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Thread: Genetic Genealogy & Ancient DNA in the News (DISCUSSION ONLY)

  1. #3001
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    Quote Originally Posted by rozenfeld View Post
    Not Ancient DNA, so I am posting it here:

    https://www.eurekalert.org/pub_relea...-ega111119.php

    Extinct giant ape directly linked to the living orangutan

    Researchers have succeeded in reconstructing the evolutionary relationship between a 2-million-year-old giant primate and the living orangutan; it is the first time genetic material this old has been retrieved from a fossil in a subtropical area


    https://www.nature.com/articles/s41586-019-1728-8

    Enamel proteome shows that Gigantopithecus was an early diverging pongine

    Frido Welker, Jazmín Ramos-Madrigal, Martin Kuhlwilm, Wei Liao, Petra Gutenbrunner, Marc de Manuel, Diana Samodova, Meaghan Mackie, Morten E. Allentoft, Anne-Marie Bacon, Matthew J. Collins, Jürgen Cox, Carles Lalueza-Fox, Jesper V. Olsen, Fabrice Demeter, Wei Wang, Tomas Marques-Bonet & Enrico Cappellini

    Nature (2019)
    There needs to be some distinction between DNA and the protein sequences that come from it.
    The reason being that if you are going back the other way - trying to estimate DNA from the protein that comes from it - you can only go so far, and will be left with uncertainties.

    Protein is NOT genetic matter, no matter how frequently commentators might say it is.

    Eurekalert (and some other news services) can be absolutely brilliant sometimes, but they can also ignore some of these distinctions.
    Read their reports with caution.
    Last edited by Saetro; 11-14-2019 at 08:50 PM.

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    Video of a lecture about ancient DNA study of Lech valley in Germany:

    https://www.youtube.com/watch?v=syej3SWtRlI

    SoHP-MHAAM Lecture Series: Alissa Mittnik "Marriage Mobility and Households in Bronze-Age Germany"

    Initiative for the Science of the Human Past at Harvard - Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean - Lecture Series at Harvard University, October 15, 2019

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    Quote Originally Posted by rozenfeld View Post
    https://www.biorxiv.org/content/10.1101/851188v1

    Neolithic genomes reveal a distinct ancient HLA allele pool and population transformation in Europe

    Alexander Immel, Christoph Rinne, John Meadows, Rodrigo Barquera, Andras Szolek, Federica Pierini, Julian Susat, Lisa Boehme, Janina Dose, Joanna Bonczarowska, Clara Drummer, Katharina Fuchs, David Ellinghaus, Jan Christian Kaessens, Martin Furholt, View ORCID ProfileOliver Kohlbacher, Sabine Schade-Lindig, Iain Mathieson, Andre Franke, Johannes Krause, Johannes Mueller, Tobias L Lenz, Almut Nebel, Ben Krause-Kyora

    doi: https://doi.org/10.1101/851188

    Abstract

    The Wartberg culture (WBC, 3,500-2,800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We perform a genome-wide analysis of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3,300-3,200 cal. BCE). Our results highlight that the Niedertiefenbach population indeed emerged at the beginning of the WBC. This farming community was genetically heterogeneous and carried a surprisingly large hunter-gatherer ancestry component (40%). We detect considerable differences in the human leukocyte antigen gene pool between contemporary Europeans and the Niedertiefenbach individuals whose immune response was primarily geared towards defending viral infections.
    Have never seen an article like this. No adequate structure of the text, some statements are repeated twice. Very few low quality illustrations, not a sigle table, no supplementary data (I would guess just because it's not ready). Expected a bit more order from Germans.
    But the topic itself, about relations between WHG and neolithic farmers is quite interesting for me. Given the fact this culture had outliers with surprisingly high WHG ancestry proves that the story of relationship between those groups did not end in expeted result of homogenous population even 2 thousand years after LBK first farmers appeared in the region.

    By the way, I expect I-L621 or maybe even I-CTS4002, happlogroups ancestral to I2a-Din to appear somewhere in that region in 4th millenium BCE, so I'm waiting for the supplementary data. There are clues in the text that Y-chromosome markers were both EEF and HG (likely both I2 and G2?), but no direct data.
    Last edited by artemv; 11-24-2019 at 11:58 AM. Reason: typo

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    R1b-V88 could also appear as I have noted that not far away in Blätterhöhle, the following yDNAs wer detected:
    MN farmer Blätterhöhle Germany I1594/Bla28 R1b1a2-V88, mtDNA J1c1b1
    MN Fisher-gatherer Blätterhöhle Germany I1593/Bla16 R1b1a2-V88, mtDNA U5b2a2
    MN Fisher-gatherer Blätterhöhle Germany I1565/Bla8 I2a1, mtDNA U5b2b2

    For example the fisher-gatherer I1593/Bla16 is ca 53% Barcin.

