1. Grey wolf genomic history reveals a dual ancestry of dogs
- Author
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Anders Bergström, David W. G. Stanton, Ulrike H. Taron, Laurent Frantz, Mikkel-Holger S. Sinding, Erik Ersmark, Saskia Pfrengle, Molly Cassatt-Johnstone, Ophélie Lebrasseur, Linus Girdland-Flink, Daniel M. Fernandes, Morgane Ollivier, Leo Speidel, Shyam Gopalakrishnan, Michael V. Westbury, Jazmin Ramos-Madrigal, Tatiana R. Feuerborn, Ella Reiter, Joscha Gretzinger, Susanne C. Münzel, Pooja Swali, Nicholas J. Conard, Christian Carøe, James Haile, Anna Linderholm, Semyon Androsov, Ian Barnes, Chris Baumann, Norbert Benecke, Hervé Bocherens, Selina Brace, Ruth F. Carden, Dorothée G. Drucker, Sergey Fedorov, Mihály Gasparik, Mietje Germonpré, Semyon Grigoriev, Pam Groves, Stefan T. Hertwig, Varvara V. Ivanova, Luc Janssens, Richard P. Jennings, Aleksei K. Kasparov, Irina V. Kirillova, Islam Kurmaniyazov, Yaroslav V. Kuzmin, Pavel A. Kosintsev, Martina Lázničková-Galetová, Charlotte Leduc, Pavel Nikolskiy, Marc Nussbaumer, Cóilín O’Drisceoil, Ludovic Orlando, Alan Outram, Elena Y. Pavlova, Angela R. Perri, Małgorzata Pilot, Vladimir V. Pitulko, Valerii V. Plotnikov, Albert V. Protopopov, André Rehazek, Mikhail Sablin, Andaine Seguin-Orlando, Jan Storå, Christian Verjux, Victor F. Zaibert, Grant Zazula, Philippe Crombé, Anders J. Hansen, Eske Willerslev, Jennifer A. Leonard, Anders Götherström, Ron Pinhasi, Verena J. Schuenemann, Michael Hofreiter, M. Thomas P. Gilbert, Beth Shapiro, Greger Larson, Johannes Krause, Love Dalén, Pontus Skoglund, Bergström, Anders [0000-0002-4096-9268], Frantz, Laurent [0000-0001-8030-3885], Sinding, Mikkel-Holger S [0000-0003-1371-219X], Lebrasseur, Ophélie [0000-0003-0687-8538], Fernandes, Daniel M [0000-0002-7434-6552], Ollivier, Morgane [0000-0002-8361-4221], Westbury, Michael V [0000-0003-0478-3930], Ramos-Madrigal, Jazmin [0000-0002-1661-7991], Feuerborn, Tatiana R [0000-0003-1610-3402], Conard, Nicholas J [0000-0002-4633-0385], Haile, James [0000-0002-8521-8337], Linderholm, Anna [0000-0002-1613-9926], Barnes, Ian [0000-0001-8322-6918], Baumann, Chris [0000-0002-1001-8621], Bocherens, Hervé [0000-0002-0494-0126], Brace, Selina [0000-0003-2126-6732], Drucker, Dorothée G [0000-0003-0854-4371], Germonpré, Mietje [0000-0001-8865-0937], Jennings, Richard P [0000-0001-9996-7518], Kuzmin, Yaroslav V [0000-0002-4512-2269], Orlando, Ludovic [0000-0003-3936-1850], Outram, Alan [0000-0003-3360-089X], Perri, Angela R [0000-0002-4349-1060], Plotnikov, Valerii V [0000-0002-4870-3499], Sablin, Mikhail [0000-0002-2773-7454], Crombé, Philippe [0000-0002-4198-8057], Hansen, Anders J [0000-0002-1890-2702], Willerslev, Eske [0000-0002-7081-6748], Leonard, Jennifer A [0000-0003-0291-7819], Pinhasi, Ron [0000-0003-1629-8131], Shapiro, Beth [0000-0002-2733-7776], Larson, Greger [0000-0002-4092-0392], Krause, Johannes [0000-0001-9144-3920], Dalén, Love [0000-0001-8270-7613], Skoglund, Pontus [0000-0002-3021-5913], Apollo - University of Cambridge Repository, The Francis Crick Institute [London], Swedish Museum of Natural History (NRM), Ludwig Maximilian University [Munich] (LMU), University of Copenhagen = Københavns Universitet (UCPH), Trinity College Dublin, University of Greenland, University of Tübingen, University of Oxford, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), University College of London [London] (UCL), IT University of Copenhagen (ITU), Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Texas A&M University System, Stockholm University, Natural History Museum [Oslo], University of Oslo (UiO), German Archaeological Institute (DAI), The Natural History Museum [London] (NHM), UCD School of Biology and Environmental Science, UCD, Royal Belgian Institute of Natural Sciences (RBINS), North-Eastern Federal University, School of Archaeology, Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Centre d'anthropologie et de génomique de Toulouse (CAGT), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), University of Vienna [Vienna], Max Planck Institute for Evolutionary Anthropology [Leipzig], This work was supported by grants to P. Skoglund from the European Research Council (grant no. 852558), the Erik Philip Sörensen Foundation and the Science for Life Laboratory, Swedish Biodiversity Program, made available by support from the Knut and Alice Wallenberg Foundation. A.B., L.S., P. Swali and P. Skoglund were supported by Francis Crick Institute core funding (FC001595) from Cancer Research UK, the UK Medical Research Council and the Wellcome Trust. P. Skoglund