Horses revolutionized human history with fast mobility1. However, the timeline between their domestication and their widespread integration as a means of transport remains contentious2-4. Here we assemble a collection of 475 ancient horse genomes to assess the period when these animals were first reshaped by human agency in Eurasia. We find that reproductive control of the modern domestic lineage emerged around 2200 BCE, through close-kin mating and shortened generation times. Reproductive control emerged following a severe domestication bottleneck starting no earlier than approximately 2700 BCE, and coincided with a sudden expansion across Eurasia that ultimately resulted in the replacement of nearly every local horse lineage. This expansion marked the rise of widespread horse-based mobility in human history, which refutes the commonly held narrative of large horse herds accompanying the massive migration of steppe peoples across Europe around 3000 BCE and earlier3,5. Finally, we detect significantly shortened generation times at Botai around 3500 BCE, a settlement from central Asia associated with corrals and a subsistence economy centred on horses6,7. This supports local horse husbandry before the rise of modern domestic bloodlines.

Ajuntament de Calafell Calafell Spain

Albrecht Daniel Thaer Institute Faculty of Life Sciences Humboldt University Berlin Berlin Germany

Archaeological Research Center and Department of Anthropology and Archaeology National University of Mongolia Ulaanbaatar Mongolia

Archaeology Department Ankara University Ankara Türkiye

Archaeology of Social Dynamics Barcelona Spain

Archéologie des Sociétés Méditeranéennes Archimède IA ANR 11 LABX 0032 01 CNRS UMR 5140 Université Paul Valéry Montpellier France

C Major 20 Norfeu Arqueologia Art i Patrimoni S C La Tallada d'Empordà Spain

Center for Animal Breeding and Genetics Department of Biosystems KU Leuven Leuven Belgium

Central Laboratory Bioarchaeology Laboratory Archaeozoology section University of Tehran Tehran Iran

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

Centre for Applied Bioanthropology Institute for Anthropological Research Zagreb Croatia

Centre for Research on Science and Geological Engineering Universidade Nova de Lisboa Lisbon Portugal

Centre National de Recherche Scientifique Muséum national d'Histoire naturelle Archéozoologie Archéobotanique CP 56 Paris France

Consell Insular d'Eivissa Eivissa Spain

Departament d'Història i Arqueologia Facultat de Geografia i Història Universitat de Barcelona Barcelona Spain

Department for Digitalization and Knowledge Transfer Federal Monuments Authority Austria Vienna Austria

Department for Prehistory Middle Ages and Renaissance National Museum of Denmark Copenhagen K Denmark

Department of Anatomy Histology and Embryology Faculty of Veterinary Medicine University of Zagreb Zagreb Croatia

Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden

Department of Anthropology Alumni Building University of North Carolina at Chapel Hill Chapel Hill NC USA

Department of Archaeological Heritage Preservation Institute of Archaeology of the Russian Academy of Sciences Moscow Russia

Department of Archaeological Monuments State Historical Museum Moscow Russian Federation

Department of Archaeological Science and Conservation Moesgaard Museum Højbjerg Denmark

Department of Archaeology and Heritage Studies Aarhus University Højbjerg Denmark

Department of Archaeology and History University of Exeter Exeter UK

Department of Archaeology Ethnography and Museology Altai State University Barnaul Russia

Department of Archaeology Faculty of Humanities and Social Sciences University of Zagreb Zagreb Croatia

Department of Archaeology History Faculty Vilnius University Vilnius Lithuania

Department of Archaeology Moesgaard Museum Højbjerg Denmark

Department of Archaeology University of York York UK

Department of Biotechnology Abdul Wali Khan University Mardan Pakistan

Department of Earth System Science University of California Irvine CA USA

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

Department of Environmental Sciences Integrative Prehistory and Archaeological Science Basel University Basel Switzerland

Department of Evolutionary Genetics Leibniz Institute for Zoo and Wildlife Research Berlin Germany

Department of Folk Studies and Anthropology Western Kentucky University Bowling Green KY USA

Department of Health Technology Section for Bioinformatics Technical University of Denmark Copenhagen Denmark

Department of History of the Institute of Humanities Ural Federal University Ekaterinburg Russia

Department of Innovation and Technology Ulaanbaatar Science and Technology Park National University of Mongolia Ulaanbaatar Mongolia

Department of Natural Sciences and Archaeometry Institute of Archaeology of the Czech Academy of Sciences Prague Czechia

Department of Prehistory and Western Asian Northeast African Archaeology Austrian Archaeological Institute Vienna Austria

Department of Russian History and Archaeology Samara State University of Social Sciences and Education Samara Russia

Department of Russian Regional Studies National and State confessional Relations Altai State University Barnaul Russia

Department of the Diversity and Evolution of Genomes Institute of Molecular and Cellular Biology Novosibirsk Russia

Dipartimento di Beni Culturali e Ambientali Università degli Studi di Milano Milan Italy

Ecole Nationale Vétérinaire d'Alfort Maisons Alfort France

Ecole Tunisienne d'Histoire et d'Anthropologie Tunis Tunisia

Eurasia Department of the German Archaeological Institute Berlin Germany

Faculdade de Ciências Humanas e Sociais Centro de Estudos de Arqueologia Artes e Ciências do Património Universidade do Algarve Faro Portugal