    This is what this new paper explains:
    "Human genomic datasets from clear archaeological MC [Michelsberg culture] contexts are not available as yet. A possible exception could be the genome-wide data of four individuals from the Blätterhöhle that may be chronologically (based on their radiocarbon dates of 4,100-3,000 BCE) and geographically linked with Late MC and/ or WBC [Wartberg culture]. However, it has to be kept in mind that the remains were found in a cave without any definite cultural assignment. Our analyses showed that the Niedertiefenbach population appeared most closely related to the Blätterhöhle collective. In particular, their large HG components (39-72% ) fell into the range observed for Niedertiefenbach. Moreover, they were the best proxies for the HG and farmer components of the Niedertiefenbach sample. In addition, our ALDER admixture date is very similar to the one obtained for the Blätterhöhle that yield ed 18-23 generations before the average sample date of 3,414 +/- 84 cal. BCE3. Thus, there is a probable genetic link between the people buried in the Blätterhöhle and those in the gallery grave of Niedertiefenbach."

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    Quote Originally Posted by Kristiina View Post
    R1b-V88 could also appear as I have noted that not far away in Blätterhöhle, the following yDNAs wer detected:
    MN farmer Blätterhöhle Germany I1594/Bla28 R1b1a2-V88, mtDNA J1c1b1
    MN Fisher-gatherer Blätterhöhle Germany I1593/Bla16 R1b1a2-V88, mtDNA U5b2a2
    MN Fisher-gatherer Blätterhöhle Germany I1565/Bla8 I2a1, mtDNA U5b2b2
    Have just checked this MN Fisher-gatherer Blätterhöhle Germany I1565/Bla8 I2a1, mtDNA U5b2b2.
    The file is not so heavy (600mb), but has calls for many Y-SNPs.
    He is https://www.yfull.com/tree/I-M838/

    A very old and rare branch, formed 11300 ybp, TMRCA 6000 ybp, no sub-branches on y-full.
    Given that all the European branches of V88 are rare, we can say that all the three Blätterhöhle male individs have Y-happlogroups that are very rare now.

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    Video of a lecture by Kristian Kristiansen

    https://www.hf.uio.no/dnir/forskning...orelesningene/

    The L'Orange Lecture 2019

    Professor Kristian Kristiansen presents the new, emerging picture of European prehistory in this year's L'Orange lecture: Towards a New European Prehistory: genes, archaeology and language.

    Tid og sted: 11. nov. 2019 18:00, The Norwegian Institute in Rome

    Towards a New European Prehistory: genes, archaeology and language.

    Ancient DNA has revolutionized our understanding of later European prehistory, from the first farmers to the Bronze Age. At the Norwegian Institute November 11, 2019, Kristiansen will present the new, emerging picture of Europe’s early history.

    Professor Kristian Kristiansen:

    Kristian Kristansen is professor of archaeology at the University of Gothenburg, Sweden. He is one of the World’s foremost archaeologists, having written extensively about the European Bronze Age, the Neolithic, archaeological theory, the history of archaeology and cultural heritage, and played a central role in the ongoing Third Science Revolution in archaeology.

    Kristiansen has led numerous international and interdisciplinary projects, served as director of the Danish Archeological Heritage Administration, was a driving force the creation of the European Association of Archaeologists and was founding editor of the European Journal of Archaeology.
    Last edited by rozenfeld; 11-26-2019 at 07:15 PM.

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    So, I watched the video, not much new, two things I noted:

    1. They are now studying thousand samples from Mediterranean, they hope to finish studying them next year.

    2. They did a study similar to the Lech valley study, but focused on a Corded ware and got similar results, it should be published in a couple of months if I have heard correctly.

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    Quote Originally Posted by artemv View Post
    Have just checked this MN Fisher-gatherer Blätterhöhle Germany I1565/Bla8 I2a1, mtDNA U5b2b2.
    The file is not so heavy (600mb), but has calls for many Y-SNPs.
    He is https://www.yfull.com/tree/I-M838/

    A very old and rare branch, formed 11300 ybp, TMRCA 6000 ybp, no sub-branches on y-full.
    Given that all the European branches of V88 are rare, we can say that all the three Blätterhöhle male individs have Y-happlogroups that are very rare now.
    Where can one obtain the files?

    Should be interesting to see which subclade(s) these R-V88 samples fall under.

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    Quote Originally Posted by rozenfeld View Post
    So, I watched the video, not much new, two things I noted:

    1. They are now studying thousand samples from Mediterranean, they hope to finish studying them next year.

    2. They did a study similar to the Lech valley study, but focused on a Corded ware and got similar results, it should be published in a couple of months if I have heard correctly.
    And Dr. Kristiansen exaggerated a bit in saying all the Neolithic male lines were completely wiped out, leaving only the steppe y-dna lines R1b and R1a.

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    Yes, below the Y DNA frequencies in France and Germany according to Eupedia (https://www.eupedia.com/europe/europ...logroups.shtml)

    France (%)
    I2*/I2a 3, I2b 3.5, I1 8.5
    G 5.5
    T 1
    E1b1b 7.5
    R1b 58.5
    R1a 3
    J2 6 J*/J1 1.5
    Q 0.5 N 0

    Germany (%)
    I2*/I2a 1.5, I2b 4.5, I1 16
    G 5
    T 1
    E1b1b 5.5
    R1b 44.5
    R1a 16
    J2 4.5, J*/J1 0
    Q 0.5 N 1

    In a country with 80 million inhabitants as Germany, a frequency of 1% still means ca 400 000 males. G, T and E1b1b form 14% of y lines in France and 11.5% in Germany and these three y lines do not cover all lines rooted in the Neolithic.
    Last edited by Kristiina; 11-27-2019 at 06:41 AM.

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