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1. Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe

Author

Adam B. Rohrlach, Luka Papac, Ainash Childebayeva, Maïté Rivollat, Vanessa Villalba-Mouco, Gunnar U. Neumann, Sandra Penske, Eirini Skourtanioti, Marieke van de Loosdrecht, Murat Akar, Kamen Boyadzhiev, Yavor Boyadzhiev, Marie-France Deguilloux, Miroslav Dobeš, Yilmaz S. Erdal, Michal Ernée, Marcella Frangipane, Mirosław Furmanek, Susanne Friederich, Emmanuel Ghesquière, Agata Hałuszko, Svend Hansen, Mario Küßner, Marcello Mannino, Rana Özbal, Sabine Reinhold, Stéphane Rottier, Domingo Carlos Salazar-García, Jorge Soler Diaz, Philipp W. Stockhammer, Consuelo Roca de Togores Muñoz, K. Aslihan Yener, Cosimo Posth, Johannes Krause, Alexander Herbig, and Wolfgang Haak

Subjects
Medicine, Science
Abstract

Abstract Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.

Published
2021
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4. Stone Age

Author

Aida, Andrades Valtueña, Gunnar U, Neumann, Maria A, Spyrou, Lyazzat, Musralina, Franziska, Aron, Arman, Beisenov, Andrey B, Belinskiy, Kirsten I, Bos, Alexandra, Buzhilova, Matthias, Conrad, Leyla B, Djansugurova, Miroslav, Dobeš, Michal, Ernée, Javier, Fernández-Eraso, Bruno, Frohlich, Mirosław, Furmanek, Agata, Hałuszko, Svend, Hansen, Éadaoin, Harney, Alina N, Hiss, Alexander, Hübner, Felix M, Key, Elmira, Khussainova, Egor, Kitov, Alexandra O, Kitova, Corina, Knipper, Denise, Kühnert, Carles, Lalueza-Fox, Judith, Littleton, Ken, Massy, Alissa, Mittnik, José Antonio, Mujika-Alustiza, Iñigo, Olalde, Luka, Papac, Sandra, Penske, Jaroslav, Peška, Ron, Pinhasi, David, Reich, Sabine, Reinhold, Raphaela, Stahl, Harald, Stäuble, Rezeda I, Tukhbatova, Sergey, Vasilyev, Elizaveta, Veselovskaya, Christina, Warinner, Philipp W, Stockhammer, Wolfgang, Haak, Johannes, Krause, and Alexander, Herbig

Subjects
Plague, Yersinia pestis, Human Migration, Animals, Genetic Variation, Humans, Animal Husbandry, DNA, Ancient, Genome, Bacterial, History, Ancient, Phylogeny
Abstract

The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development. Here, we present 17 Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide geographic expanse across Eurasia. This increased dataset enabled us to explore correlations between temporal, geographical, and genetic distance. Our results suggest a nonflea-adapted and potentially extinct single lineage that persisted over millennia without significant parallel diversification, accompanied by rapid dispersal across continents throughout this period, a trend not observed in other pathogens for which ancient genomes are available. A stepwise pattern of gene loss provides further clues on its early evolution and potential adaptation. We also discover the presence of the flea-adapted form of Y. pestis in Bronze Age Iberia, previously only identified in in the Caucasus and the Volga regions, suggesting a much wider geographic spread of this form of Y. pestis. Together, these data reveal the dynamic nature of plague’s formative years in terms of its early evolution and ecology.

Published
2022

5. Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague

Author

Aida Andrades Valtueña, Gunnar U. Neumann, Maria A. Spyrou, Lyazzat Musralina, Franziska Aron, Arman Beisenov, Andrey B. Belinskiy, Kirsten I. Bos, Alexandra Buzhilova, Matthias Conrad, Leyla B. Djansugurova, Miroslav Dobeš, Michal Ernée, Javier Fernández-Eraso, Bruno Frohlich, Mirosław Furmanek, Agata Hałuszko, Svend Hansen, Éadaoin Harney, Alina N. Hiss, Alexander Hübner, Felix M. Key, Elmira Khussainova, Egor Kitov, Alexandra O. Kitova, Corina Knipper, Denise Kühnert, Carles Lalueza-Fox, Judith Littleton, Ken Massy, Alissa Mittnik, José Antonio Mujika-Alustiza, Iñigo Olalde, Luka Papac, Sandra Penske, Jaroslav Peška, Ron Pinhasi, David Reich, Sabine Reinhold, Raphaela Stahl, Harald Stäuble, Rezeda I. Tukhbatova, Sergey Vasilyev, Elizaveta Veselovskaya, Christina Warinner, Philipp W. Stockhammer, Wolfgang Haak, Johannes Krause, Alexander Herbig, Max Planck Society, Max Planck - Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, European Research Council, Heidelberg Academy of Sciences and Humanities, Academy of Sciences of the Czech Republic, Ministerio de Ciencia e Innovación (España), German Research Foundation, Diputación Foral de Álava, Eusko Jaurlaritza, and Ministry of Education and Science (Kazakhstan)

