This is a repository copy of Ancient DNA suggests modern wolves trace their origin to a late Pleistocene expansion from Beringia. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/154615/ Version: Published Version Article: Loog, Liisa, Thalmann, Olaf, Sinding, Mikkel-Holger S. et al. (33 more authors) (2019) Ancient DNA suggests modern wolves trace their origin to a late Pleistocene expansion from Beringia. Molecular Ecology. ISSN 0962-1083 https://doi.org/10.1111/mec.15329 Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Received: 5 October 2018 | Revised: 16 October 2019 | Accepted: 3 December 2019 DOI: 10.1111/mec.15329 FROM THE COVER Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia Liisa Loog1,2,3,4 | Olaf Thalmann5 | Mikkel-Holger S. Sinding6,7,8 | Verena J. Schuenemann9,10,11 | Angela Perri12 | Mietje Germonpré13 | Herve Bocherens10,14 | Kelsey E. Witt15 | Jose A. Samaniego Castruita6 | Marcela S. Velasco6 | Inge K. C. Lundstrøm6 | Nathan Wales6,16 | Gontran Sonet17 | Laurent Frantz2 | Hannes Schroeder6 | Jane Budd18 | Elodie-Laure Jimenez13 | Sergey Fedorov19 | Boris Gasparyan20 | Andrew W. Kandel21 | Martina Lázničková-Galetová22,23,24 | Hannes Napierala25 | Hans-Peter Uerpmann9 | Pavel A. Nikolskiy26,27 | Elena Y. Pavlova27,28 | Vladimir V. Pitulko27 | Karl-Heinz Herzig5,29 | Ripan S. Malhi30 | Eske Willerslev2,31,32 | Anders J. Hansen8,31 | Keith Dobney33,34,35 | M. Thomas P. Gilbert6,36 | Johannes Krause9,37 | Greger Larson1 | Anders Eriksson2,38,39 | Andrea Manica2 1Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK 2Department of Zoology, University of Cambridge, Cambridge, UK 3Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester, UK 4Department of Genetics, University of Cambridge, Cambridge, UK 5Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland 6EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark 7Natural History Museum, University of Oslo, Oslo, Norway 8The Qimmeq Project, University of Greenland, Nuussuaq, Greenland 9Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany 10Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany 11Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland 12Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 13OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium 14Department of Geosciences, Palaeobiology, University of Tübingen, Tübingen, Germany 15School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA 16BioArch, Department of Archaeology, University of York, York, UK, USA 17OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium 18Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates 19Mammoth Museum, Institute of Applied Ecology of the North of the North-Eastern Federal University, Yakutsk, Russia 20Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Republic of Armenia 21Heidelberg Academy of Sciences and Humanities: The Role of Culture in Early Expansions of Humans, Tübingen, Germany 22Department of Anthropology, University of West Bohemia, Pilzen, Czech Republic 23Moravian museum, Brno, Czech Republic Thalmann, Sinding, and Schuenemann contributed equally to this work. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2019 The Authors. Molecular Ecology published by John Wiley & Sons Ltd Molecular Ecology. 2019;00:1–15. wileyonlinelibrary.com/journal/mec | 1 2 | LOOG ET AL. 24Hrdlička Museum of Man, Faculty of Science, Charles University, Praha, Czech Republic 25Institute of Palaeoanatomy, Domestication Research and History of Veterinary Medicine, Ludwig-Maximilians-University Munich, Munich, Germany 26Geological Institute, Russian Academy of Sciences, Moscow, Russia 27Institute for Material Culture History, Russian Academy of Sciences, St Petersburg, Russia 28Arctic and Antarctic Research Institute, St Petersburg, Russia 29Institute of Biomedicine and Biocenter of Oulu, Medical Research Center and University Hospital, University of Oulu, Oulu, Finland 30Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA 31Centre for GeoGenetics Globe Institute, University of Copenhagen, Copenhagen, Denmark 32Wellcome Trust Sanger Institute, Cambridge, UK 33Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK 34Department of Archaeology, University of Aberdeen, Aberdeen, UK 35Department of Archaeology, Simon Fraser University, Burnaby, BC, Canada 36Norwegian University of Science and Technology, University Museum, Trondheim, Norway 37Max Planck Institute for the Science of Human History, Jena, Germany 38Department of Medical & Molecular Genetics, King's College London, Guys Hospital, London, UK 39cGEM, Institute of Genomics, University of Tartu, Tartu, Estonia Correspondence Liisa Loog, Department of Genetics, Markova,Abstract 2016), and both the palaeontological and archaeological records attest to the continu- University of Cambridge, Cambridge, UK. ousGrey presence wolves of (greyCanis wolves lupus across) are theone Northern of the Hemispherefew large terrestrialfor at least thecarnivores last 300,000 that years have Email: [email protected] (Sotnikovamaintained & Rook, a wide 2010) geographical(reviewed in Appendix distribution S1). This across geogr aphicalthe Nor andthern temporal Hemisphere continuity Greger Larson, Research Laboratory for across the Northern Hemisphere contrasts with analyses of complete modern genomes, which throughout the Pleistocene and Holocene. Recent geneticstudies have suggested Archaeology and History of Art, University have suggested that all contemporary wolves and dogs descend from a common ancestral popula- of Oxford, Oxford, UK. that, despite this continuous presence, major demographic hangesc occurred in wolf tion that existed as recently as 20,000 years ago (Fan et al., 2016; Freedman et al., 2014; Skoglund, Email: [email protected] Ersmark,populations Palkopoulou, between & Dalén, the Late 2015). Pleistocene and early Holocene, and that extant wolves Anders Eriksson, cGEM, Institute of traceThese their analyses ancestry point to aa bottleneck single Late followed Pleistocene by a rapid populati radiationon. Bothfrom anthe ancestral geographical popula- Genomics, University of Tartu, Tartu, Estonia. tionorigin around of thisor just ancestral after the populationLGM. The geographical and how itorigin became and dynamics widespread of thisremain radiation unknown. remain Email: [email protected] unknown.Here, we Resolving used a thesespatially demographic and temporally changes explicit is necessary modell ingfor understandingframework to the analyse ecologi a- cal circumstances that allowed wolves to survive the Late Pleistocene megafaunal extinctions. Andrea Manica, Department of Zoology, data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the University of Cambridge, Cambridge, UK. Furthermore, because dogs were domesticated from Late Pleistocene grey wolves (Larson et al., Northern Hemisphere, spanning the last 50,000 years. Our results suggest that con- Email: [email protected] 2012), a detailed insight into wolf demography during this time period would provide an essential contexttemporary for reconstructing wolf populations the history trace of their dog domestication. ancestry to an expansion from Beringia at the Funding information Russian Science Foundation, Grant/Award endReconstructing of the Last Glacialpast demographic Maximum, events and that solely this from process modern was genomesost m likely is drivenchallenging by Late be- Number: N16-18-10265 RNF; Grantová causePleistocene multiple demographicecological fluctuations histories can thatlead tooccurred similar ge acrossnetic patternsthe Northern in present-day Hemisphere. samples Agentura České Republiky, Grant/Award (Groucutt et al., 2015). Analyses that incorporate ancient DNA sequences can eliminate some of Number: GAČR15-06446S; Polish National This study provides direct ancient genetic evidence that long-range migration has Science Center, Grant/Award Number: theseplayed alternative an important histories role by quantifying in the population changes in history population of agenetic large carnivore, differences and through provides