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Thread: Z40481 Splits R-P312

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    Z40481 Splits R-P312

    There is an STR at position hg19:chrY:23316016 that is known to split the various branches of R-P312. For convenience, I've named the STR mutation from 12 repeats of TTTA to 11 repeats as Z40481 and have added it to my "Big Tree", www.ytree.net. R-ZZ11 (parent of R-U152 and R-DF27), R-DF99 and R-ZZ37 are Z40481+. R-L238, R-DF19 and R-L21 are Z40481-. The status for the two newest and smallest branches is still unknown. The hg19 and hg38 reference sequences are Z40481+.

    I found this STR earlier this year, but Richard Rocca wrote about it back in April of 2012 on the World Families forum:

    http://www.worldfamilies.net/forum/i...topic=9930.151

    I'm not aware of any mention of it prior to that. At that time, DF27 was recently discovered and much work was going into figuring out the relationship of the known P312 children.

    This is what Richard Rocca had to say:

    "Based on repeat value of 'TATT' at Build 37 position ChrY:23316016, I think that DF27 and U152 might have more in common with each other. L21 and DF19 also seem closer to each other due to this repeat. There was no data at that location for L238, but I would bet it is the same as L21 and DF19."

    We now know from various NGS tests that Richard was correct and that L238 is ancestral for Z40481. Richard was also correct in surmising the closer relationship between DF27 and U152. Neither DF99 nor ZZ37 was known at the time.

    I understand that an STR is not an ideal candidate for a phylogenetic tree. However, there is a lot of expansion and a lot of branching around the time of P312. This reduces the opportunity for a subsequent mutation of the STR before additional branching has taken place.

    The table below summarizes what I know about the status of Z40481 for the various branches of R-P312 that I have on my tree. What is given in the table is actually the status for each of the sub-branches, from which the status of the branch can be inferred. BigY files have coverage for the region of this STR about 1/3 of the time. 1000 genomes kits do a little a better and it is generally covered by FGC tests. It can be ordered from YSEQ.net.

    Branches/Sub-branches of R-P312 Status
    DF19
    S233/Z302
    DF88

    Z40481-
    Z40481-
    L238
    Z2247
    Martin (410754)

    Z40481-
    ?
    L21
    DF13
    DF63
    BY2899
    A5846
    A7900

    Z40481-
    Z40481-
    Z40481-
    ?
    ?
    ZZ11
    U152
    ZZ45
    Z193
    L2
    Z43
    22047046-C-T (hg19)
    Y17059
    U152* Sinclair (216196)
    DF27
    Z195
    ZZ12


    Z40481+
    Z40481+
    Z40481+
    Z40481+
    ?
    Z40481+
    ?

    Z40481+
    Z40481+
    DF99
    FGC846/Y2834
    Y5049
    BY3449

    Z40481+
    Z40481+
    ?
    ZZ37
    Z29644
    L624
    Z39300
    Lee (306861)

    ?
    Z40481+
    ?
    ?
    A9063
    McFarlane (51865)
    Morrison (423789)

    ?
    ?
    Y18209
    Harbottle (278973)
    Powell (8640)

    ?
    ?
    P312* Keyes (104079)
    ?

    Z40481 seems stable enough to be useful and too significant to be ignored.

    Alex

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    Quote Originally Posted by Williamson View Post
    There is an STR at position hg19:chrY:23316016 that is known to split the various branches of R-P312. For convenience, I've named the STR mutation from 12 repeats of TTTA to 11 repeats as Z40481 and have added it to my "Big Tree", www.ytree.net. R-ZZ11 (parent of R-U152 and R-DF27), R-DF99 and R-ZZ37 are Z40481+. R-L238, R-DF19 and R-L21 are Z40481-. The status for the two newest and smallest branches is still unknown. The hg19 and hg38 reference sequences are Z40481+.

    I found this STR earlier this year, but Richard Rocca wrote about it back in April of 2012 on the World Families forum:

    http://www.worldfamilies.net/forum/i...topic=9930.151

    I'm not aware of any mention of it prior to that. At that time, DF27 was recently discovered and much work was going into figuring out the relationship of the known P312 children.

    This is what Richard Rocca had to say:

    "Based on repeat value of 'TATT' at Build 37 position ChrY:23316016, I think that DF27 and U152 might have more in common with each other. L21 and DF19 also seem closer to each other due to this repeat. There was no data at that location for L238, but I would bet it is the same as L21 and DF19."

    We now know from various NGS tests that Richard was correct and that L238 is ancestral for Z40481. Richard was also correct in surmising the closer relationship between DF27 and U152. Neither DF99 nor ZZ37 was known at the time.

    I understand that an STR is not an ideal candidate for a phylogenetic tree. However, there is a lot of expansion and a lot of branching around the time of P312. This reduces the opportunity for a subsequent mutation of the STR before additional branching has taken place.