Faculty of Archaeology Adam Mickiewicz University Poznań Poland

Faculty of Arts and Humanities University of Southampton Southampton UK

Faculty of History University of Oxford Oxford UK

Génomique Métabolique Genoscope Institut François Jacob CEA CNRS Université d'Évry Université Paris Saclay Évry France

Genoscope Institut de Biologie François Jacob CEA CNRS Université d'Évry Université Paris Saclay Évry France

ICAC Tarragona Spain

ICArEHB Campus de Gambelas University of Algarve Faro Portugal

ICREA Catalan Institution for Research and Advanced Studies Barcelona Spain

IEC Institut d'Estudis Catalans Barcelona Spain

Ilok Town Museum Ilok Croatia

Independent researcher Prague Czechia

INRAE Division Ecology and Biodiversity Castanet Tolosan Cedex France

INRAE GeT PlaGe Genotoul Castanet Tolosan France

Institut d'Arqueologia de la Universitat de Barcelona Barcelona Spain

Institut de Biologia Evolutiva Barcelona Spain

Institut de Paléontologie Humaine Fondation Albert Ier Paris UMR 7194 HNHP MNHN CNRS UPVD EPCC Centre Européen de Recherche Préhistorique Tautavel France

Institute for Anthropological Research Zagreb Croatia

Institute for Caucasus Archaeology Nalchik Russian Federation

Institute for Humanities Research and Indigenous Studies of the North Yakutsk Russia

Institute of Animal Breeding and Genetics Department of Biomedical Sciences University of Veterinary Medicine Vienna Vienna Austria

Institute of Archaeology Faculty of History Nicolaus Copernicus University Toruń Poland

Institute of Archaeology Maria Curie Skłodowska University Lublin Poland

Institute of Archaeology Mongolian Academy of Science Ulaanbaatar Mongolia

Institute of Archaeology National Academy of Sciences of Ukraine Kyiv Ukraine

Institute of Archaeology Russian Academy of Sciences Moscow Russia

Institute of the History of Material Culture Russian Academy of Sciences St Petersburg Russia

Kh Ibragimov Complex Institute of the Russian Academy of Sciences Grozny Russia

Kremenetsko Pochaivskii Derzhavnyi Istoriko arkhitekturnyi Zapovidnik Kremenets Ukraine

Laboratory for Archaeological Research Akhmet Baitursynuly Kostanay Regional University Kostanay Kazakhstan

Landesamt für Denkmalpflege und Archäologie Sachsen Anhalt Landesmuseum für Vorgeschichte Halle Germany

Leibniz Zentrum für Archäologie Mainz Germany

Lundbeck Foundation GeoGenetics Centre Globe Institute University of Copenhagen Copenhagen Denmark

Max Planck Institute of Geoanthropology Jena Germany

Mon IberRocs SCL Vilanova i la Geltrú Spain

Mosaïques Archéologie Espace d'activités de la Barthe Cournonterral France

Museu d'Arqueologia de Catalunya Ullastret Spain

Museum of Natural History Vienna Austria

Museum Østjylland Grenaa Denmark

Museum Vestsjælland Holbæk Denmark

Narodni muzej Slovenije Ljubljana Slovenia

Nasledie Cultural Heritage Unit Stavropol Russia

National Institute of Archaeology Hungarian National Museum Budapest Hungary

National Natural History Collections Edmond J Safra Campus Givat Ram The Hebrew University Jerusalem Israel

Osteoarchaeology Practice and Research Center and Department of Anatomy Faculty of Veterinary Medicine Istanbul University Cerrahpaşa Istanbul Türkiye

Östra Greda Research Group Borgholm Sweden

Paleoecology Laboratory Institute of Plant and Animal Ecology Ural Branch of the Russian Academy of Sciences Ekaterinburg Russia

Peter the Great Museum of Anthropology and Ethnography Russian Academy of Sciences St Petersburg Russia

Research Institute and Museum of Anthropology Lomonosov Moscow State University Moscow Russia

School of Archaeology and Ancient History University of Leicester Leicester UK

School of Archaeology University College Dublin Dublin Ireland

Secció de Prehistòria i Arqueologia IAUB Institut d'Arqueologia de la Universitat de Barcelona Barcelona Spain

Smurfit Institute of Genetics Trinity College Dublin Dublin Ireland

Taku Skan Skan Wasakliyapi Global Institute for Traditional Sciences Rapid City SD USA

The Royal Danish Academy Institute of Conservation Copenhagen Denmark

Toraighyrov University Joint Research Center for Archeological Studies Pavlodar Kazakhstan

UMR 5199 De la Préhistoire à l'Actuel Culture Environnement et Anthropologie CNRS Université de Bordeaux Pessac Cédex France

UMR du CNRS 8215 Trajectoires Institut d'Art et Archéologie Paris France

UNIARQ Unidade de Arqueologia Universidade de Lisboa Alameda da Universidade Lisboa Portugal

Universidade Aberta Lisbon Portugal

Université Paris Saclay AgroParisTech INRAE GABI UMR1313 Jouy en Josas France

University of Tunis Institut National du Patrimoine Tunis Tunisia

Vinkovci Municipal Museum Vinkovci Croatia

Zoological institute Department of Environmental Sciences University of Basel Basel Switzerland

Zoological Institute Russian Academy of Sciences St Petersburg Russia

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