Little studied" would be true.
    Joe, if something is not published in a peer-review scientific journal this means it is unknown for science yet.

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    The Z2103 clade was identified, but not discussed, in Hallast et al 2015 (and Batini et al 2015 using the same data), and in Karmin et al 2015, where it is called R1b11 - Balanovsky was actually a co-author on the latter. Hopefully it is not just Z2103, but I am not holding my breath. By "not studied" he may just mean it has not been tested for in a proper survey with representative samples of many populations.

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