Subjects
Plague, Multidisciplinary, Ancient DNA, Yersinia pestis
Abstract

[Significance] The bacterium Yersinia pestis has caused numerous historically documented outbreaks of plague and research using ancient DNA could demonstrate that it already affected human populations during the Neolithic. However, the pathogen’s genetic diversity, geographic spread, and transmission dynamics during this early period of Y. pestis evolution are largely unexplored. Here, we describe a set of ancient plague genomes up to 5,000 y old from across Eurasia. Our data demonstrate that two genetically distinct forms of Y. pestis evolved in parallel and were both distributed across vast geographic distances, potentially occupying different ecological niches. Interpreted within the archeological context, our results suggest that the spread of plague during this period was linked to increased human mobility and intensification of animal husbandry., The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development. Here, we present 17 Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide geographic expanse across Eurasia. This increased dataset enabled us to explore correlations between temporal, geographical, and genetic distance. Our results suggest a nonflea-adapted and potentially extinct single lineage that persisted over millennia without significant parallel diversification, accompanied by rapid dispersal across continents throughout this period, a trend not observed in other pathogens for which ancient genomes are available. A stepwise pattern of gene loss provides further clues on its early evolution and potential adaptation. We also discover the presence of the flea-adapted form of Y. pestis in Bronze Age Iberia, previously only identified in in the Caucasus and the Volga regions, suggesting a much wider geographic spread of this form of Y. pestis. Together, these data reveal the dynamic nature of plague’s formative years in terms of its early evolution and ecology., This study was funded by the Max Planck Society, Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean and the European Research Council under the European Union’s Horizon 2020 research and innovation program under Grant Agreement 771234 – PALEoRIDER (to W.H.), 856453 – HistoGenes (to J.K.), and 834616 – ARCHCAUCASUS (to S.H.). The Heidelberg Academy of Science financed the genetic and archeological research on human individuals from the Augsburg region within the project WIN Kolleg: “Times of Upheaval: Changes of Society and Landscape at the Beginning of the Bronze Age. M.E. was supported by the award “Praemium Academiae” of the Czech Academy of Sciences. M.D. was supported by the project RVO 67985912 of the Institute of Archaeology of the Czech Academy of Sciences, Prague. I.O. was supported by the Ramón y Cajal grant from Ministerio de Ciencia e Innovación, Spanish Government (RYC2019-027909-I). A. H€ubner was supported by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy (EXC 2051 – Project-ID 390713860). J.F.-E. and J.A.M.-A. were supported by the Diputación Foral de Alava, IT 1223-19, Gobierno Vasco. A. Buzhilova was supported by the Center of Information Technologies and Systems (CITIS), Moscow, Russia 121041500329-0. L. M., L.B.D., and E. Khussainova were supported by the Grant AP08856654, Ministry of Education and Science of the Republic of Kazakhstan. A. Beisenov was supported by the Grant AP08857177, Ministry of Education and Science of the Republic of Kazakhstan.

Published
2022

6. Large-scale migration into Britain during the Middle to Late Bronze Age

Author

Nick Patterson, Michael Isakov, Thomas Booth, Lindsey Büster, Claire-Elise Fischer, Iñigo Olalde, Harald Ringbauer, Ali Akbari, Olivia Cheronet, Madeleine Bleasdale, Nicole Adamski, Eveline Altena, Rebecca Bernardos, Selina Brace, Nasreen Broomandkhoshbacht, Kimberly Callan, Francesca Candilio, Brendan Culleton, Elizabeth Curtis, Lea Demetz, Kellie Sara Duffett Carlson, Ceiridwen J. Edwards, Daniel M. Fernandes, M. George B. Foody, Suzanne Freilich, Helen Goodchild, Aisling Kearns, Ann Marie Lawson, Iosif Lazaridis, Matthew Mah, Swapan Mallick, Kirsten Mandl, Adam Micco, Megan Michel, Guillermo Bravo Morante, Jonas Oppenheimer, Kadir Toykan Özdoğan, Lijun Qiu, Constanze Schattke, Kristin Stewardson, J. Noah Workman, Fatma Zalzala, Zhao Zhang, Bibiana Agustí, Tim Allen, Katalin Almássy, Luc Amkreutz, Abigail Ash, Christèle Baillif-Ducros, Alistair Barclay, László Bartosiewicz, Katherine Baxter, Zsolt Bernert, Jan Blažek, Mario Bodružić, Philippe Boissinot, Clive Bonsall, Pippa Bradley, Marcus Brittain, Alison Brookes, Fraser Brown, Lisa Brown, Richard Brunning, Chelsea Budd, Josip Burmaz, Sylvain Canet, Silvia Carnicero-Cáceres, Morana Čaušević-Bully, Andrew Chamberlain, Sébastien Chauvin, Sharon Clough, Natalija Čondić, Alfredo Coppa, Oliver Craig, Matija Črešnar, Vicki Cummings, Szabolcs Czifra, Alžběta Danielisová, Robin Daniels, Alex Davies, Philip de Jersey, Jody Deacon, Csilla Deminger, Peter W. Ditchfield, Marko Dizdar, Miroslav Dobeš, Miluše Dobisíková, László Domboróczki, Gail Drinkall, Ana Đukić, Michal Ernée, Christopher Evans, Jane Evans, Manuel Fernández-Götz, Slavica Filipović, Andrew Fitzpatrick, Harry Fokkens, Chris Fowler, Allison Fox, Zsolt Gallina, Michelle Gamble, Manuel R. González Morales, Borja González-Rabanal, Adrian Green, Katalin Gyenesei, Diederick Habermehl, Tamás Hajdu, Derek Hamilton, James Harris, Chris Hayden, Joep Hendriks, Bénédicte Hernu, Gill Hey, Milan Horňák, Gábor Ilon, Eszter Istvánovits, Andy M. Jones, Martina Blečić Kavur, Kevin Kazek, Robert A. Kenyon, Amal Khreisheh, Viktória Kiss, Jos Kleijne, Mark Knight, Lisette M. Kootker, Péter F. Kovács, Anita Kozubová, Gabriella Kulcsár, Valéria Kulcsár, Christophe Le Pennec, Michael Legge, Matt Leivers, Louise Loe, Olalla López-Costas, Tom Lord, Dženi Los, James Lyall, Ana B. Marín-Arroyo, Philip Mason, Damir Matošević, Andy Maxted, Lauren McIntyre, Jacqueline McKinley, Kathleen McSweeney, Bernard Meijlink, Balázs G. Mende, Marko Menđušić, Milan Metlička, Sophie Meyer, Kristina Mihovilić, Lidija Milasinovic, Steve Minnitt, Joanna Moore, Geoff Morley, Graham Mullan, Margaréta Musilová, Benjamin Neil, Rebecca Nicholls, Mario Novak, Maria Pala, Martin Papworth, Cécile Paresys, Ricky Patten, Domagoj Perkić, Krisztina Pesti, Alba Petit, Katarína Petriščáková, Coline Pichon, Catriona Pickard, Zoltán Pilling, T. Douglas Price, Siniša Radović, Rebecca Redfern, Branislav Resutík, Daniel T. Rhodes, Martin B. Richards, Amy Roberts, Jean Roefstra, Pavel Sankot, Alena Šefčáková, Alison Sheridan, Sabine Skae, Miroslava Šmolíková, Krisztina Somogyi, Ágnes Somogyvári, Mark Stephens, Géza Szabó, Anna Szécsényi-Nagy, Tamás Szeniczey, Jonathan Tabor, Károly Tankó, Clenis Tavarez Maria, Rachel Terry, Biba Teržan, Maria Teschler-Nicola, Jesús F. Torres-Martínez, Julien Trapp, Ross Turle, Ferenc Ujvári, Menno van der Heiden, Petr Veleminsky, Barbara Veselka, Zdeněk Vytlačil, Clive Waddington, Paula Ware, Paul Wilkinson, Linda Wilson, Rob Wiseman, Eilidh Young, Joško Zaninović, Andrej Žitňan, Carles Lalueza-Fox, Peter de Knijff, Ian Barnes, Peter Halkon, Mark G. Thomas, Douglas J. Kennett, Barry Cunliffe, Malcolm Lillie, Nadin Rohland, Ron Pinhasi, Ian Armit, David Reich, European Research Council, Croatian Science Foundation, Ministry of Culture (Czech Republic), Academy of Sciences of the Czech Republic, Leverhulme Trust, Culture Vannin, Hungarian Academy of Sciences, National Research, Development and Innovation Office (Hungary), Ministerio de Ciencia e Innovación (España), National Institutes of Health (US), John Templeton Foundation, Paul G. Allen Family Foundation, Howard Hughes Medical Institute, Geology and Geochemistry, and Archaeology of Northwestern Europe

