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Thread: Genetic Genealogy and Ancient DNA in the News

  1. #1521
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    http://advances.sciencemag.org/content/3/7/e1700186

    A fourth Denisovan individual

    Viviane Slon1,*, Bence Viola2,3,4, Gabriel Renaud1, Marie-Theres Gansauge1, Stefano Benazzi3,5, Susanna Sawyer1, Jean-Jacques Hublin3, Michael V. Shunkov4,6, Anatoly P. Derevianko4,7, Janet Kelso1, Kay Prüfer1, Matthias Meyer1 and Svante Pääbo1

    Science Advances 07 Jul 2017:

    DOI: 10.1126/sciadv.1700186

    Abstract

    The presence of Neandertals in Europe and Western Eurasia before the arrival of anatomically modern humans is well supported by archaeological and paleontological data. In contrast, fossil evidence for Denisovans, a sister group of Neandertals recently identified on the basis of DNA sequences, is limited to three specimens, all of which originate from Denisova Cave in the Altai Mountains (Siberia, Russia). We report the retrieval of DNA from a deciduous lower second molar (Denisova 2), discovered in a deep stratigraphic layer in Denisova Cave, and show that this tooth comes from a female Denisovan individual. On the basis of the number of “missing substitutions” in the mitochondrial DNA determined from the specimen, we find that Denisova 2 is substantially older than two of the other Denisovans, reinforcing the view that Denisovans were likely to have been present in the vicinity of Denisova Cave over an extended time period. We show that the level of nuclear DNA sequence diversity found among Denisovans is within the lower range of that of present-day human populations.

    Open Access

    It's all nice and great, but basically thus far they are literally digging one single cave in Russia.

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  3. #1522
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    Normandie Wallonia
    Quote Originally Posted by rms2 View Post
    At least they tried:
    I am sceptical about their technological material means and their experiences to find nuclear and Y DNA. It is not a critic of their personal qualities.
    Last edited by palamede; 07-07-2017 at 10:57 PM.

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  5. #1523
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    http://www.biorxiv.org/content/early/2017/07/17/164400

    Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation

    View ORCID ProfileTorsten Günther, View ORCID ProfileHelena Malmström, View ORCID ProfileEmma Svensson, Ayça Omrak, Federico Sánchez-Quinto, Gülşah M Kılınç, Maja Krzewińska, View ORCID ProfileGunilla Eriksson, Magdalena Fraser, Hanna Edlund, Arielle R. Munters, Alexandra Coutinho, Luciana G. Simões, Mário Vicente, Anders Sjölander, Berit Jansen Sellevold, Roger Jørgensen, View ORCID ProfilePeter Claes, View ORCID ProfileMark D. Shriver, View ORCID ProfileCristina Valdiosera, View ORCID ProfileMihai G. Netea, Jan Apel, Kerstin Lidén, Birgitte Skar, Jan Storå, View ORCID ProfileAnders Götherström, View ORCID ProfileMattias Jakobsson

    doi: https://doi.org/10.1101/164400

    Abstract

    Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the last glaciation. However, the origin(s) of the first colonizers and their migration routes remain unclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavated across Scandinavia and dated to 9,500-6,000 years before present. Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. This result suggests that Scandinavia was initially colonized following two different routes: one from the south, the other from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These adaptations include high frequencies of low pigmentation variants and a gene-region associated with physical performance, which shows strong continuity into modern-day northern Europeans. Finally, we were able to compute a 3D facial reconstruction of a Mesolithic woman from her high-coverage genome, giving a glimpse into an individual's physical appearance in the Mesolithic.

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  7. #1524
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    Meanwhile Dan Bradley is studying genetics of medieval manuscripts: http://www.sciencemag.org/news/2017/...ncient-gospels

    Preprint: http://www.biorxiv.org/content/early/2017/07/24/146324

    The York Gospels: a one thousand year biological palimpsest

    View ORCID ProfileMatthew D. Teasdale, Sarah Fiddyment, Jiří Vnouček, Valeria Mattiangeli, Camilla Speller, Annelise Binois, Martin Carver, Catherine Dand, Timothy P. Newfield, Christopher C. Webb, View ORCID ProfileDaniel G. Bradley, View ORCID ProfileMatthew J. Collins

    doi: https://doi.org/10.1101/146324

    Abstract

    Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA we report a cost effective and simple-to-use biomolecular sampling technique. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1,000 year lifespan of this cherished object that remains an active participant in the life of York Minster. This biological data provides insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object.

