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Thread: More Bell Beaker U152 and one ZZ11?

  1. #11
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    Thanks Rich for taking a deeper look at these samples.

    I'm not sure I agree with you that I0805 is PF6658+. I took a look at the BAM files for a couple PF6658+ men and the reads look homogeneous. Moreover, the ancestral read is a perfect match to the reference sequence while the derived read differs from the reference sequence at a number of positions. If the sample does belong to R-U152, I don't think this is the proof of it.

    The situation for I0806 is very different. I agree with you that the sample does look to be ZZ11+. I double checked a number of ZZ11+ and ZZ11- BAM files and the read you found is only found in the ZZ11+ files. As such, that ZZ11+ read likely doesn't originate from some other unrelated region. I used grep and samtools to search for the read within the BAM files.

    I also found that I0806 is positive for Z38841. This mutation is in the same block as ZZ11. It is an STR so I wouldn't trust it on its own. Although it's fairly stable, I know there are subsequent mutations along some lines. Negative men have 10 copies of the GAATG motif, while positive men agree with the reference sequence and have just 9. Sample I0806 is lucky to have one read long enough to contain the whole STR and it has only 9 repeats.

    I couldn't find any R-U152 mutations for I0806, but there is one read in the 390k BAM file which could indicate that I0806 is positive for DF27. The read is fairly short however, just 64bp, and may actually belong to chromosomes 2 or 5.

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  3. #12
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    Quote Originally Posted by Williamson View Post
    I couldn't find any R-U152 mutations for I0806, but there is one read in the 390k BAM file which could indicate that I0806 is positive for DF27. The read is fairly short however, just 64bp, and may actually belong to chromosomes 2 or 5.
    Apparently, I0806's grave contained mixed cultural features, including a Corded Ware shaft-hole axe and a perfect bell beaker.

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  5. #13
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    Quote Originally Posted by Williamson View Post
    Thanks Rich for taking a deeper look at these samples.

    I'm not sure I agree with you that I0805 is PF6658+. I took a look at the BAM files for a couple PF6658+ men and the reads look homogeneous. Moreover, the ancestral read is a perfect match to the reference sequence while the derived read differs from the reference sequence at a number of positions. If the sample does belong to R-U152, I don't think this is the proof of it.
    Good thing I asked you privately to jump in here... always good to have a second set of eyes

    Even though most PF6658+ samples are overwhelmingly 'G' but still have 'A' reads and visa-versa, I have no problem with your assessment. While I can 'suspect' he 'may be' PF6658+, the confidence level is likely low.

    Quote Originally Posted by Williamson View Post
    The situation for I0806 is very different. I agree with you that the sample does look to be ZZ11+. I double checked a number of ZZ11+ and ZZ11- BAM files and the read you found is only found in the ZZ11+ files. As such, that ZZ11+ read likely doesn't originate from some other unrelated region. I used grep and samtools to search for the read within the BAM files.

    I also found that I0806 is positive for Z38841. This mutation is in the same block as ZZ11. It is an STR so I wouldn't trust it on its own. Although it's fairly stable, I know there are subsequent mutations along some lines. Negative men have 10 copies of the GAATG motif, while positive men agree with the reference sequence and have just 9. Sample I0806 is lucky to have one read long enough to contain the whole STR and it has only 9 repeats.

    I couldn't find any R-U152 mutations for I0806, but there is one read in the 390k BAM file which could indicate that I0806 is positive for DF27. The read is fairly short however, just 64bp, and may actually belong to chromosomes 2 or 5.
    Excellent! I hadn't even looked at STRs, but I am pleasantly surprised that I0806 contains the entire Z38841 read. So it is a near certainty that it is ZZ11+.
    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 Williamson View Post
    I couldn't find any R-U152 mutations for I0806, but there is one read in the 390k BAM file which could indicate that I0806 is positive for DF27. The read is fairly short however, just 64bp, and may actually belong to chromosomes 2 or 5.
    So that's a second "maybe" DF27 guy in a "German" Bell Beaker context. Anyhow, ZZ11 from the East is still looking pretty good, to me. We shall see (with the usual caveat: if we live long enough).