Subjects
Europe, Farmers, Multidisciplinary, Archaeology, Genome, Human, Britain, prehistory, genetics, language, Human Migration, Humans, Infant, France, United Kingdom, Article
Abstract

Present-day people from England and Wales have more ancestry derived from early European farmers (EEF) than did people of the Early Bronze Age1. To understand this, here we generated genome-wide data from 793 individuals, increasing data from the Middle to the Late Bronze Age and Iron Age in Britain by 12-fold, and western and central Europe by 3.5-fold. Between 1000 and 875 BC, EEF ancestry increased in southern Britain (England and Wales) but not northern Britain (Scotland) due to incorporation of migrants who arrived at this time and over previous centuries, and who were genetically most similar to ancient individuals from France. These migrants contributed about half the ancestry of people of England and Wales from the Iron Age, thereby creating a plausible vector for the spread of early Celtic languages into Britain. These patterns are part of a broader trend of EEF ancestry becoming more similar across central and western Europe in the Middle to the Late Bronze Age, coincident with archaeological evidence of intensified cultural exchange2-6. There was comparatively less gene flow from continental Europe during the Iron Age, and the independent genetic trajectory in Britain is also reflected in the rise of the allele conferring lactase persistence to approximately 50% by this time compared to approximately 7% in central Europe where it rose rapidly in frequency only a millennium later. This suggests that dairy products were used in qualitatively different ways in Britain and in central Europe over this period., This work was funded in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 834087; the COMMIOS Project to I.A.). M.N. was supported by the Croatian Science Fund grant (HRZZ IP-2016-06-1450). P.V., M.Dobeš and Z.V. were supported by the Ministry of Culture of the Czech Republic (DKRVO 2019-2023/7.I.c, 00023272). M.E. was supported by Czech Academy of Sciences award Praemium Academiae. M.Dobisíková and A.Danielisová were supported by the grant RVO 67985912 of the Institute of Archaeology of the Czech Academy of Sciences. M.G.B.F. was funded by The Leverhulme Trust via a Doctoral Scholarship scheme awarded to M.Pala and M.B.R. Support to M.Legge came from the South, West & Wales Doctoral Training Partnership. M.G.’s osteological analyses were funded by Culture Vannin. A.S.-N. was supported by the János Bolyai Research Scholarship of the Hungarian Academy of Sciences. T.H., T.S. and K.K.’s work was supported by a grant from the Hungarian Research, Development and Innovation Office (project number: FK128013). We acknowledge support for radiocarbon dating and stable isotope analyses as well as access to skeletal material from Manx National Heritage and A. Fox. Dating analysis was funded by Leverhulme Trust grant RPG-388. M.G.T. and I.B. were supported by a Wellcome Trust Investigator Award (project 100713/Z/12/Z). I.O. was supported by a Ramón y Cajal grant from Ministerio de Ciencia e Innovación, Spanish Government (RYC2019-027909-I). The research directed at Harvard was funded by NIH grants GM100233 and HG012287, by John Templeton Foundation grant 61220, by a gift from Jean-François Clin, and by the Allen Discovery Center program, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation. D.R. is also an Investigator of the Howard Hughes Medical Institute.

Published
2021
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7. Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe