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    http://www.biorxiv.org/content/early/2017/07/26/168658

    Relationships between clans and genetic kin explain cultural similarities over vast distances: the case of Yakutia

    Vincent Zvenigorosky, Sylvie Duchesne, Patrice Gerard, Anatoly Alexeev, Nikolai Kirianov, Dariya Nikolaeva, Vassili Popov, Christiane Petit, Jean Guilaine, Sergei Kodolesnikov, Michel Petit, Liubomira Romanova, Alexandre Riberon, Annie Geraut, Catherine Cannet, Jean-Luc Fausser, Veronica Pereda, Olga Meniltchuk, Xavier Mata, Catherine Theves, Rozalia Bravina, Ludovic Orlando, Christine Keyser, Bertrand Ludes, Eric Crubezy

    doi: https://doi.org/10.1101/168658

    Abstract

    Archaeological studies sample ancient human populations one site at a time, often limited to a fraction of the regions and periods occupied by a given group. While this bias is known and discussed in the literature, few model populations span areas as large and unforgiving as the Yakuts of Eastern Siberia. We systematically surveyed 31,000 square kilometres in the Sakha Republic (Yakutia) and completed the archaeological study of 174 frozen graves, assembled between the 15th and the 19th century. We analysed genetic data (autosomal genotypes, Y-chromosome haplotypes and mitochondrial haplotypes) for all ancient subjects and confronted it to the study of 190 modern subjects from the same area and the same population. Ancient familial links and paternal clan were identified between graves up to 1500 km apart and we provide new data concerning the origins of the contemporary Yakut population and demonstrate that cultural similarities in the past were linked to (i) the expansion of specific paternal clans, (ii) preferential marriage among the elites and (iii) funeral choices that could constitute a bias in any ancient population study.

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    https://www.cambridge.org/core/journ...C16012F1D21FD9

    Discussion: Are the Origins of Indo-European Languages Explained by the Migration of the Yamnaya Culture to the West?

    Leo S. Klejn (a1), Wolfgang Haak (a2), Iosif Lazaridis (a3), Nick Patterson (a3), David Reich (a3), Kristian Kristiansen (a4), Karl-Göran Sjögren (a4), Morten Allentoft (a5), Martin Sikora (a5) and Eske Willerslev (a5)

    (a1) 1 Saint Petersburg University, Russia
    (a2) 2 Max Planck Institute for the Science of Human History, Iena, Germany
    (a3) 3 Department of Genetics, Harvard Medical School, USA
    (a4) 4 Department of Historical Studies, University of Gothenburg, Sweden
    (a5) 5 Centre for Geogenetics, Natural History Museum of Denmark, Copenhagen, Denmark

    DOI: https://doi.org/10.1017/eaa.2017.35
    Published online: 28 July 2017

    Abstract

    Two co-authored articles in Nature (Haak et al., 2015; Allentoft et al., 2015) caused a sensation. They revealed genetically the mass migration of steppe Yamnaya culture people in the Early Bronze Age to central and northern Europe. The authors considered this event as the basis of the spread of Indo-European languages. In response, the Russian archaeologist, Leo S. Klejn, expresses critical remarks on the genetic inference, and in particular its implications for the problem of the origins of Indo-European languages. These remarks were shown to the authors and they present their objections. Klejn, however, has come to the conclusion that the authors’ objections do not assuage his doubts. He analyses these objections in a further response.

