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Thread: U152 > L2 > ZZ48

  1. #1
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    U152 > L2 > ZZ48

    This thread is to keep folks up to date on L2 subclade ZZ48. This mutation is on palindrome P6 and shows up as a mixture of ancestral and derived reads at position ZZ48_1 and ZZ48_2. The positions are as follows:

    ZZ48_1:
    18316065(A>G)
    ZZ48_2:
    18493038(T>C)

    Current subclades include:

    Group A: FGC10516+ FGC10536+ FGC10543+
    Rocca (Italy), Simonetti (Italy), Bonfanti (Italy), Gronella (Italy), Fiero (Italy), two anonymous Sardinians, England (England), Curtis (England), Lambert (France), Robert (France), two anonymous Bristol England samples
    Group B: FGC5301 et al
    Eaton (England), Whitney (England), Day (England)
    Group C: FGC5336 et al
    Montaguti (Italy), two anonymous Sardinians
    Group D: BY3477+ BY3486+ L199+
    Neese (German), Epstein (German Ashkenazi)

    Groups A and D have an almost absolute DYS442=11 modal value.
    Last edited by R.Rocca; 05-21-2016 at 02:55 PM.
    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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  3. #2
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    Rich, thanks for starting this thread. I have had a hard time understanding specifics of ZZ SNP first identified by Alex Williamson for The Big Tree:

    http://www.ytree.net/DisplayTree.php?blockID=1431

    Is there something specific that connects the two locations for ZZ48 in the Palindrome?

    Also, to identify a ZZ SNP it seems like other samples do not have heterozygous results which it a sign that it is unique. Is there a way to sample all the public samples to support the validity of ZZ type SNPs?

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  5. #3
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    First of all I thank Richard and Alex for the fantastic job that they have done.
    After long years in which I thought to be the last of the Mohicans of the FGC5336+ al. (along with 2 Sardinian anonymous), finally I found out that I belong to a new subgroup.

    First of all I ask you a question:
    Richard reported that ZZ48+ is divided into four distinct subgroups, while the site http://www.ytree.net indicates that there are only three subgroup (Group D: BY3477+, BY3486+, L199+ is to be located under Group A: FGC10516+, FGC10536+, FGC10543+).
    What is the truth?

    In any case, I tell you that based on some of my analysis I think is very likely that these samples belong to group D):
    1) Simon Shonkwiler (sample FTDNA No. 238720);
    2) Szarvas (sample FTDNA No. 194683), this sample should belonging to the Epstein group;

    I think it is interesting that even the Shonkwiller family is originally from Germany, even near Frankfurt.
    The Szarvas family should be more connected with the Epstein family. It may not be a coincidence that this family is originally from Bukovina.

    In conclusion I make this last reflection. If it is confirmed that the ZZ48 + group has 4 sub-groups, it is clear that it was the most prolific direct subgroup of R1b-L2. This could be an indication to understand the historical position of the person who developed the ZZ48+ mutation.

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    Quote Originally Posted by haleaton View Post
    Rich, thanks for starting this thread. I have had a hard time understanding specifics of ZZ SNP first identified by Alex Williamson for The Big Tree:

    http://www.ytree.net/DisplayTree.php?blockID=1431

    Is there something specific that connects the two locations for ZZ48 in the Palindrome?

    Also, to identify a ZZ SNP it seems like other samples do not have heterozygous results which it a sign that it is unique. Is there a way to sample all the public samples to support the validity of ZZ type SNPs?
    Hal, this may help explain the relationship, especially the graphic of the palindromic arms and the correlation between genes on both sides... https://phylogenous.wordpress.com/20...y-palindromes/
    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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  8. #5
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    Quote Originally Posted by Acque agitate View Post
    First of all I thank Richard and Alex for the fantastic job that they have done.
    After long years in which I thought to be the last of the Mohicans of the FGC5336+ al. (along with 2 Sardinian anonymous), finally I found out that I belong to a new subgroup.