Author

Marie-France Deguilloux, Agata Hałuszko, Maïté Rivollat, Sandra Penske, J. S. Díaz, Michal Ernée, Eirini Skourtanioti, Miroslav Dobeš, Cosimo Posth, Mario Küßner, Stéphane Rottier, Gunnar U. Neumann, Emmanuel Ghesquière, Susanne Friederich, Yılmaz Selim Erdal, Adam Ben Rohrlach, Rana Özbal, Svend Hansen, Marcella Frangipane, Marcello A. Mannino, Ainash Childebayeva, Consuelo Roca de Togores Muñoz, Sabine Reinhold, Murat Akar, Wolfgang Haak, Alexander Herbig, Luka Papac, Yavor Boyadzhiev, Domingo C. Salazar-García, Vanessa Villalba-Mouco, Kamen Boyadzhiev, Johannes Krause, K. Aslıhan Yener, Mirosław Furmanek, Marieke Sophia van de Loosdrecht, Philipp W. Stockhammer, European Commission, Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, University of Adelaide, De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Spanish National Research Council (CSIC), Mustafa Kemal University, Bulgarian Academy of Sciences (BAS), Czech Academy of Sciences [Prague] (CAS), Hacettepe University = Hacettepe Üniversitesi, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], University of Wrocław [Poland] (UWr), State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Institut national de recherches archéologiques préventives (Inrap), Centre de Recherche en Archéologie, Archéosciences, Histoire (CReAAH), Le Mans Université (UM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC)-Nantes Université (NU), German Archaeological Institute (DAI), Aarhus University [Aarhus], Koç University, Basque Foundation for Science (Ikerbasque), University of Cape Town, Departamento de Inteligencia Artificial [UPM, Spain] (DIA), Universidad Politécnica de Madrid (UPM), Universitat de València (UV), Medizinische Klinik und Poliklinik III [Bonn, Germany], Universitätsklinikum Bonn (UKB), MARQ - Museo Arqueológico Provincial de Alicante (MARQ), Ludwig Maximilian University [Munich] (LMU), New York University [New York] (NYU), NYU System (NYU), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, University of South Australia [Adelaide], Max Planck Society Foundation CELLEX, French (ANR) French National Research Agency (ANR), German (DFG) Research Foundations under the INTERACT project German Research Foundation (DFG) [ANR17-FRAL-0010, DFG-HA-5407/4-1], European Research Council (ERC) under the European Union European Research Council (ERC) [771234-PALEoRIDER], Czech Academy of Sciences Czech Academy of Sciences, Institute of Archaeology of the Czech Academy of Sciences, Prague Czech Academy of Sciences [RVO 67985912], Projekt DEAL, ANR-17-FRAL-0010,INTERACT,Interactions entre groupes humains en Europe de l'Ouest durant la transition Mésolithique-Néolithique: la double perspective des échanges biologiques et culturels(2017), Özbal, Rana (ORCID 0000-0001-6765-2765 & YÖK ID 55583), Rohrlach, A.B., Papac, L., Childebayeva, A., Rivollat, M., Villalba Mouco, V., Neumann, G.U., Penske, S., Skourtanioti, E., van de Loosdrecht, M., Akar, M., Boyadzhiev, K., Boyadzhiev, Y., Deguilloux, M.F., Dobes, M., Erdal, Y.S., Ernée, M., Frangipane, M., Furmanek, M., Friederich, S., Ghesquière, E., Ha?uszko, A., Hansen, S., Küßner, M., Mannino, M., Reinhold, S., Rottier, S., Salazar García, D.C., Diaz, J.S., Stockhammer, P.W., de Togores Muñoz, C.R., Yener, K.A., Posth, C., Krause, J., Herbig, A., Haak, W., College of Social Sciences and Humanities, Department of Archeology and History of Art, Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), Université de Nantes (UN)-Le Mans Université (UM)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR Histoire, Histoire de l'Art et Archéologie (UFR HHAA), Université de Nantes (UN)-Université de Nantes (UN)-Ministère de la Culture (MC), Max Planck Society, Agence Nationale de la Recherche (France), German Research Foundation, European Research Council, Academy of Sciences of the Czech Republic, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Le Mans Université (UM)-Université de Rennes (UR)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR Histoire, Histoire de l'Art et Archéologie (UFR HHAA), and Ikerbasque - Basque Foundation for Science

Subjects
Czech, SELECTION, Population genetics, MITOCHONDRIAL-DNA, early farmers, DIVERSITY, mitochondrial DNA, shotgun sequencing, Prehistòria, Haplogroup, German, 0302 clinical medicine, Medicine and Health Sciences, DNA sequencing, Science and technology, media_common, 0303 health sciences, Multidisciplinary, Horizon (archaeology), Critical event, Shotgun sequencing, chromosomal haplogroups, European research, STEPPE, Western europe, language, Medicine, Genetic Markers, Mitochondrial DNA, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, uniparentally-inherited markers, Science, Library science, Biology, Y chromosome, DNA, Mitochondrial, Polymorphism, Single Nucleotide, Target enrichment, Article, 03 medical and health sciences, Political science, Humans, media_common.cataloged_instance, ANCIENT DNA, Genetic Testing, European union, Alleles, 030304 developmental biology, MUTATION-RATE, Chromosomes, Human, Y, Saturation (genetic), History and Archaeology, Y-mappable capture assay, Ancient DNA, Neanderthals, Anatomically modern humans, language.human_language, Neolithic transition, Genetics, Population, Haplotypes, Evolutionary biology, GENOMIC HISTORY, 030217 neurology & neurosurgery
Abstract

Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe., Open Access funding enabled and organized by Projekt DEAL. This study was funded by the Max Planck Society, the French (ANR) and German (DFG) Research Foundations under the INTERACT project (ANR-17-FRAL-0010, DFG-HA-5407/4-1, 2018-2021) to M.R. and W.H., the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program under Grant agreement no. 771234-PALEoRIDER to W.H., the award Praemium Academiae of the Czech Academy of Sciences to M.E. and the project RVO 67985912 of the Institute of Archaeology of the Czech Academy of Sciences, Prague to M.S.

Published
2021
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8. Dynamic changes in genomic and social structures in third millennium BCE central Europe

Author

Michaela Langová, Petr Limburský, Radka Šumberová, Martin Kuna, Adam Ben Rohrlach, Jana Kuljavceva Hlavová, Maria A. Spyrou, Erika Průchová, Drahomíra Malykova, Alžběta Danielisová, Milan Kuchařík, Petr Velemínský, Hana Brzobohatá, Johannes Krause, Franziska Aron, David Reich, Brendan J. Culleton, Luka Papac, Miluše Dobisíková, Ron Pinhasi, Volker M Heyd, Jan Kolář, Jana Klementová, Lubor Smejtek, Michal Ernée, David Daněček, Petr Krištuf, Lucia Mattiello, Ondřej Švejcar, Miloš Vávra, Douglas J. Kennett, Martin Trefný, Miroslav Dobeš, Wolfgang Haak, Jaroslav Špaček, Stephan Schiffels, Josef Hložek, Katarína Petriščáková, Gunnar U. Neumann, Michal Kostka, Monika Pecinovská, Nadin Rohland, Petra Stránská, Department of Cultures, Helsinki Institute of Sustainability Science (HELSUS), YMPACT: The Yamnaya Impact on Prehistoric Europe, Archaeology, and Faculty Common Matters (Faculty of Arts)