    Oddly enough, I0806 has previously reared his bony head here, in connection with a little intrusion of Corded Ware material culture into a Bell Beaker burial. http://www.anthrogenica.com/showthre...ll=1#post69762

    Edit (9/11/16): I should link to the post by rms2 that started the previous discussion here of sample I0806, just a bit higher on that same thread: http://www.anthrogenica.com/showthre...ll=1#post68771
    Last edited by razyn; 09-11-2016 at 11:14 PM.

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  9. #15
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    Quote Originally Posted by razyn View Post
    So that's a second "maybe" DF27 guy in a "German" Bell Beaker context. Anyhow, ZZ11 from the East is still looking pretty good, to me. We shall see (with the usual caveat: if we live long enough).

    Oddly enough, I0806 has previously reared his bony head here, in connection with a little intrusion of Corded Ware material culture into a Bell Beaker burial. http://www.anthrogenica.com/showthre...ll=1#post69762
    I think this case is more than just a "maybe". Sample i0806 was sequenced twice and the file I initially looked at (i0806.1240k.bam) did not have a read at DF27, but I just checked file i0806.390k.bam and the single read at the DF27 position is positive. So, I think there is very little doubt it is DF27+, especially since it is also positive for a ZZ11 equivalent and also previously confirmed P312+. Congratulations to all our DF27 cousins!
    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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  11. #16
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    I'll drink to that.

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    I0806 from Germany, Quedlinburg (2431-2150 BC) is pretty close to the YFull DF27 TMRCA of 4500 ybp. Now I wonder if we will ever get a P312 ancient specimen that has a radiocarbon date that has an SNP that is slightly older than the TMRCA date at YFull.

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  15. #18
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    This ties in rather well with my assumption that U152 was a major lineage in the "eastern" and "central" parts of the BB horizon, what I'm more interested in though is whether U152 was a major Urnfield lineage, if so this would have important ramifications for the initial spread of Celtic and Italic.
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    ᾽Άλλο δέ τοι ἐρέω, σὺ δ᾽ ἐνὶ φρεσὶ βάλλεο σῇσιν:
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    νῆα κατισχέμεναι: ἐπεὶ οὐκέτι πιστὰ γυναιξίν.


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  17. #19
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    Quote Originally Posted by Agamemnon View Post
    This ties in rather well with my assumption that U152 was a major lineage in the "eastern" and "central" parts of the BB horizon, what I'm more interested in though is whether U152 was a major Urnfield lineage, if so this would have important ramifications for the initial spread of Celtic and Italic.
    When you look at an Urnfield culture map and a map of the present day distribution for U152 it's reasonable to think there may be a connection.

    Genetic correlations with Urnfield

    The distribution of the Urnfield Culture is very similar to that of the Y-DNA Haplogroup R1b-U152. The density of R1b-U152 is greatest in Northern Italy and radiates out from there.7Fulvio Cruciani et al., Strong intra- and inter-continental differentiation revealed by Y chromosome SNPs M269, U106 and U152, Forensic Science International: Genetics, (advance online publication, 22 August 2010); http://www.u152.org/ . A distribution in all directions from a high density centre is what we would expect if a mutation occurs with a comparatively static population. It will percolate gradually outwards from its origin point.8J. Chiaroni, P. Underhill and L.L. Cavelli-Sforza, Y chromosome diversity, human expansion, drift and cultural evolution, PNAS, vol. 106, no. 48 (1 Dec 2009), pp. 20174-79. The barrier of the Alps may be responsible for the highest density in this case being offset from centre. The origin point may have been north of the Alps. If R1b-U152 did spread initially with Urnfield, then we can be sure that later Iron Age movements by the Celts also contributed to the distribution we see today
    http://thewaythetruthandthelife.net/...erian-celt.htm
    Last edited by MitchellSince1893; 09-09-2016 at 01:50 AM.
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    ^^It would also make a whole lot of sense from a linguistic standpoint, assuming there is a correlation to be found.
    מכורותיך ומולדותיך מארץ הכנעני אביך האמורי ואמך חתית
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    ᾽Άλλο δέ τοι ἐρέω, σὺ δ᾽ ἐνὶ φρεσὶ βάλλεο σῇσιν:
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    νῆα κατισχέμεναι: ἐπεὶ οὐκέτι πιστὰ γυναιξίν.


    -Αγαμέμνων; H Οδύσσεια, Ραψωδία λ

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