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Thread: Age of PF6658/Z193?

  1. #11
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    Quote Originally Posted by Richard A. Rocca View Post
    Looks like he belongs to the CTS2617+CTS4562+ branch which had all 11 samples thus far from Italy (between FTDNA, 1KG and Francalacci data).
    I see now. I missed this subclade because its only member only appears in the R-U152 Project results when specifically logged in to a kit in that project. (The owner has marked his results to be Members Only.)

    Yes, our Polish kit 148821 tested positive at
    CTS2617
    CTS4562
    18414951
    23580754

    But here's the odd thing: That CTS2617+ already in the R-U152 Project, kit N42592 of Sicily, has a corresponding mtDNA kit, N39236, in the Polish Project! His matrilineal ancestor is from Poznań!
    Last edited by lgmayka; 05-18-2015 at 07:38 PM.

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  3. #12
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    Quote Originally Posted by Richard A. Rocca View Post
    It was only one 1KG sample (NA20792), so it makes sense since they did not have anything else to match it to. The other 9 samples were from the Sardinian Francalacci et al dataset and the last one was FTDNA kit no. N42592 from Sicily.
    Vladimir Tagankin of YFull writes:
    ---
    Z193 - It has a high degree of homology. When reading the short length it is 100% corresponds to a different portion of the Y chromosome.
    ...
    This SNP is in a difficult region for aligned (224xxxxx). At least in the results of the NGS this SNP is not reliable.
    This SNP is necessary to remove the tree.

    Z193 (G->T) for NA20792 — 2T1G

    PF6658. Here, almost all the same.
    PF6658 (A->G) for NA20792 — 1A1T
    Position 224xxxxx
    ---

    Dropping Z193 and PF6658 from the haplotree would not seriously affect the new subclade we are discussing, since we have at least four other SNPs (CTS2617, CTS4562, 18414951, and 23580754) to define it. But it brings into question any relationship with the PF6660 subclade or the two singletons on the current tree.

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  5. #13
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    H4a1-T152C!

    United States of America Italy 1861-1946 Spain
    Quote Originally Posted by lgmayka View Post
    Vladimir Tagankin of YFull writes:
    ---
    Z193 - It has a high degree of homology. When reading the short length it is 100% corresponds to a different portion of the Y chromosome.
    ...
    This SNP is in a difficult region for aligned (224xxxxx). At least in the results of the NGS this SNP is not reliable.
    This SNP is necessary to remove the tree.

    Z193 (G->T) for NA20792 — 2T1G

    PF6658. Here, almost all the same.
    PF6658 (A->G) for NA20792 — 1A1T
    Position 224xxxxx
    ---

    Dropping Z193 and PF6658 from the haplotree would not seriously affect the new subclade we are discussing, since we have at least four other SNPs (CTS2617, CTS4562, 18414951, and 23580754) to define it. But it brings into question any relationship with the PF6660 subclade or the two singletons on the current tree.
    Z193 and PF6658 are impossible to test via Sanger sequencing, but make up a pretty substantial subclade directly below U152. The heterozygosity at these two positions are unique to U152 minus all other major subclades L2, Z36, etc. (...that I know of).
    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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  7. #14
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    Quote Originally Posted by Richard A. Rocca View Post
    Z193 and PF6658 are impossible to test via Sanger sequencing, but make up a pretty substantial subclade directly below U152.
    But can they be reliably detected via microarray? ISOGG's rules appear to say that for full (non-italicized) status, a SNP must be reliably detectable via either
    - Sanger sequencing, or
    - Both next-generation sequencing and microarrays.

    Slightly off-topic: Has FTDNA officially announced the technology used in its SNP panels? At one time, Janine Cloud of FTDNA wrote:
    ---
    They won't be using Sanger sequencing, but it won't be a Big Y-type sequencing either. I don't have clearance to discuss the specifics of the technology involved, but I can tell you it's not either of those.
    ---

    Is everyone just assuming that the SNP panels must be using microarrays?

  8. #15
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    Quote Originally Posted by lgmayka View Post
    But can they be reliably detected via microarray? ISOGG's rules appear to say that for full (non-italicized) status, a SNP must be reliably detectable via either
    - Sanger sequencing, or
    - Both next-generation sequencing and microarrays.