Subjects
Steppe, media_common.quotation_subject, 615 History and Archaeology, Prehistory, 03 medical and health sciences, social structure, Beaker, Bronze Age, 0601 history and archaeology, genomic structure, Social organization, Research Articles, 030304 developmental biology, media_common, 0303 health sciences, Bohemia, aDNA, migration, Neolithic, Eneolithic, ancestry, geography.geographical_feature_category, Multidisciplinary, 060102 archaeology, Central Europe, 1184 Genetics, developmental biology, physiology, SciAdv r-articles, 06 humanities and the arts, DNA, 3th millennium BC, Social processes, Geography, Anthropology, Ethnology, Social structure, Diversity (politics), Research Article
Abstract

Archaeogenetic time transect in Europe unravels genetic and social changes before and after the arrival of “steppe” ancestry., Europe’s prehistory oversaw dynamic and complex interactions of diverse societies, hitherto unexplored at detailed regional scales. Studying 271 human genomes dated ~4900 to 1600 BCE from the European heartland, Bohemia, we reveal unprecedented genetic changes and social processes. Major migrations preceded the arrival of “steppe” ancestry, and at ~2800 BCE, three genetically and culturally differentiated groups coexisted. Corded Ware appeared by 2900 BCE, were initially genetically diverse, did not derive all steppe ancestry from known Yamnaya, and assimilated females of diverse backgrounds. Both Corded Ware and Bell Beaker groups underwent dynamic changes, involving sharp reductions and complete replacements of Y-chromosomal diversity at ~2600 and ~2400 BCE, respectively, the latter accompanied by increased Neolithic-like ancestry. The Bronze Age saw new social organization emerge amid a ≥40% population turnover.

Published
2021
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9. Ten millennia of hepatitis B virus evolution

Author

Oleg Balanovsky, Lourdes Marquez-Morfin, Magdalena Zoledziewska, Susannah J. Salter, Cody E. Parker, Kirsten I. Bos, Kathrin Nägele, Domingo C. Salazar-García, Kerttu Majander, Vittorio Mazzarello, Cosimo Posth, Kurt W. Alt, Elmira Khussainova, Silvia Teresita Hernández Godoy, Richard Mortimer, Ayshin Ghalichi, Alexander Herbig, Lars Fehren-Schmitz, Leyla B. Djansugurova, Dmitry A. Stashenkov, Raiko Krauß, Mikhail S. Chaplygin, Tiago Ferraz, Patrick Semal, Eva Rosenstock, Michal Kostka, Yavor Boyadzhiev, Harald Meller, Petr Limburský, Mario Küßner, Tara Ingman, Maïté Rivollat, Eva Fernández-Domínguez, Rodrigo Barquera, Robin Skeates, Kamen Boyadzhiev, Denise Kühnert, Mirjana Roksandic, Adam Ben Rohrlach, Alexandra P. Buzhilova, Alissa Mittnik, Yadira Chinique de Armas, Johannes Krause, Marie-France Deguilloux, Aleksandr Khokhlov, Rezeda I. Tukhbatova, Elizabeth Popescu, Lucy C. Salazar, Andrey A. Chizhevsky, Christopher Read, Hubert Steiner, Melanie Van Twest, Eveline Altena, Diana Iraíz Hernández-Zaragoza, Lyazzat Musralina, Megan Michel, Íñigo García-Martínez de Lagrán, Anatoly R. Kantorovich, Katrien Van de Vijver, Alžbeta Danielisová, Rachel Clarke, Duncan Sayer, Bastien Llamas, Nikolaj Makarov, Alejandro Romero, Luka Papac, Alessandra Sperduti, Vladimir E. Maslov, Rafael Garrido-Pena, Gunnar U. Neumann, Arman Z. Beisenov, Zainolla Samashev, Guido Alberto Gnecchi-Ruscone, Päivi Onkamo, Eduardo Carmona Ballestero, Javier Jimenez-Echevarria, Valery Khartanovich, Manuel Rojo-Guerra, Fredrik Hallgren, Eirini Skourtanioti, Natalia Shishlina, Luca Lai, Petr Velemínský, Antti Sajantila, Peter C. Ramsl, Claudia Sagona, Susanne Friederich, Miroslav Dobeš, Marcel Keller, Francesco Cucca, Sabine Reinhold, Florian van Bömmel, Luc Amkreutz, Vittoria Schimmenti, Raphaela Stahl, Douglas Baird, Marina K. Karapetian, Kurt Rademaker, Stephan Schiffels, Sacha Kacki, Evelyn K. Guevara, Michael Francken, Christina Warinner, Kay Prüfer, Karen Giffin, Felix M. Key, Joscha Gretzinger, Alexey Kalmykov, Svetlana Shnaider, Sandra Penske, Antje Wissgott, Tiffiny A. Tung, Biaslan Ch. Atabiev, Philippe Lefranc, Elizabeth A. Nelson, Peter de Knijff, Vladimir Slavchev, Jessica Pearson, Yılmaz Selim Erdal, Louise Loe, Jan Nováček, Micaela Alvarez Calmet, José I. Royo-Guillén, Richard L. Burger, Kristiina Mannermaa, K. Aslıhan Yener, Maria Pfefferkorn, Vyacheslav Moiseyev, Svend Hansen, Didier Binder, Michal Ernée, Maria A. Spyrou, Michal Feldman, Vladimir V. Kufterin, Murat Akar, Héctor Arcusa-Magallón, Andrej B. Belinskiy, Egor Kitov, Franziska Aron, Ron Hübler, Vanessa Villalba-Mouco, Sophie Beckett, Jessica Beckett, Arthur Kocher, Michael Schultz, Elena Batieva, Pilar Utrilla, Cristina Tejedor-Rodríguez, Kristin von Heyking, Masnav Navruzbekov, Michaela Langová, Maria Paz Miguel de Ibáñez, Stéphane Rottier, Maria V. Dobrovolskaya, Sandra Lösch, Emma D. Zilivinskaya, Dmitry V. Vasilev, Gabriel García Atiénzar, Marcello A. Mannino, Wolfgang Haak, Philipp W. Stockhammer, Sylvie Saintot, Alice Lyons, Ken Massy, Elena Kaverzneva, Susanna Sabin, Carmen Alonso-Fernández, Anna F. Kochkina, Marieke Sophia van de Loosdrecht, Stefanie Eisenmann, Max Planck Society, European Commission, Slovak Academy of Sciences, Academy of Sciences of the Czech Republic, Russian Foundation for Basic Research, German Research Foundation, Agence Nationale de la Recherche (France), Wenner-Gren Foundation, Ministry of Education and Science (Kazakhstan), Universidad de Alicante. Departamento de Prehistoria, Arqueología, Historia Antigua, Filología Griega y Filología Latina, Universidad de Alicante. Departamento de Biotecnología, Universidad de Alicante. Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico, Prehistoria y Protohistoria, Grupo de Inmunología, Biología Celular y del Desarrollo, Ingman, Tara, Kocher, A., Papac, L., Barquera, R., Key, FM., Spyrou, MA., Hubler, R., Rohrlach, AB., Aron, F., Stahl, R., Wissgott, A., van Bommel, F., Pfefferkorn, M., Mittnik, A., Villalba-Mouco, V., Neumann, GU., Rivollat, M., van de Loosdrecht, MS., Majander, K., Tukhbatova, RI., Musralina, L., Ghalichi, A., Penske, S., Sabin, S., Michel, M., Gretzinger, J., Nelson, EA., Ferraz, T., Nagele, K., Parker, C., Keller, M., Guevara, EK., Feldman, M., Eisenmann, S., Skourtanioti, E., Giffin, K., Gnecchi-Ruscone, GA., Friederich, S., Schimmenti, V., Khartanovich, V., Karapetian, MK., Chaplygin, MS., Kufterin, VV., Khokhlov, AA., Chizhevsky, AA., Stashenkov, DA., Kochkina, AF., Tejedor-Rodriguez, C., de Lagran, IGM., Arcusa-Magallon, H., Garrido-Pena, R., Royo-Guillen, JI., Novacek, J., Rottier, S., Kacki, S., Saintot, S., Kaverzneva, E., Belinskiy, AB., Veleminsky, P., Limbursky, P., Kostka, M., Loe, L., Popescu, E., Clarke, R., Lyons, A., Mortimer, R., Sajantila, A., de Armas, YC., Godoy, STH., Hernandez-Zaragoza, DI., Pearson, J., Binder, D., Lefranc, P., Kantorovich, AR., Maslov, VE., Lai, L., Zoledziewska, M., Beckett, JF., Langova, M., Atienzar, GG., Ibanez, MPD, Romero, A., Sperduti, A., Beckett, S., Salter, SJ., Zilivinskaya, ED., Vasil, DV., von Heyking, K., Burger, RL., Salazar, LC., Amkreutz, L., Navruzbekov, M., Rosenstock, E., Alonso-Fernandez, C., Slavchev, V., Kalmykov, AA., Atabiev, BC., Batieva, E, Calmet, MA., Llamas, B., Schultz, M., Krauss, R., Jimenez-Echevarria, J., Francken, M., Shnaider, S., de Knijff, P., Altena, E., Van de Vijver, K., Fehren-Schmitz, L., Tung, TA., Losch, S., Dobrovolskaya, M., Makarov, N., Read, C., Van Twest, M., Sagona, C., Ramsl, PC., Akar, M., Yener, KA., Ballestero, EC., Cucca, F., Mazzarello, V., Utrilla, P., Rademaker, K., Fernandez-Dominguez, E., Baird, D., Semal, P., Marquez-Morfin, L, Roksandic, M., Steiner, H., Salazar-Garcia, DC., Shishlina, N. Erdal, YS., Hallgren, F., Boyadzhiev, Y., Boyadzhiev, K., Kussner, M., Sayer, D., Onkamo, P., Skeates, R., Rojo-Guerra, M., Buzhilova, A., Khussainova, E., Djansugurova, LB., Beisenov, AZ., Samashev, Z., Massy, K., Mannino, M., Moiseyev, V., Mannermaa, K., Balanovsky, O., Deguilloux, MF., Reinhold, S., Hansen, S., Kitov, EP., Dobes, M., Ernee, M., Meller, H., Prufer, Kay., Warinner, C., Schiffels, S., Stockhammer, PW., Bos, K., Posth, C., Herbig, A., Haak, W., Krause, J., Kuhnert, D., and Koç University Research Center for Anatolian Civilizations (ANAMED) / Koç Üniversitesi Anadolu Medeniyetleri Araştırma Merkezi (ANAMED)