    The table below summarizes what I know about the status of Z40481 for the various branches of R-P312 that I have on my tree. What is given in the table is actually the status for each of the sub-branches, from which the status of the branch can be inferred. BigY files have coverage for the region of this STR about 1/3 of the time. 1000 genomes kits do a little a better and it is generally covered by FGC tests. It can be ordered from YSEQ.net.

    Z40481 seems stable enough to be useful and too significant to be ignored.

    Alex
    Thanks for following up on this Alex. I never did have enough non-U152 data to follow up on it myself, but it looks like your dataset is paying off very well in many aspects.
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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    This is pretty exciting, so I am surprised by the lack of comments. I did not expect to see DF99 share anything upstream with DF27 and U152. I would have thought it more likely to share upstream markers with at least DF19 and L238. However, L21 does not surprise me too much.

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    Quote Originally Posted by Webb View Post
    This is pretty exciting, so I am surprised by the lack of comments. I did not expect to see DF99 share anything upstream with DF27 and U152. I would have thought it more likely to share upstream markers with at least DF19 and L238. However, L21 does not surprise me too much.
    I would have suspected that DF99 would have clustered together with L238 and DF19, and L21 with DF27 and U152. I'm not entirely sure what to make of it.

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    Quote Originally Posted by Webb View Post
    This is pretty exciting, so I am surprised by the lack of comments. I did not expect to see DF99 share anything upstream with DF27 and U152. I would have thought it more likely to share upstream markers with at least DF19 and L238. However, L21 does not surprise me too much.
    It would be very interesting if an ancient dna sample is found that is positive for Z40481 and/or ZZ11 but negative for all downstream SNPs. It's location and age would be huge in understanding the history of P312 migration and subsequent divisions.

    Can we go back and see if the individuals at Kromsdorf (M269+ U106-, P312 not tested) and Quedlinburg (P312+), are positive for either of these?
    Last edited by MitchellSince1893; 05-11-2016 at 05:02 AM.
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    Quote Originally Posted by Webb View Post
    This is pretty exciting, so I am surprised by the lack of comments. I did not expect to see DF99 share anything upstream with DF27 and U152. I would have thought it more likely to share upstream markers with at least DF19 and L238. However, L21 does not surprise me too much.
    I think the lack of comments may be due to people trying to analyse these results. I agree with your assessment re L21. When I looked at Alex's superb Big Y Tree the nationalities who are in the majority for L21 are fairly predictable. Some of the other groups contained fairly geographically diverse mixtures - Scandinavian,German, French, Spanish & Portuguese etc, etc. My interest is largely focused on the ancient tribes who settled in Britain, but I'm not quite sure what to make of this data.
    Last edited by castle3; 05-11-2016 at 10:44 AM.

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    Quote Originally Posted by Webb View Post
    This is pretty exciting, so I am surprised by the lack of comments. I did not expect to see DF99 share anything upstream with DF27 and U152. I would have thought it more likely to share upstream markers with at least DF19 and L238. However, L21 does not surprise me too much.
    I would have commented sooner, but I just did not see this thread. I've been pretty busy with work lately as we near exams at my school and have not had as much time for Anthrogenica as I would like. The weekend is better for me.

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    Quote Originally Posted by GoldenHind View Post
    I would have suspected that DF99 would have clustered together with L238 and DF19, and L21 with DF27 and U152. I'm not entirely sure what to make of it.
    Yeah, I agree. Odd!

    I need to think about this and hear what others have to say, but surely it says something about where Z40481 and xZ40481 started from relative to each other.

    I really want to see some western Yamnaya results.

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    For completeness I can report that FGC Y-Elite 2.0 kit X5ZNK below U152>22047046-C-T (aka FGC43778) has no insertion when looking at the raw data with IGV (so only 11 copies and therefore Z40481+). It has solid coverage of that region with at least 5 reads. Alex, you can check it with the .bam that I shared with you through the FGC website. Bam file for 388170 has been requested with FTDNA but isn't as relevant as the raw data of kit B3492 would be.

    It is available for testing as an indel at YSEQ: https://www.yseq.net/product_info.ph...ff789dcbfc9a99.

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    We know RISE563 was U152+ and so Z40481+. That puts Z40481+ in eastern Bell Beaker, but I don't see a date for RISE563. RISE563 came from Osterhofen-Altenmarkt, down in the SE corner of Germany near the Danube and wedged in between the Czech Republic and Austria. Maybe that is an indicator of where the Z40481+ clades came from, but I am just thinking out loud and not trying to lay down doctrine.

    Perhaps L21, DF19, and L238 will be found in Rhenish Bell Beaker (except that probably came up from east central Europe, as well). L238 is the real mystery. Looks like it or its P312* progenitor took off for Scandinavia at some early point and did so pretty much lock, stock, and barrel.

    In other words, L238 probably originated in Scandinavia from a xZ40481 progenitor who went to Norway with the Beaker Folk who settled there.
    Last edited by rms2; 05-11-2016 at 11:39 AM.

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