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Thread: The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early Europea

  1. #491
    The PCA plot below confirms the results of my admixture analyses showing Eastern European admixture in many of the El Portalón samples, and further refutes Wesolowski's above claim that all of them except for ATP9 "have exactly none" such admixture.

    Samples with lower values of the second principal component are shifted away from the early European farmers and toward the ancient populations of Eastern Europe. Below are the eight El Portalón samples, listed in decreasing order of the second principal component:

    Code:
    ATP12  3010–2879 BC
    ATP16  3261–2916 BC
    ATP2   2899–2678 BC
    ATP17  3007–2871 BC
    ATP7   3345–2944 BC
    ATP20  2289–2050 BC
    ATP9   1750–1618 BC
    ATP3   3516–3362 BC
    ATP17 has a lower PC 2 value than all but one El Mirador sample, and ATP7 and ATP20 have lower values than all of them. The Middle Bronze Age sample ATP9 has a lower value still, and the oldest sample, ATP3, has the lowest value of all, making its position the closest to modern Spaniards and Basques.

    The above ordering of the eight samples is similar to their ordering by increasing amount of the medium blue Eastern European component in my admixture analyses (e.g., here), shown below:

    Code:
    ATP12  3010–2879 BC
    ATP17  3007–2871 BC
    ATP16  3261–2916 BC
    ATP2   2899–2678 BC
    ATP20  2289–2050 BC
    ATP7   3345–2944 BC
    ATP9   1750–1618 BC
    ATP3   3516–3362 BC

  2. The Following 2 Users Say Thank You to genetiker For This Useful Post:

     parasar (02-16-2017),  Silesian (02-16-2017)

  3. #492
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    Quote Originally Posted by genetiker View Post
    The PCA plot below confirms the results of my admixture analyses showing Eastern European admixture in many of the El Portalón samples, and further refutes Wesolowski's above claim that all of them except for ATP9 "have exactly none" such admixture.

    Samples with lower values of the second principal component are shifted away from the early European farmers and toward the ancient populations of Eastern Europe. Below are the eight El Portalón samples, listed in decreasing order of the second principal component:

    Code:
    ATP12  3010–2879 BC
    ATP16  3261–2916 BC
    ATP2   2899–2678 BC
    ATP17  3007–2871 BC
    ATP7   3345–2944 BC
    ATP20  2289–2050 BC
    ATP9   1750–1618 BC
    ATP3   3516–3362 BC
    ATP17 has a lower PC 2 value than all but one El Mirador sample, and ATP7 and ATP20 have lower values than all of them. The Middle Bronze Age sample ATP9 has a lower value still, and the oldest sample, ATP3, has the lowest value of all, making its position the closest to modern Spaniards and Basques.

    The above ordering of the eight samples is similar to their ordering by increasing amount of the medium blue Eastern European component in my admixture analyses (e.g., here), shown below:

    Code:
    ATP12  3010–2879 BC
    ATP17  3007–2871 BC
    ATP16  3261–2916 BC
    ATP2   2899–2678 BC
    ATP20  2289–2050 BC
    ATP7   3345–2944 BC
    ATP9   1750–1618 BC
    ATP3   3516–3362 BC
    ...
    Looks counterintuitive to a later movement from the east - that the oldest sample ATP3 is most like a modern as well most towards eastern Europe.
    As we can discount contamination, do you suppose poor and deficient sequences are causing a problem?

  4. #493
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    Genetiker,

    Can you e-mail me the genotypes for these samples?

  5. #494
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    Quote Originally Posted by Generalissimo View Post
    Genetiker,

    Can you e-mail me the genotypes for these samples?
    You have ATP 3, don't you?

  6. #495
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    Quote Originally Posted by Gravetto-Danubian View Post
    You have ATP 3, don't you?
    I had it, but it was crap so got rid of it.

  7. #496
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    This is old but I have not seen it posted anywhere any idea what it means? Q or R in ancient central asia maybe?

    Parallel tagged amplicon sequencing of highly degraded Ychromosomal
    DNA from archaeological skeletons
    Silja Dillenberger1
    , Sandra Wilde1
    , Martina Unterländer1 & Joachim Burger1
    1
    Palaeogenetics Group, Institute of Anthropology, Johannes Gutenberg-University,
    Colonel Kleinmann-Weg 2, 55128 Mainz, Germany
    The intent of the study was to develop a Y-SNP multiplex-PCR suitable for genetic
    analysis of ancient human remains. Therefore 37 SNPs characterizing Eurasian
    haplogroups, with a focus on Europe and Central Asia, were selected in order to get a
    high phylogeographic resolution.
    The 37 SNPs, using amplicon lengths between 64 and 107bp, were co-amplified
    within 2 multiplex PCRs followed by parallel tagged sequencing on the 454 platform.
    After testing on 3 recent male and 2 recent female individuals it was applied to 8 male
    prehistoric samples from Central Asia and Europe. One sample was too poorly
    preserved for haplogroup identification. Another individual could be narrowed down
    to Q or R*. The haplogroups of the remaining 6 samples could unambiguously be
    defined. This shows that this approach is adequate for Y-chromosomal typing of
    highly degraded ancient human remains.
    http://pure.au.dk/portal/files/34337330/ISBA4_FINAL.pdf

    I contacted Sandra Wilde more than a year ago with no luck maybe I should contact the others.
    Its been almost 7 years and still this paper is a mystery.
    Last edited by venustas; 02-16-2017 at 07:05 AM.
    Maternal Uncle y-line= F0R1b1-L21

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  9. #497
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    Quote Originally Posted by venustas View Post
    This is old but I have not seen it posted anywhere any idea what it means? Q or R in ancient central asia maybe?