Subjects
Phylogeographic history, Hepatitis B/history, 01 natural sciences, The Republic, Communicable Diseases, Emerging, German, Communicable Diseases, Emerging/history, Agency (sociology), Science and technology, ComputingMilieux_MISCELLANEOUS, History, Ancient, Phylogeny, media_common, 0303 health sciences, Multidisciplinary, Ancient DNA, European research, virus diseases, Genomics, Hepatitis B, 3. Good health, Europe, language, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Christian ministry, Paleogenomic analyses, Asian Continental Ancestry Group, 010506 paleontology, Hepatitis B virus, Asia, Hepatitis B virus/classification, European Continental Ancestry Group, Library science, Biología Celular, White People, Marie curie, Evolution, Molecular, 03 medical and health sciences, American Natives, Asian People, Political science, Genomic data, media_common.cataloged_instance, Humans, Slovak, European union, American Indian or Alaska Native, 030304 developmental biology, 0105 earth and related environmental sciences, Genetic Variation, Paleontology, Prehistoria, A300, language.human_language, digestive system diseases, American natives, Americas, Asian continental ancestry group, Communicable diseases, Emerging, European continental ancestry group, Evolution, molecular, Genetic variation
Abstract

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic., The research was funded by the Max Planck Society, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (771234–PALEoRIDER, to W.H.; 805268–CoDisEASe to K. Bos; 834616–ARCHCAUCASUS to S.H.), the Slovak Academy of Sciences and the European Union’s Seventh Framework Programme and Marie Curie Actions under the Programme SASPRO (1340/03/03 to P.C.R.), the ERA.NET RUS Plus–S&T programm of the European Union’s Seventh Framework Programme (277–BIOARCCAUCASUS to S.Re. and S.H.), the Werner Siemens Stiftung (“Paleobiochemistry”, to CW), the Award Praemium Academiae of the Czech Academy of Sciences (to M.E.), the Institute of Archaeology of the Czech Academy of Sciences (RVO 67985912, to M.Dobe.), the Russian Foundation for Basic Research (19-09-00354a, to M.K.K. and V.V.K.; 19-78-10053 to SSh), the German Research Foundation (DFG-HA-5407/4-1–INTERACT to W.H. and RE2688/2 to S.Re.), the French National Research Agency (ANR-17-FRAL-0010–INTERACT, to M.F.D., M.Ri., S.Ro., S.Sai., D.Bi., and P.Le.), the Wenner-Gren Dissertation Fieldwork Grant (9558 to S.Sab.), and the Ministry of Education and Science of the Republic of Kazakhstan (AP08856654 to L.B.D., L.M., and E.Kh. and AP08857177 to A.Z.B.).