    Deux articles parus dans la revue Nature (Haak et al., 2015 ; Allentoft et al., 2015) firent sensation. Ils révélaient, du point de vue génétique, qu'une migration de masse de peuples des steppes appartenant à la culture Yamna affecta l'Europe du centre et du nord à l’âge du Bronze Ancien. Leurs auteurs tiennent cet évènement comme formant la base de la diffusion des langues indo-européennes. En réponse, Prof. L.S. Klejn, archéologue à Saint Pétersbourg (Russie), émit certaines critiques à l’égard des déductions basées sur la génétique, en particulier ses répercussions sur la question des origines des langues indo-européennes. Ses remarques furent soumises aux auteurs des deux articles, qui à leur tour présentèrent leurs contre-arguments. Cependant Klejn en vint à conclure que les objections de ces auteurs n'ont pas atténué ses doutes, ce qui l'amène à une seconde réponse. Translation by Madeleine Hummler

    Zwei Artikel, welche die Zeitschrift Nature in 2015 veröffentlichte (Haak et al., 2015; Allentoft et al., 2015), haben großes Aufsehen erregt. Diese lassen, aus genetischer Sicht, eine Massenmigration der Steppenvölker der Jamnaja-Kultur nach Mittel- und Nordeuropa in der Bronzezeit erkennen. Nach Auffassung der Verfasser bildet dieses Ereignis die Grundlage der Verbreitung der indoeuropäischen Sprachen. Als Antwort darauf äußerte sich Prof. L.S. Klejn (Archäologe in Sankt Petersburg, Russland) kritisch über die genetischen Rückschlüsse, besonders über die Auswirkungen auf die Frage des Ursprungs der indoeuropäischen Sprachen. Diese kritischen Bemerkungen wurden den Verfassern der Artikel vorgelegt und die Letzteren haben dann ihre Einwände dargelegt. Klejn ist aber zum Schluss gekommen, dass die Einwände der Verfasser ihn nicht überzeugen, und untersucht diese Gegenargumente in einer zweiten Antwort. Translation by Madeleine Hummler

    and relevant tweets by Iosif Lazaridis: https://twitter.com/iosif_lazaridis/...14969581023237 and the subsequent ones

    I do not have access to the paper.

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    Quote Originally Posted by rozenfeld View Post
    I do not have access to the paper.
    I do. If you want it, PM me.
    Hidden Content

    Ancestral paternal origin: Roman-era Egyptian/Levantine
    Ancestral maternal origin: Langobardic

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    Quote Originally Posted by rozenfeld View Post
    https://www.cambridge.org/core/journ...C16012F1D21FD9

    Discussion: Are the Origins of Indo-European Languages Explained by the Migration of the Yamnaya Culture to the West?

    Leo S. Klejn (a1), Wolfgang Haak (a2), Iosif Lazaridis (a3), Nick Patterson (a3), David Reich (a3), Kristian Kristiansen (a4), Karl-Göran Sjögren (a4), Morten Allentoft (a5), Martin Sikora (a5) and Eske Willerslev (a5)

    (a1) 1 Saint Petersburg University, Russia
    (a2) 2 Max Planck Institute for the Science of Human History, Iena, Germany
    (a3) 3 Department of Genetics, Harvard Medical School, USA
    (a4) 4 Department of Historical Studies, University of Gothenburg, Sweden
    (a5) 5 Centre for Geogenetics, Natural History Museum of Denmark, Copenhagen, Denmark

    DOI: https://doi.org/10.1017/eaa.2017.35
    Published online: 28 July 2017

    Abstract

    Two co-authored articles in Nature (Haak et al., 2015; Allentoft et al., 2015) caused a sensation. They revealed genetically the mass migration of steppe Yamnaya culture people in the Early Bronze Age to central and northern Europe. The authors considered this event as the basis of the spread of Indo-European languages. In response, the Russian archaeologist, Leo S. Klejn, expresses critical remarks on the genetic inference, and in particular its implications for the problem of the origins of Indo-European languages. These remarks were shown to the authors and they present their objections. Klejn, however, has come to the conclusion that the authors’ objections do not assuage his doubts. He analyses these objections in a further response.