was also supported by the Vallee Foundation, the European Molecular Biology Organisation and the Wellcome Trust (217223/Z/19/Z). Computations were supported by SNIC-UPPMAX. We also acknowledge support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council and the Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We thank the Yukon gold mining community and First Nations, including the Tr’ondëk Hwëch’in, for continued support of our palaeontology research in the Yukon Territories, Canada. We thank the Danish National High-Throughput Sequencing Centre and BGI-Europe for assistance in sequencing data generation and the Danish National Supercomputer for Life Sciences–Computerome (https://computerome.dtu.dk) for computational resources. We thank National Museum Wales for continued sampling support. M. Germonpré acknowledges support from the Brain.be 2.0 ICHIE project (BELSPO B2/191/P2/ICHIE). M.T.P.G. was supported by the European Research Council (grant no. 681396). M.-H.S.S. was supported by the Velux Foundations through the Qimmeq Project, the Aage og Johanne Louis-Hansens Fond and the Independent Research Fund Denmark (8028-00005B). L.D. acknowledges support from FORMAS (2018-01640). D.W.G.S. received funding for this project from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 796877. M.P. was supported by the Polish National Agency for Academic Exchange–NAWA (grant no. PPN/PPO/2018/1/00037). V.J.S. was supported by the University of Zurich’s University Research Priority Program ‘Evolution in Action: From Genomes to Ecosystems’. This research was done with the participation of ZIN RAS (grant no. 075-15-2021-1069). We are grateful to the museum of the Institute of Plant and Animal Ecology UB RAS (Ekaterinburg, Russia) for provision of samples. R.P.J. and C.O’D. were supported by the Standing Committee for Archaeology of the Royal Irish Academy through the Archaeological Excavation Research Grant Scheme. E.Y.P., P.N. and V.V.P. are supported by the Russian Science Foundation (grant no. 16-18-10265-RNF and 21-18-00457-RNF). Y.V.K. was supported by the Russian Science Foundation (grant no. 20-17-00033). M.H. was supported by the European Research Council (consolidator grant GeneFlow no. 310763). M.L.-G. was supported by the Czech Science Foundation GAČR (grant no. 15-06446S) and institutional financing of the Moravian Museum from the Czech Ministry of Culture (IP DKRVO 2019-2023, MK000094862). L.S. is supported by the Sir Henry Wellcome fellowship (220457/Z/20/Z). We thank Staatliches Museum für Naturkunde Stuttgart for sample access. L.F. and G.L. were supported by European Research Council grants (ERC-2013-StG-337574-UNDEAD and ERC-2019-StG-853272-PALAEOFARM) and Natural Environmental Research Council grants (NE/K005243/1, NE/K003259/1, NE/S007067/1 and NE/S00078X/1). L.F. was also supported by the Wellcome Trust (210119/Z/18/Z). This research was funded in whole, or in part, by the Wellcome Trust (FC001595). For the purpose of open access, the author has applied a CC-BY public copyright licence to any author accepted manuscript version arising from this submission., Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Department of Geosciences and Geography, and Faculty of Science
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History ,RUSSIAN FEDERATION ,631/158/2464 ,CANIS LUPUS ,ANIMAL EXPERIMENT ,Domestication ,Ecology,Evolution & Ethology ,MIDDLE EAST ,DOG ,History, Ancient ,Phylogeny ,CANID ,WOLF ,Multidisciplinary ,Genome ,ORIGIN ,article ,45/77 ,Genomics ,CC ,ADMIXTURE ,CONTAMINATION ,Europe ,GENOME ,EXTINCTION ,DOGS ,COMPLETE MITOCHONDRIAL GENOME ,Genetics & Genomics ,NATURAL SELECTION ,1171 Geosciences ,AFRICA ,EUROPE ,NORTH AMERICA ,GENETICS ,SIBERIA ,General Science & Technology ,PHYLOGENY ,PLEISTOCENE ,LIBRARY PREPARATION ,45/23 ,Infectious Disease ,ANCESTRY ,SEQUENCE ,EURASIA ,Ancient ,TIME SERIES ANALYSIS ,631/181/27 ,Middle East ,QH301 ,Dogs ,UPPER PLEISTOCENE ,Genetic ,EVOLUTIONARY HISTORY ,WOLVES ,GENE MUTATION ,ANCIENT DNA ,Animals ,NONHUMAN ,631/181/457 ,DNA, Ancient ,Selection, Genetic ,ARTICLE ,Selection ,QH426 ,QL ,Wolves ,History and Archaeology ,Tumor Suppressor Proteins ,ANIMALS ,Biology and Life Sciences ,DNA ,ANIMAL ,GENE ,Siberia ,CONTROLLED STUDY ,DOMESTICATION ,631/181/2474 ,Africa ,Mutation ,North America ,570 Life sciences ,biology ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,GENOMICS - Abstract