Published
2021
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11. Scapulae and phalanges as grave goods: a mystery from the Early Bronze Age

Author

Michaela Langová, Radka Šumberová, René Kyselý, Petr Limburský, and Michal Ernée

Subjects
Archeology, Rite, Grave goods, History, media_common.quotation_subject, Ancient history, Phalanx, Magic (paranormal), Digging, Divination, Bronze Age, Anthropology, Realm, media_common
Abstract

Based on a study of animal bone finds from the Unětice Culture cemeteries (2200–1700 BC) in Bohemia, Czech Republic, the study analyses selected aspects of the funeral rite in the Early Bronze Age in Central Europe. The focus is on unworked and unburned cattle, pig, sheep/goat and red deer scapulae, phalanges (+ some astragali) and ribs—significant burial phenomena in the Unětice Culture—determined as undoubtedly intentional components of funerals, that is, as grave goods. Radiocarbon and other evidence show that the phenomena existed for the whole of the Unětice Culture and perhaps longer. The presence of scapulae in 41% of the graves in the cemetery at Mikulovice and tens of other cemeteries in Bohemia and Moravia, and the complete domination of phalanges among the animal bones in graves in the funerary area at Vliněves provide evidence of the importance of these customs in the funerary rite. Rib cuts certainly represent meat offerings but the meaning of isolated (unarticulated) scapulae and phalanges/astragali is difficult to determine. The hypothesis that scapulae found always singly could also be real meat offerings is difficult to accept, so further roles, whether practical or symbolic, should be considered. An earlier suggestion that scapulae were used as a trowel for digging grave pits is highly improbable, as follows from our analysis, and we were unable to confirm the use of the flat scapula as a plate for other offerings or a base for paintings. The choice of the (near-triangular) scapula to symbolise the triangle must be left in the realm of speculation. Unworked and variably positioned phalanges and astragali are unlikely to have been used for clothing or hair decoration but, based on analogies, might have been used in magic or games (amulets, tokens, dice, game pieces). The possible use of scapulae and phalanges + astragali in divination is considered in the light of ethnographic and historical records of scapulimancy and astragalomancy on four continents. As scapulae and phalanges do not usually appear together in a single grave, they could represent attributes of different social groups or statuses.

Published
2020
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12. The beaker phenomenon and the Genomic transformations of Northwest Europe