    First of all I ask you a question:
    Richard reported that ZZ48+ is divided into four distinct subgroups, while the site http://www.ytree.net indicates that there are only three subgroup (Group D: BY3477+, BY3486+, L199+ is to be located under Group A: FGC10516+, FGC10536+, FGC10543+).
    What is the truth?

    In any case, I tell you that based on some of my analysis I think is very likely that these samples belong to group D):
    1) Simon Shonkwiler (sample FTDNA No. 238720);
    2) Szarvas (sample FTDNA No. 194683), this sample should belonging to the Epstein group;

    I think it is interesting that even the Shonkwiller family is originally from Germany, even near Frankfurt.
    The Szarvas family should be more connected with the Epstein family. It may not be a coincidence that this family is originally from Bukovina.

    In conclusion I make this last reflection. If it is confirmed that the ZZ48 + group has 4 sub-groups, it is clear that it was the most prolific direct subgroup of R1b-L2. This could be an indication to understand the historical position of the person who developed the ZZ48+ mutation.
    Alex is still looking at the Epstein/Newman files, so they are temporarily placed there. Remember that Big-Y misses a lot of positions, so some SNPs are not covered and therefore other samples like FullGenomes, 1000 Genomes etc need to be looked at to properly place them.
    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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    Quote Originally Posted by Richard A. Rocca View Post
    Hal, this may help explain the relationship, especially the graphic of the palindromic arms and the correlation between genes on both sides... https://phylogenous.wordpress.com/20...y-palindromes/
    Thanks, My question is in a Palindrome of known length and postion, to the extent the reference sequence can determine, is a SNP location on one arm determine the location on the other arm or was this done empirically by Alex--though there really is limited Big Y data in this case. Is there a mathematical formula given one location for the other?

    I include my results for myself (FGC, BigY), Whitney(BigY), and my 11th 1R Eaton cousin (FGC). Comparing the others in the YFull U152 group only one other, who is anonymous as far as paper ancestry, has this level of heterozygosity to indicate a SNP.

    However it would be interesting to see the heterozygosity accross a larger sample of all human Y haplogroups.

    ZZ48_1:
    18316065(A>G)

    YF01461 (R-A197) 32A 39G Eaton#1 FGC Elite 1.0 BGI
    YF02170 (R-A197) 51A 39G Eaton#1 Big Y
    YF04174 (R-A197) 35A 28G Whitney Big Y
    YF05537 (R-A197) 57A 49G Eaton#2 11th 1R Eaton#1 cousin Elite 2.0

    YF02458 (L-2*) 35A 53G (Big Y) Anonymous in YFull U-152 Group (probably one of the samples in Rich's post)

    ZZ48_2:
    18493038(T>C)

    YF01461 (R-A197) 30T 27C
    YF02170 (R-A197) 1T (Big Y)
    YF04174 (R-A197) no call position (Big Y)
    YF05537 (R-A197) 63T 48C

    YF02458 no call (Big Y)

    I have three Elite 2.1 samples (Eaton#3, Whitney, Day) in batch 8007 due in September. While all of these samples are probably related within the last 2000 years at most, the may show the same clear evidence for ZZ48 as my FGC sample and my 11th 1R cousin, separated by 500 years.
    Last edited by haleaton; 05-22-2016 at 03:12 PM.

  11. #7
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    Quote Originally Posted by haleaton View Post
    Thanks, My question is in a Palindrome of known length and postion, to the extent the reference sequence can determine, is a SNP location on one arm determine the location on the other arm or was this done empirically by Alex--though there really is limited Big Y data in this case. Is there a mathematical formula given one location for the other?

    I include my results for myself (FGC, BigY), Whitney(BigY), and my 11th 1R Eaton cousin (FGC). Comparing the others in the YFull U152 group only one other, who is anonymous as far as paper ancestry, has this level of heterozygosity to indicate a SNP.