The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located. © 2022, The Author(s). 8028-00005B; IP DKRVO 2019-2023, MK000094862; 220457/Z/20/Z, ERC-2013-StG-337574-UNDEAD, ERC-2019-StG-853272-PALAEOFARM; 075-15-2021-1069; European Molecular Biology Organization, EMBO: 217223/Z/19/Z; Vallee Foundation; Velux Fonden; Wellcome Trust, WT; Francis Crick Institute, FCI: FC001595; Horizon 2020 Framework Programme, H2020: 796877; Medical Research Council, MRC; Natural Environment Research Council, NERC: 210119/Z/18/Z, NE/K003259/1, NE/K005243/1, NE/S00078X/1, NE/S007067/1; Cancer Research UK, CRUK; European Research Council, ERC: 852558; Grantová Agentura České Republiky, GA ČR: 15-06446S; Svenska Forskningsrådet Formas: 2018-01640; Knut och Alice Wallenbergs Stiftelse; Vetenskapsrådet, VR: 681396, BELSPO B2/191/P2/ICHIE; Russian Science Foundation, RSF: 16-18-10265-RNF, 20-17-00033, 21-18-00457-RNF, 310763; Science for Life Laboratory, SciLifeLab; Narodowa Agencja Wymiany Akademickiej, NAWA: PPN/PPO/2018/1/00037 This work was supported by grants to P. Skoglund from the European Research Council (grant no. 852558), the Erik Philip Sörensen Foundation and the Science for Life Laboratory, Swedish Biodiversity Program, made available by support from the Knut and Alice Wallenberg Foundation. A.B., L.S., P. Swali and P. Skoglund were supported by Francis Crick Institute core funding (FC001595) from Cancer Research UK, the UK Medical Research Council and the Wellcome Trust. P. Skoglund was also supported by the Vallee Foundation, the European Molecular Biology Organisation and the Wellcome Trust (217223/Z/19/Z). Computations were supported by SNIC-UPPMAX. We also acknowledge support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council and the Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We thank the Yukon gold mining community and First Nations, including the Tr’ondëk Hwëch’in, for continued support of our palaeontology research in the Yukon Territories, Canada. We thank the Danish National High-Throughput Sequencing Centre and BGI-Europe for assistance in sequencing data generation and the Danish National Supercomputer for Life Sciences–Computerome ( https://computerome.dtu.dk ) for computational resources. We thank National Museum Wales for continued sampling support. M. Germonpré acknowledges support from the Brain.be 2.0 ICHIE project (BELSPO B2/191/P2/ICHIE). M.T.P.G. was supported by the European Research Council (grant no. 681396). M.-H.S.S. was supported by the Velux Foundations through the Qimmeq Project, the Aage og Johanne Louis-Hansens Fond and the Independent Research Fund Denmark (8028-00005B). L.D. acknowledges support from FORMAS (2018-01640). D.W.G.S. received funding for this project from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 796877. M.P. was supported by the Polish National Agency for Academic Exchange–NAWA (grant no. PPN/PPO/2018/1/00037). V.J.S. was supported by the University of Zurich’s University Research Priority Program ‘Evolution in Action: From Genomes to Ecosystems’. This research was done with the participation of ZIN RAS (grant no. 075-15-2021-1069). We are grateful to the museum of the Institute of Plant and Animal Ecology UB RAS (Ekaterinburg, Russia) for provision of samples. R.P.J. and C.O’D. were supported by the Standing Committee for Archaeology of the Royal Irish Academy through the Archaeological Excavation Research Grant Scheme. E.Y.P., P.N. and V.V.P. are supported by the Russian Science Foundation (grant no. 16-18-10265-RNF and 21-18-00457-RNF). Y.V.K. was supported by the Russian Science Foundation (grant no. 20-17-00033). M.H. was supported by the European Research Council (consolidator grant GeneFlow no. 310763). M.L.-G. was supported by the Czech Science Foundation GAČR (grant no. 15-06446S) and institutional financing of the Moravian Museum from the Czech Ministry of Culture (IP DKRVO 2019-2023, MK000094862). L.S. is supported by the Sir Henry Wellcome fellowship (220457/Z/20/Z). We thank Staatliches Museum für Naturkunde Stuttgart for sample access. L.F. and G.L. were supported by European Research Council grants (ERC-2013-StG-337574-UNDEAD and ERC-2019-StG-853272-PALAEOFARM) and Natural Environmental Research Council grants (NE/K005243/1, NE/K003259/1, NE/S007067/1 and NE/S00078X/1). L.F. was also supported by the Wellcome Trust (210119/Z/18/Z). This research was funded in whole, or in part, by the Wellcome Trust (FC001595). For the purpose of open access, the author has applied a CC-BY public copyright licence to any author accepted manuscript version arising from this submission.
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- 2022
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