Author

Matthew Ferry, Nasreen Broomandkhoshbacht, Anna Endrődi, César Heras Martínez, Balázs Gusztáv Mende, Fraser Brown, András Czene, Morten E. Allentoft, Anna Szécsényi-Nagy, Ian Barnes, Roberto Risch, Milan Kuchařík, Clive Waddington, Benjamin Neil, Róbert Patay, Ignacio Soriano, Jocelyne Desideri, Luc Vergnaud, Gordon Cook, Denise Keating, Francesca Candilio, Karl-Göran Sjögren, Iosif Lazaridis, Kristin Stewardson, Harry Fokkens, Virginia Galera Olmo, Tamás Hajdu, David Caramelli, Aurore Schmitt, Philippe Lefranc, Maya Hoole, Stephany Leach, Megan Michel, Alessandra Modi, Daniel Fernandes, Viktória Kiss, João Luís Cardoso, Václav Smrčka, Swapan Mallick, Zuzana Faltyskova, Wolfgang Haak, Eszter Bánffy, David Billoin, Ron Pinhasi, T. Douglas Price, Ian Armit, Michiel Gazenbeek, Piotr Włodarczak, Eadaoin Harney, Marie Besse, Tim Allen, Douglas J. Kennett, Christopher Evans, Carles Lalueza-Fox, Alessandro Zanini, Selina Brace, Manuel Ángel Rojo Guerra, Philipp W. Stockhammer, Mike Luke, Zsolt Bernert, Peter de Knijff, Richard Mortimer, Michal Ernée, Gill Hey, Emiliano Carnieri, Elżbieta Haduch, Kitti Köhler, Laura Bonsall, João Zilhão, Thomas J. Booth, Mike Parker Pearson, Germán Delibes, Yoan Diekmann, Olivier Lemercier, Iñigo Olalde, János Dani, Eveline Altena, Alistair Barclay, Ken Massy, Sebastiano Tusa, Antonella Valenti, David Reich, Jonas Oppenheimer, Nadin Rohland, Clive Bonsall, Ana Maria Silva, Pierre-Jérôme Rey, Joaquín Lomba Maurandi, Alison Sheridan, Tona Majó, Chris Fowler, Petr Velemínský, Natasha Dodwell, Luigi Lentini, Katina T. Lillios, Miroslav Dobeš, Azucena Avilés Fernández, Olivia Cheronet, Mark G. Thomas, Ana-Mercedes Herrero-Corral, María Haber-Uriarte, Maria Bernabò-Brea, Agata Hałuszko, Ana Bastida Ramírez, Concepción Blasco, Alissa Mittnik, Roberto Menduiña García, Marcus Brittain, Nick Patterson, Tamás Szeniczey, Maksym Mackiewicz, Raúl Flores Fernández, Sophie Carver, Timothy D J Knowles, Volker M Heyd, Rafael Garrido Pena, Arnaud Lefebvre, Kathleen McSweeney, Lindsey Büster, Joël Serralongue, Mirosław Furmanek, Laura Castells Navarro, Kirsten Egging Dinwiddy, Artur Rapiński, Thomas K. Harper, Corina Liesau, Kristian Kristiansen, Barry Cunliffe, Oliver E. Craig, Patricia Ríos, Gabriella Kulcsár, Joan Francès Farré, Pilar Prieto, Jorge Vega de Miguel, Johannes Krause, Saskia Pfrengle, Thomas Higham, Elisa Guerra-Doce, Anthony Denaire, Nick Jowett, Kurt W. Alt, Mark Lipson, Jacqueline I. McKinley, Günter Brücken, Universitat Pompeu Fabra [Barcelona] (UPF), Egham TW20 0EX, Middlesex University, Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft, Harvard School of Public Health, Max Planck Institute for the Science of Human History (MPI-SHH), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], School of Archaeology [Dublin], University College Dublin [Dublin] (UCD), Center for Human and Clinical Genetics, Leiden University Medical Center (LUMC), Institut national de recherches archéologiques préventives (Inrap), Haematology, St James' Institute of Oncology, Etude des Civilisations de l'Antiquité (UMR 7044), Centre National de la Recherche Scientifique (CNRS)-Université Marc Bloch - Strasbourg II-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA)), Department of Psychiatry and Biobehavioral Sciences, University of California [Los Angeles] (UCLA), University of California-University of California-Shirley and Stefan Hatos Center for Neuropharmacology, Archéologie, Terre, Histoire, Sociétés [Dijon] (ARTeHiS), Ministère de la Culture et de la Communication (MCC)-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Institute of Archaeology [Budapest], Research Centre for The Humanities [Budapest], Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Department of Anthropology [University of Vienna], University of Vienna [Vienna], Department of Anthropology, Národní muzeum, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Laboratoire d'archéologie préhistorique et anthropologie, Université de Genève (UNIGE), Instytut Archeologii Uniwersytetu Wrocławskiego, Institute for Health and Consumer Protection, European Commission - Joint Research Centre, Environnements, Dynamiques et Territoires de la Montagne (EDYTEM), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Universidad de Valladolid [Valladolid] (UVa), Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Service archéologique de la Haute-Savoie, Office départemental d'animation culturelle de la Haute-Savoie, University of Minho [Braga], Department of Archaeology and Anthropology, University of Bristol [Bristol], Laboratorio di Antropologia, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Oxford Radiocarbon Accelerator Unit, RLAHA, National Museums of Scotland, Department of Archaeogenetics [Jena] (DAG), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, School of Archaeology, Departament de biologia animal, Universitad de barcelona, Universiteit Leiden-Universiteit Leiden, Étude des Civilisations de l'Antiquité : de la Préhistoire à Byzance (ARCHIMEDE), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université Marc Bloch - Strasbourg II-Centre National de la Recherche Scientifique (CNRS), University of California (UC)-University of California (UC)-Shirley and Stefan Hatos Center for Neuropharmacology, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Université de Genève = University of Geneva (UNIGE), Environnements, Dynamiques et Territoires de Montagne (EDYTEM), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Firenze = University of Florence (UniFI), National Museums Scotland (NMS), Repositório da Universidade de Lisboa, Universitat de Barcelona, Desideri, Jocelyne, and Besse, Marie

Subjects
Male, 0301 basic medicine, Steppe, ADN, Néolithique, Bell Beaker, Arqueologia, Bell Beaker culture, genome wide ancient DNA, 0302 clinical medicine, Archéologie, Phenomenon, ddc:550, 0601 history and archaeology, Suisse, History, Ancient, 0303 health sciences, education.field_of_study, geography.geographical_feature_category, Multidisciplinary, 060102 archaeology, [SDE.IE]Environmental Sciences/Environmental Engineering, Human migration, Préhistoire, Neolithic period, Gene Pool, Genomics, [SHS.GEO]Humanities and Social Sciences/Geography, 06 humanities and the arts, bell Beaker, Europe, Geography, Archaeology, Ceràmica, Ethnology, Mégalithisme, Archaeogenetics, Campaniforme, Pottery, Human Migration, [SDE.MCG]Environmental Sciences/Global Changes, Population, Ancient history, Article, 03 medical and health sciences, Spatio-Temporal Analysis, popular genetics, Bronze Age, Beaker, Cultural Evolution, Neolític, genomics, Humans, DNA, Ancient, education, 030304 developmental biology, Chromosomes, Human, Y, Genome, Human, business.industry, Northwest Europe, Chalcolithic, [SDE.ES]Environmental Sciences/Environmental and Society, Ancient DNA, Genetics, Population, 030104 developmental biology, Haplotypes, Period (geology), Genomic, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, 030217 neurology & neurosurgery
Abstract

Bell Beaker pottery spread across western and central Europe beginning around 2750 BCE before disappearing between 2200–1800 BCE. The mechanism of its expansion is a topic of long-standing debate, with support for both cultural diffusion and human migration. We present new genome-wide ancient DNA data from 170 Neolithic, Copper Age and Bronze Age Europeans, including 100 Beaker-associated individuals. In contrast to the Corded Ware Complex, which has previously been identified as arriving in central Europe following migration from the east, we observe limited genetic affinity between Iberian and central European Beaker Complex-associated individuals, and thus exclude migration as a significant mechanism of spread between these two regions. However, human migration did have an important role in the further dissemination of the Beaker Complex, which we document most clearly in Britain using data from 80 newly reported individuals dating to 3900–1200 BCE. British Neolithic farmers were genetically similar to contemporary populations in continental Europe and in particular to Neolithic Iberians, suggesting that a portion of the farmer ancestry in Britain came from the Mediterranean rather than the Danubian route of farming expansion. Beginning with the Beaker period, and continuing through the Bronze Age, all British individuals harboured high proportions of Steppe ancestry and were genetically closely related to Beaker-associated individuals from the Lower Rhine area. We use these observations to show that the spread of the Beaker Complex to Britain was mediated by migration from the continent that replaced >90% of Britain’s Neolithic gene pool within a few hundred years, continuing the process that brought Steppe ancestry into central and northern Europe 400 years earlier.

Published
2017
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