    Deux articles parus dans la revue Nature (Haak et al., 2015 ; Allentoft et al., 2015) firent sensation. Ils révélaient, du point de vue génétique, qu'une migration de masse de peuples des steppes appartenant à la culture Yamna affecta l'Europe du centre et du nord à l’âge du Bronze Ancien. Leurs auteurs tiennent cet évènement comme formant la base de la diffusion des langues indo-européennes. En réponse, Prof. L.S. Klejn, archéologue à Saint Pétersbourg (Russie), émit certaines critiques à l’égard des déductions basées sur la génétique, en particulier ses répercussions sur la question des origines des langues indo-européennes. Ses remarques furent soumises aux auteurs des deux articles, qui à leur tour présentèrent leurs contre-arguments. Cependant Klejn en vint à conclure que les objections de ces auteurs n'ont pas atténué ses doutes, ce qui l'amène à une seconde réponse. Translation by Madeleine Hummler

    Zwei Artikel, welche die Zeitschrift Nature in 2015 veröffentlichte (Haak et al., 2015; Allentoft et al., 2015), haben großes Aufsehen erregt. Diese lassen, aus genetischer Sicht, eine Massenmigration der Steppenvölker der Jamnaja-Kultur nach Mittel- und Nordeuropa in der Bronzezeit erkennen. Nach Auffassung der Verfasser bildet dieses Ereignis die Grundlage der Verbreitung der indoeuropäischen Sprachen. Als Antwort darauf äußerte sich Prof. L.S. Klejn (Archäologe in Sankt Petersburg, Russland) kritisch über die genetischen Rückschlüsse, besonders über die Auswirkungen auf die Frage des Ursprungs der indoeuropäischen Sprachen. Diese kritischen Bemerkungen wurden den Verfassern der Artikel vorgelegt und die Letzteren haben dann ihre Einwände dargelegt. Klejn ist aber zum Schluss gekommen, dass die Einwände der Verfasser ihn nicht überzeugen, und untersucht diese Gegenargumente in einer zweiten Antwort. Translation by Madeleine Hummler

    and relevant tweets by Iosif Lazaridis: https://twitter.com/iosif_lazaridis/...14969581023237 and the subsequent ones

    I do not have access to the paper.
    I read the paper. Nothing special.

    Klejn gets totally owned. He doesn't even understand the basics of the genetic data.

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    Quote Originally Posted by rozenfeld View Post
    https://www.cambridge.org/core/journ...C16012F1D21FD9

    Discussion: Are the Origins of Indo-European Languages Explained by the Migration of the Yamnaya Culture to the West?

    Leo S. Klejn (a1), Wolfgang Haak (a2), Iosif Lazaridis (a3), Nick Patterson (a3), David Reich (a3), Kristian Kristiansen (a4), Karl-Göran Sjögren (a4), Morten Allentoft (a5), Martin Sikora (a5) and Eske Willerslev (a5)

    (a1) 1 Saint Petersburg University, Russia
    (a2) 2 Max Planck Institute for the Science of Human History, Iena, Germany
    (a3) 3 Department of Genetics, Harvard Medical School, USA
    (a4) 4 Department of Historical Studies, University of Gothenburg, Sweden
    (a5) 5 Centre for Geogenetics, Natural History Museum of Denmark, Copenhagen, Denmark

    DOI: https://doi.org/10.1017/eaa.2017.35
    Published online: 28 July 2017

    Abstract

    Two co-authored articles in Nature (Haak et al., 2015; Allentoft et al., 2015) caused a sensation. They revealed genetically the mass migration of steppe Yamnaya culture people in the Early Bronze Age to central and northern Europe. The authors considered this event as the basis of the spread of Indo-European languages. In response, the Russian archaeologist, Leo S. Klejn, expresses critical remarks on the genetic inference, and in particular its implications for the problem of the origins of Indo-European languages. These remarks were shown to the authors and they present their objections. Klejn, however, has come to the conclusion that the authors’ objections do not assuage his doubts. He analyses these objections in a further response.

