The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we first generate a de novo genome assembly of the black rat. We then sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of our newly reported sequences, together with published mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.

ArchaeoBone Blekenweg 61 9753 JN Haren The Netherlands

Archaeological Services University of Durham Durham UK

Archaeology of Social Dynamics IMF CSIC Barcelona 08001 Spain

Archaeozoology Archaeobotany Societies Practices Environments Paris France

Archeoplan Eco 2616 LZ Delft Netherlands

Austrian Academy of Sciences Austrian Archaeological Institute Hollandstraße 11 13 1020 Vienna Austria

BioArCh Department of Archaeology University of York York YO1 7EP UK

Canterbury Archaeological Trust 92a Broad Street Canterbury Kent CT1 2LU UK

Centre for Palaeogenetics and Department of Geological Sciences Stockholm University Stockholm 10691 Sweden

Centre National de la Recherche Scientifique University of Lille Lille France

Centro de Arqueologia da Universidade de Lisboa Faculdade de Letras Universidade de Lisboa 1600 214 Lisboa Portugal

Charité Universitätsmedizin Berlin Institut für Pathologie Charitéplatz 1 10117 Berlin Germany

Christian Archaeology and Byzantine Art History Philipps University of Marburg 35037 Marburg Germany

Consell Insular d'Eivissa i Formentera Avenida de España 49 07800 Eivissa Illes Balears Spain

Cultural Heritage Agency of the Netherlands Smallepad 5 3811 MG Amersfoort The Netherlands

Department of Anthropology Rice University 6100 Main St Houston TX 77005 USA

Department of Anthropology University of British Columbia Vancouver BC Canada

Department of Anthropology University of California Santa Cruz 1156 High St Santa Cruz CA 95064 USA

Department of Archaeogenetics Max Planck Institute for Evolutionary Anthropology 04103 Leipzig Germany

Department of Archaeogenetics Max Planck Institute for the Science of Human History 07745 Jena Germany

Department of Archaeology and Anthropology Bournemouth University Poole BH12 5BB UK

Department of Archaeology Classics and Egyptology University of Liverpool Liverpool L69 7WZ UK

Department of Archaeology Durham University Durham UK

Department of Archaeology Institute of History and Archaeology University of Tartu 2 Jakobi St 51005 Tartu Estonia

Department of Archaeology Max Planck Institute for the Science of Human History 07745 Jena Germany

Department of Archaeology Simon Fraser University Burnaby BC V5 1S6 Canada

Department of Archaeology Sir Marcus Fernando Mawatha Colombo 07 Sri Lanka

Department of Archaeology University of Aberdeen Aberdeen AB24 3UF UK

Department of Archaeology University of Reading Berkshire RG6 6AB UK

Department of Archaeology University of Sydney Sydney NSW 2006 Australia

Department of Archaeology University of York York YO1 7EP UK

Department of Culture University of Helsinki P O Box 59 FI 00014 Helsinki Finland

Department of Ecology and Evolutionary Biology Cornell University Ithaca NY 14853 USA

Department of History and Archaeology University of Ruhuna Matara 81000 Sri Lanka

Department of Natural Sciences and Archaeometry Institute of Archaeology of the Czech Academy of Sciences Prague Letenská 4 118 01 Prague Czech Republic

Department of Philosophy Institute of Prehistoric Archaeology Friedrich Alexander University of Erlangen Nürnberg 91054 Erlangen Germany

Departmento de Biología Universidad Autónoma de Madrid 28049 Madrid Spain

Fell View Park Gosforth Seascale Cumbria CA20 1HY UK

Freelance archaeozoologist Liliom u 4 1 1 Balatonfüred 8230 Hungary

Institut National de Patrimoine Tunis 1008 Tunisia

Institute of Archaeology 11000 Belgrade Serbia

Institute of Archaeology University College London London WC1H 0PY UK

Institute of Clinical Molecular Biology Kiel University Kiel 24105 Germany

L'Ecole Tunisienne de l'Histoire et l'Anthropologie Tunis Tunisia

Laboratory of Biodiversity and Evolutionary Genomics Katholieke Universiteit Leuven 3000 Leuven Belgium

Museum of Vertebrate Zoology University of California Berkeley Berkeley CA 94720 3160 USA

Negaunee Integrative Research Center Field Museum of Natural History Chicago IL 60605 USA

Osteological Research Laboratory University of Stockholm 10691 Stockholm Sweden

Palaeogenomics and Bio Archaeology Research Network Research Laboratory for Archaeology and History of Art University of Oxford Oxford OX1 3QY UK

Postgraduate Institute of Archaeology 407 Bauddhaloka Mawatha Colombo 7 Sri Lanka

Research Centre in Evolutionary Anthropology and Palaeoecology Liverpool John Moores University Liverpool L3 3AF UK

Römisch Germanisches Zentralmuseum Leibniz Forschungsinstitut für Archäologie Ernst Ludwig Platz 2 55116 Mainz Germany

Royal Belgian Institute of Natural Sciences Vautierstraat 29 1000 Brussels Belgium

Schmalhausen Institute of Zoology National Academy of Sciences of Ukraine Kyiv 01030 Ukraine

School of Life Sciences Peking University 100871 Beijing China

School of Social Science The University of Queensland St Lucia QLD Australia

Secció de Prehistòria i Arqueologia University of Barcelona Barcelona Spain

Ukrainian Scientific Center of Ecology of the Sea Odessa 65009 Ukraine

University of Tunis Tunis Tunisia

VIAS Vienna Institute for Archaeological Science University of Vienna Althanstraße 14 1090 Vienna Austria

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