Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

Yu H, Jamieson A, Hulme-Beaman A, Conroy CJ, Knight B, Speller C, Al-Jarah H, Eager H, Trinks A, Adikari G, Baron H, Boehlendorf-Arslan B, Bohingamuwa W, Crowther A, Cucchi T, Esser K, Fleisher J, Gidney L, Gladilina E, Gol'Din P, Goodman SM, Hamilton-Dyer S, Helm R, Hillman C, Kallala N, Kivikero H, Kovacs ZE, Kunst GK, Kysely R, Linderholm A, Maraoui-Telmini B, Markovic N, Morales-Muniz A, Nabais M, O'Connor T, Oueslati T, Morales EMQ, Pasda K, Perera J, Perera N, Radbauer S, Ramon J, Rannamae E, Grego JS, Treasure E, Valenzuela-Lamas S, Van Der Jagt I, Van Neer W, Vigne JD, Walker T, Wynne-Jones S, Zeiler J, Dobney K, Boivin N, Searle JB, Krause-Kyora B, Krause J, Larson G, Orton D (2022)

Publication Type: Journal article

Publication year: 2022


Book Volume: 13

Article Number: 2399

Journal Issue: 1

DOI: 10.1038/s41467-022-30009-z


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.

Authors with CRIS profile

Involved external institutions

Max Planck Institute for Evolutionary Anthropology / Max-Planck-Institut für evolutionäre Anthropologie DE Germany (DE) University of Oxford GB United Kingdom (GB) The University of Liverpool GB United Kingdom (GB) University of California, Berkeley US United States (USA) (US) University of York GB United Kingdom (GB) Philipps-Universität Marburg DE Germany (DE) Ukrainian Scientific Center of Ecology of the Sea (UkrSCES) / Український науковий центр екології моря (УкрНЦЕМ) UA Ukraine (UA) Universidad Autónoma de Madrid (UAM) ES Spain (ES) University College London (UCL) GB United Kingdom (GB) LILLE 1 University - Science and Technology FR France (FR) University of California Santa Cruz US United States (USA) (US) Österreichische Akademie der Wissenschaften AT Austria (AT) University of Tartu EE Estonia (EE) Universitat de Barcelona (UB) / University of Barcelona ES Spain (ES) Durham University GB United Kingdom (GB) Institucion Mila y Fontanals ES Spain (ES) Cultural Heritage Agency of the Netherlands NL Netherlands (NL) University of Kelaniya LK Sri Lanka (LK) Römisch-Germanisches Zentralmuseum - Leibniz-Forschungsinstitut für Archäologie (RGZM) DE Germany (DE) Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (MPG) / Max Planck Society for the Advancement of Science DE Germany (DE) Muséum National d’Histoire Naturelle (MNHN) FR France (FR) Archeoplan Eco NL Netherlands (NL) Rice University US United States (USA) (US) Field Museum of Natural History US United States (USA) (US) Bournemouth University GB United Kingdom (GB) Helsingin yliopisto / University of Helsinki FI Finland (FI) Academy of Sciences of the Czech Republic (ASCR) / Akademie věd České republiky (AVČR) CZ Czech Republic (CZ) Université de Tunis / جامعة تونس‎ TN Tunisia (TN) ArchaeoBone NL Netherlands (NL) Cornell University US United States (USA) (US) Christian-Albrechts-Universität zu Kiel DE Germany (DE) University of Ruhuna / රුහුණ විශ්වවිද්‍යාලය, රෝහණ සරසවිය LK Sri Lanka (LK) National Academy of Sciences of Ukraine (NAN) / Національна академія наук України UA Ukraine (UA) Universität Wien / University of Vienna AT Austria (AT) University of Reading GB United Kingdom (GB) Canterbury Archaeological Trust GB United Kingdom (GB) Royal Belgian Institute of Natural Sciences BE Belgium (BE)

How to cite


Yu, H., Jamieson, A., Hulme-Beaman, A., Conroy, C.J., Knight, B., Speller, C.,... Orton, D. (2022). Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history. Nature Communications, 13(1).


Yu, He, et al. "Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history." Nature Communications 13.1 (2022).

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