    Deux articles parus dans la revue Nature (Haak et al., 2015 ; Allentoft et al., 2015) firent sensation. Ils révélaient, du point de vue génétique, qu'une migration de masse de peuples des steppes appartenant à la culture Yamna affecta l'Europe du centre et du nord à l’âge du Bronze Ancien. Leurs auteurs tiennent cet évènement comme formant la base de la diffusion des langues indo-européennes. En réponse, Prof. L.S. Klejn, archéologue à Saint Pétersbourg (Russie), émit certaines critiques à l’égard des déductions basées sur la génétique, en particulier ses répercussions sur la question des origines des langues indo-européennes. Ses remarques furent soumises aux auteurs des deux articles, qui à leur tour présentèrent leurs contre-arguments. Cependant Klejn en vint à conclure que les objections de ces auteurs n'ont pas atténué ses doutes, ce qui l'amène à une seconde réponse. Translation by Madeleine Hummler

    Zwei Artikel, welche die Zeitschrift Nature in 2015 veröffentlichte (Haak et al., 2015; Allentoft et al., 2015), haben großes Aufsehen erregt. Diese lassen, aus genetischer Sicht, eine Massenmigration der Steppenvölker der Jamnaja-Kultur nach Mittel- und Nordeuropa in der Bronzezeit erkennen. Nach Auffassung der Verfasser bildet dieses Ereignis die Grundlage der Verbreitung der indoeuropäischen Sprachen. Als Antwort darauf äußerte sich Prof. L.S. Klejn (Archäologe in Sankt Petersburg, Russland) kritisch über die genetischen Rückschlüsse, besonders über die Auswirkungen auf die Frage des Ursprungs der indoeuropäischen Sprachen. Diese kritischen Bemerkungen wurden den Verfassern der Artikel vorgelegt und die Letzteren haben dann ihre Einwände dargelegt. Klejn ist aber zum Schluss gekommen, dass die Einwände der Verfasser ihn nicht überzeugen, und untersucht diese Gegenargumente in einer zweiten Antwort. Translation by Madeleine Hummler

    and relevant tweets by Iosif Lazaridis: https://twitter.com/iosif_lazaridis/...14969581023237 and the subsequent ones

    I do not have access to the paper.
    http://sci-hub.cc/saveme/b03a/10.1017@eaa.2017.35.pdf

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    http://www.biorxiv.org/content/early/2017/08/06/172890

    Archaeogenetics of Late Iron Age Çemialo Sırtı, Batman: Investigating maternal genetic continuity in North Mesopotamia since the Neolithic

    Reyhan Yaka, Ayşegül Birand, Yasemin Yılmaz, Ceren Caner, Sinan Can Açan, Sidar Gündüzalp, Poorya Parvizi, Aslı Erim Özdoğan, Zehra İnci Togan, Mehmet Somel
    doi: https://doi.org/10.1101/172890

    Abstract


    North Mesopotamia has witnessed dramatic political and social change since the Bronze Age, but the impact of these events on its demographic history is little understood. Here we study this question by analysing the recently excavated Late Iron Age settlement of Çemialo Sırtı in Batman, southeast Turkey. Archaeological and/or radiocarbon evidence indicate that the site was inhabited during two main periods: the first half of the 2nd millennium BCE and the first millennium BCE. Çemialo Sırtı reveals nomadic items of the Early Iron Age, as well as items associated with the Late Achaemenid and subsequent Hellenistic Periods. Mitochondrial DNA (mtDNA) haplotypes from 12 Çemialo Sırtı individuals reveal high genetic diversity in this population, conspicuously higher than early Holocene west Eurasian populations, which supports the notion of increasing population admixture in west Eurasia through the Holocene. Still, in its mtDNA composition, Çemialo Sırtı shows highest affinity to Neolithic north Syria and Neolithic Anatolia among ancient populations studied, and to modern-day southwest Asian populations. Population genetic simulations do not reject continuity between Neolithic and Iron Age, nor between Iron Age and present-day populations of the region. Despite the region's complex political history and indication for increased genetic diversity over time, we find no evidence for sharp shifts in north Mesopotamian maternal genetic composition within the last 10,000 years.

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