    Slightly off-topic: Has FTDNA officially announced the technology used in its SNP panels? At one time, Janine Cloud of FTDNA wrote:
    ---
    They won't be using Sanger sequencing, but it won't be a Big Y-type sequencing either. I don't have clearance to discuss the specifics of the technology involved, but I can tell you it's not either of those.
    ---

    Is everyone just assuming that the SNP panels must be using microarrays?
    I'm not sure if they can be detected via microarrays, but certainly via NGS. Derived samples meet the reporting threshold of both Big-Y and Full Genomes.
    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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  10. #16
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    YFull's latest (3.11) haplotree has dropped Z193 and PF6658. In its stead are two subclades directly under U152:

    - CTS2617, CTS4562. Right now, this includes only the Polish YF03574 and the Tuscan NA20792. YFull loosely estimates a TMRCA of 3200 ybp between the two. I am trying to persuade the FTDNA customer of Sicilian patrilineage to submit his BAM file to YFull. His example would refine the TMRCA.

    - Z192/PF6660. This has 4 Tuscan and Mexican research samples.

    PF6658 is found in multiple places in haplogroup J as well, so its prospects for inclusion in the tree are pretty low. Z193 is not found anywhere else in the haplotree, so perhaps additional examples might convince YFull of its phylogenetic reliability in uniting R-CTS2617 and R-Z192.
    Last edited by lgmayka; 06-06-2015 at 10:35 PM.

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  12. #17
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    Quote Originally Posted by lgmayka View Post
    Yes, our Polish kit 148821 tested positive at
    CTS2617
    CTS4562
    18414951
    23580754

    But here's the odd thing: That CTS2617+ already in the R-U152 Project, kit N42592 of Sicily, has a corresponding mtDNA kit, N39236, in the Polish Project! His matrilineal ancestor is from Poznań!
    The Shared Novel Variants feature of FTDNA's Big Y Matches page is finally working again, so I can now easily see that kits 148821 and N42592 share the following additional reliable SNPs (besides those listed above). Classification (best vs. acceptable) is by YFull.

    Best quality
    8681571
    14928150
    17579504
    18984799

    Acceptable quality
    15207741

    Thus, this relationship is quite significant, though still ancient.

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  14. #18
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    England Wales Scotland Ireland European Union
    On the U152 project it is suggested some test for PF6658. Wasn't this unreliable as can come in positive or negative due to heterozygous properties. Or was this Z193?

    I digress, but I am restricted to my tablet at present as sitting at my PC is uncomfortable, I am recovering from a radical prostatectomy (cancer).

    On the mend though as you probably know we U152s don't give in easily


    S.
    LivingDNA:

    GB and Ire 98.5%
    South Germanic 1.5%


    Ancestry:

    Eng, Wales & NW Euro 50%
    North Eng, Ire and Scot 39%
    Norway 5%
    Sweden 4%
    Germanic Europe 2%

    NatGen:

    42% North Euro
    37% Mediterranean
    19% SW Asian

    Known ancestral lines:

    U152: BY3644 @ Vallum Aelium
    H1c3b Salford (mother)
    U4a3a Biddick, Durham (pat grandfather's mother)
    U198 Stanhope, Durham (pat gg grandfather)
    K1a-T195C! Wigan, Lancs (pat grandmother)

  15. #19
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    Quote Originally Posted by Solothurn View Post
    On the U152 project it is suggested some test for PF6658. Wasn't this unreliable as can come in positive or negative due to heterozygous properties. Or was this Z193?

    I digress, but I am restricted to my tablet at present as sitting at my PC is uncomfortable, I am recovering from a radical prostatectomy (cancer).

    On the mend though as you probably know we U152s don't give in easily


    S.
    I agree, at the moment it is a bit confusing, now it reads; "Please order PF6658", it would be better if it reads; "Please test PF6658 (by ordering Big-Y)".

    I wish you a speedy recovery!
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    Roman helmet, gilded silver, 319-323 A.D. Made by Marcus Titus Lunamis. Found in 1910, Helenaveen, The Netherlands.
    Its owner belonged to the sixth cavalry unit of the Equites Stablesiani. On the right side of the helmet cap it says ‘Stablesia VI'.

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  17. #20
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    On YFull's branch of PF6658 I do not recognize any SNPs that my group has? Will they have another name or is it that nobody submitted with our SNPs yet?

    http://www.yfull.com/arch-3.8/tree/R-PF6658/
    LivingDNA:

    GB and Ire 98.5%
    South Germanic 1.5%


    Ancestry:

    Eng, Wales & NW Euro 50%
    North Eng, Ire and Scot 39%
    Norway 5%
    Sweden 4%
    Germanic Europe 2%

    NatGen:

    42% North Euro
    37% Mediterranean
    19% SW Asian

    Known ancestral lines:

    U152: BY3644 @ Vallum Aelium
    H1c3b Salford (mother)
    U4a3a Biddick, Durham (pat grandfather's mother)
    U198 Stanhope, Durham (pat gg grandfather)
    K1a-T195C! Wigan, Lancs (pat grandmother)

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