    Parallel tagged amplicon sequencing of highly degraded Ychromosomal
    DNA from archaeological skeletons
    Silja Dillenberger1
    , Sandra Wilde1
    , Martina Unterländer1 & Joachim Burger1
    1
    Palaeogenetics Group, Institute of Anthropology, Johannes Gutenberg-University,
    Colonel Kleinmann-Weg 2, 55128 Mainz, Germany
    The intent of the study was to develop a Y-SNP multiplex-PCR suitable for genetic
    analysis of ancient human remains. Therefore 37 SNPs characterizing Eurasian
    haplogroups, with a focus on Europe and Central Asia, were selected in order to get a
    high phylogeographic resolution.
    The 37 SNPs, using amplicon lengths between 64 and 107bp, were co-amplified
    within 2 multiplex PCRs followed by parallel tagged sequencing on the 454 platform.
    After testing on 3 recent male and 2 recent female individuals it was applied to 8 male
    prehistoric samples from Central Asia and Europe. One sample was too poorly
    preserved for haplogroup identification. Another individual could be narrowed down
    to Q or R*. The haplogroups of the remaining 6 samples could unambiguously be
    defined. This shows that this approach is adequate for Y-chromosomal typing of
    highly degraded ancient human remains.
    http://pure.au.dk/portal/files/34337330/ISBA4_FINAL.pdf

    I contacted Sandra Wilde more than a year ago with no luck maybe I should contact the others.
    Its been almost 7 years and still this paper is a mystery.
    Both Q and R have been reported since then in various Central Asian remains, like Okunevo, Andronovo etc.

  10. #498
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    Italy Spain Andalucia
    I have debian mint installed with 64bit architecture and I have installed / opt / AdmixTools-master, although for the moment I am learning, little by little, to use AdmixTools.

    Quote Originally Posted by anglesqueville View Post
    Tried with my parents:

    [1] "distance%=0.6859 / distance=0.006859"
    anglesqueville:dad
    "Barcin_Neolithic:I1099" 40.45
    "Latvia_HG:ZVEJ32" 29.2
    "Samara_HG:I0124" 17.15
    "Kotias:KK1" 13.2


    [1] "distance%=0.2797 / distance=0.002797"
    anglesqueville:mom
    "Barcin_Neolithic:I1099" 40.55
    "Latvia_HG:ZVEJ32" 33.8
    "Samara_HG:I0124" 12.1
    "Kotias:KK1" 10.45
    "Iran_Neolithic:I1290" 3.1

    That said, nMonte is only nMonte, and I'm sure that I can tell that because Huijbregts knows I have a great admiration for his work. For example, if you run this dataset with Saami, you get a very bad model ( d>3%) and more than 30% Barcin. I think it's impossible to explore gene flows with nMonte, this calc is not made for this job. I am beginning to wonder whether I should not install a linux and qpAdm on my computer ( bad memories of a previous double OS and major problems with it....)

    edit: ArmandoR1b is right. People some years ago imagine the Basque were pure HG, then pure EEF ( in spite of their Y haplos...) . Both are absurdus.
    Paternal: R1b-U152+ L2+ BY4245+ BY3485+ BY3478+ , Giovanni Domenicus Rabai, b. 1609, Savona, Italy
    Maternal: Haplogroup H65, María García Martínez, b. 1746, Cuenca, Spain

    Manuel David Rabaez 1974, Manuel Rabaez 1948, Manuel Rabaez 1912, Antonio Rabay 1868, Antonio Rabay 1833, Manuel Rabay 1791, Manuel Rabay 1764, Pedro Rabai 1727, Pedro Joseph Rabai 1691, Giovanni Battista Rabai 1647, Jo. Domenicus Rabai 1609, Pietrus Rabai (work in progress...)

  11. #499
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    Quote Originally Posted by Ravai View Post
    I have debian mint installed with 64bit architecture and I have installed / opt / AdmixTools-master, although for the moment I am learning, little by little, to use AdmixTools.
    I just installed Ubuntu on my own PC. I would like to start learning, but I still have some problems with the compilation of admixtools. While I'm at it, two questions:
    1) Did you ever use the aConv tool of Felix for converting 23&me or ftdna datas in eigenstrat format? Does it work?
    2) Which tool do you intend to use in order to merge eigenstrat datas? Eigensoft or something else?
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

  12. #500
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    Italy Spain Andalucia
    Hello anglesqueville,

    How to install AdmixTools

    Code:
    Download: https://github.com/DReichLab/AdmixTools
    
    apt-get install libopenblas-base libopenblas-dev
    apt-get install libgsl0ldbl libgsl0-dev libgsl0-dbg
    cd /opt/AdmixTools-master
    cd src; make clobber; make all; make install
    1) and 2) I have not yet used these tools.

    Regards
    Paternal: R1b-U152+ L2+ BY4245+ BY3485+ BY3478+ , Giovanni Domenicus Rabai, b. 1609, Savona, Italy
    Maternal: Haplogroup H65, María García Martínez, b. 1746, Cuenca, Spain

    Manuel David Rabaez 1974, Manuel Rabaez 1948, Manuel Rabaez 1912, Antonio Rabay 1868, Antonio Rabay 1833, Manuel Rabay 1791, Manuel Rabay 1764, Pedro Rabai 1727, Pedro Joseph Rabai 1691, Giovanni Battista Rabai 1647, Jo. Domenicus Rabai 1609, Pietrus Rabai (work in progress...)

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