    However it would be interesting to see the heterozygosity accross a larger sample of all human Y haplogroups.

    ZZ48_1:
    18316065(A>G)

    YF01461 (R-A197) 32A 39G Eaton#1 FGC Elite 1.0 BGI
    YF02170 (R-A197) 51A 39G Eaton#1 Big Y
    YF04174 (R-A197) 35A 28G Whitney Big Y
    YF05537 (R-A197) 57A 49G Eaton#2 11th 1R Eaton#1 cousin Elite 2.0

    YF02458 (L-2*) 35A 53G (Big Y) Anonymous in YFull U-152 Group (probably one of the samples in Rich's post)

    ZZ48_2:
    18493038(T>C)

    YF01461 (R-A197) 30T 27C
    YF02170 (R-A197) 1T (Big Y)
    YF04174 (R-A197) no call position (Big Y)
    YF05537 (R-A197) 63T 48C

    YF02458 no call (Big Y)

    I have three Elite 2.1 samples (Eaton#3, Whitney, Day) in batch 8007 due in September. While all of these samples are probably related within the last 2000 years at most, the may show the same clear evidence for ZZ48 as my FGC sample and my 11th 1R cousin, separated by 500 years.
    My understanding is that, once you know the length of the palindrome, you will now the relationship of both values. I suspect Alex just checks a site like NCBI or the like, as he already knows that a specific location is located in a specific arm of a palindrome.
    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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  13. #8
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    Hal, this is the explanation I received from Alex via PM...

    Thomas Krahn has the positions of the majority of the palindromes loaded into YBrowse (attached). I also went through the reference sequence myself trying to identify the boundaries of each of the palindromes. I did that before Thomas added palindromes to YBrowse, but I haven't tried to compare them. I think they could both be tweaked a little.

    By your second question, I take it you're asking how to find the "same" position on the various other arms of the palindromes? If not, let me know.

    I use BLAT to find them.

    https://genome.ucsc.edu/cgi-bin/hgBlat?command=start

    Take ZZ48 for example. ZZ48_1 = 18316065-A-G. It is on palindrome P6. To find the same position on the opposite arm, I first retrieve the reference sequence with say 200 bp on either side of 18316065. Then I search for that sequence in BLAT. There will be two possibilities with about a 100% match. One of them will be ZZ48_1 and the other ZZ48_2.

    In the other palindromes, there may be 3 or 4 different matches. They tend not to show up as well in BigY results, and seem a little patchy. That's probably because only 1/3 or 1/4 of the reads will have the desired mutation and it won't always be called.

    Regards,
    Alex
    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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  15. #9
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    In an interesting twist, these two groups now share a subclade below ZZ48 known as ZZ56:

    Group A: FGC10516+ FGC10536+ FGC10543+
    Group D: BY3477+ BY3486+ L199+

    As mentioned in the opening thread, both groups have an almost absolute DYS442=11 modal value, so it looks like the lone FGC10516+ FGC10536+ FGC10543+ sample with DYS442=12 was a back mutation to the P312 modal value.
    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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  17. #10
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    Quote Originally Posted by Richard A. Rocca View Post
    In an interesting twist, these two groups now share a subclade below ZZ48 known as ZZ56:

    Group A: FGC10516+ FGC10536+ FGC10543+
    Group D: BY3477+ BY3486+ L199+

    As mentioned in the opening thread, both groups have an almost absolute DYS442=11 modal value, so it looks like the lone FGC10516+ FGC10536+ FGC10543+ sample with DYS442=12 was a back mutation to the P312 modal value.
    Congratulations Richard,
    I propose you a daring hypothesis:
    1) the ZZ48 group could share DYS449 = 30-31
    2) the Venetian subgroup of FGC10530 (Gronella, Bonfant, Simonetti) might have had a strong back mutation from DYS449 = 30-31 to DYS449 = 27

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