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.

Academy of Sciences of Sakha Republic Yakutsk Russian Federation

Ancient Genomics Laboratory The Francis Crick Institute London UK

Arctic and Antarctic Research Institute St Petersburg Russian Federation

Biogeology Department of Geosciences University of Tübingen Tübingen Germany

Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288 CNRS Faculté de Médecine Purpan Université Paul Sabatier Toulouse France

Centre for Palaeogenetics Stockholm Sweden

CIAS Department of Life Sciences University of Coimbra Coimbra Portugal

Collections and Research Canadian Museum of Nature Ottawa Ontario Canada

Department of Anthropology University of Nevada Las Vegas Las Vegas NV USA

Department of Archaeology Ethnology and Museology Al Farabi Kazakh State University Almaty Kazakhstan

Department of Archaeology Ghent University Ghent Belgium

Department of Archaeology School of Geosciences University of Aberdeen Aberdeen UK

Department of Archaeology University of Exeter Exeter UK

Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden

Department of Early Prehistory and Quaternary Ecology University of Tübingen Tübingen Germany

Department of Earth Sciences Natural History Museum London UK

Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz CA USA

Department of Evolutionary Anthropology University of Vienna Vienna Austria

Department of Geological Sciences Stockholm University Stockholm Sweden

Department of Geosciences and Geography Faculty of Science University of Helsinki Helsinki Finland

Department of Zoology University of Cambridge Cambridge UK

Estación Biológica de Doñana Sevilla Spain

Evolutionary Adaptive Genomics Institute of Biochemistry and Biology University of Potsdam Potsdam Germany

Genetics Institute University College London London UK

Geological Institute Russian Academy of Sciences Moscow Russian Federation

German Archaeological Institute Berlin Germany

Greenland Institute of Natural Resources Nuuk Greenland

Howard Hughes Medical Institute University of California Santa Cruz Santa Cruz CA USA

Human Evolution and Archaeological Sciences University of Vienna Vienna Austria

Hungarian Natural History Museum Budapest Hungary

Ice Age Museum Shidlovskiy National Alliance 'Ice Age' Moscow Russian Federation

INRAP Metz France

Institute for Archaeological Sciences University of Tübingen Tübingen Germany

Institute for the History of Material Culture Russian Academy of Sciences St Petersburg Russian Federation

Institute of Archaeology and Steppe Civilizations Al Farabi Kazakh National University Almaty Kazakhstan

Institute of Ecology and Evolution University of Bern Bern Switzerland

Institute of Evolutionary Medicine University of Zurich Zurich Switzerland

Max Planck Institute for Evolutionary Anthropology Leipzig Germany

Max Planck Institute for the Science of Human History Jena Germany

Moravian Museum Brno Czech Republic

Museum 'Severnyi Mir' Yakutsk Russian Federation

Museum and Institute of Zoology Polish Academy of Sciences Gdańsk Poland

National Monuments Service Department of Housing Local Government and Heritage Dublin Ireland

Naturhistorisches Museum Bern Bern Switzerland

North Eastern Federal University Yakutsk Russian Federation

Palaeogenomics Group Department of Veterinary Sciences Ludwig Maximilian University Munich Germany

PaleoWest Henderson NV USA

Royal Belgian Institute of Natural Sciences Brussels Belgium

School of Archaeology University College Dublin Dublin Ireland

School of Biological and Behavioural Sciences Queen Mary University of London London UK

School of Biological and Environmental Sciences Liverpool John Moores University Liverpool UK

Senckenberg Centre for Human Evolution and Palaeoenvironment University of Tübingen Tübingen Germany

Service Régional de l'Archéologie Orléans France

Smurfit Institute of Genetics Trinity College Dublin Dublin Ireland

Sobolev Institute of Geology and Mineralogy Siberian Branch of the Russian Academy of Sciences Novosibirsk Russian Federation

Stockholm University Stockholm Sweden

Texas A and M University College Station TX USA

The GLOBE Institute University of Copenhagen Copenhagen Denmark

The Palaeogenomics and Bio Archaeology Research Network Research Laboratory for Archaeology and History of Art University of Oxford Oxford UK

The Qimmeq Project University of Greenland Nuuk Greenland

University Museum NTNU Trondheim Norway

University of Alaska Fairbanks AK USA

University of Leiden Leiden the Netherlands

University of Rennes CNRS ECOBIO UMR 6553 Rennes France

Ural Federal University Yekaterinburg Russian Federation

VNIIOkeangeologiya St Petersburg Russian Federation

Yukon Palaeontology Program Whitehorse Yukon Territories Canada

Zoological Institute of the Russian Academy of Sciences St Petersburg Russian Federation

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