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

Author

Listed:
  • He Yu

    (Max Planck Institute for Evolutionary Anthropology
    Peking University
    Max Planck Institute for the Science of Human History)

  • Alexandra Jamieson

    (University of Oxford)

  • Ardern Hulme-Beaman

    (University of Liverpool
    Liverpool John Moores University)

  • Chris J. Conroy

    (University of California, Berkeley)

  • Becky Knight

    (University of York)

  • Camilla Speller

    (University of York
    University of British Columbia)

  • Hiba Al-Jarah

    (University of York)

  • Heidi Eager

    (Cornell University)

  • Alexandra Trinks

    (University of Oxford
    Institut für Pathologie)

  • Gamini Adikari

    (Postgraduate Institute of Archaeology)

  • Henriette Baron

    (Leibniz-Forschungsinstitut für Archäologie)

  • Beate Böhlendorf-Arslan

    (Philipps University of Marburg)

  • Wijerathne Bohingamuwa

    (University of Ruhuna)

  • Alison Crowther

    (Max Planck Institute for the Science of Human History
    The University of Queensland)

  • Thomas Cucchi

    (National Museum of Natural History (MNHN))

  • Kinie Esser

    (Archeoplan Eco)

  • Jeffrey Fleisher

    (Rice University)

  • Louisa Gidney

    (University of Durham)

  • Elena Gladilina

    (Ukrainian Scientific Center of Ecology of the Sea)

  • Pavel Gol’din

    (National Academy of Sciences of Ukraine)

  • Steven M. Goodman

    (Field Museum of Natural History)

  • Sheila Hamilton-Dyer

    (Bournemouth University (Visiting Fellow))

  • Richard Helm

    (Canterbury Archaeological Trust)

  • Jesse C. Hillman

    (6 Fell View Park, Gosforth, Seascale)

  • Nabil Kallala

    (L’Ecole Tunisienne de l’Histoire et l’Anthropologie
    University of Tunis)

  • Hanna Kivikero

    (University of Helsinki
    University of Stockholm)

  • Zsófia E. Kovács

    (Freelance archaeozoologist, Liliom u. 4. 1/1)

  • Günther Karl Kunst

    (University of Vienna)

  • René Kyselý

    (Institute of Archaeology of the Czech Academy of Sciences, Prague)

  • Anna Linderholm

    (University of Oxford
    Stockholm University)

  • Bouthéina Maraoui-Telmini

    (Institut National de Patrimoine)

  • Nemanja Marković

    (Institute of Archaeology)

  • Arturo Morales-Muñiz

    (Universidad Autónoma de Madrid)

  • Mariana Nabais

    (University College London
    Universidade de Lisboa)

  • Terry O’Connor

    (University of York)

  • Tarek Oueslati

    (University of Lille)

  • Eréndira M. Quintana Morales

    (University of California, Santa Cruz)

  • Kerstin Pasda

    (Friedrich-Alexander-University of Erlangen-Nürnberg)

  • Jude Perera

    (Sir Marcus Fernando Mawatha)

  • Nimal Perera

    (Sir Marcus Fernando Mawatha)

  • Silvia Radbauer

    (Austrian Archaeological Institute)

  • Joan Ramon

    (Consell Insular d’Eivissa i Formentera)

  • Eve Rannamäe

    (University of Tartu)

  • Joan Sanmartí Grego

    (University of Barcelona)

  • Edward Treasure

    (Durham University)

  • Silvia Valenzuela-Lamas

    (IMF-CSIC)

  • Inge Jagt

    (Cultural Heritage Agency of the Netherlands)

  • Wim Neer

    (Royal Belgian Institute of Natural Sciences
    Katholieke Universiteit Leuven)

  • Jean-Denis Vigne

    (National Museum of Natural History (MNHN))

  • Thomas Walker

    (University of Reading)

  • Stephanie Wynne-Jones

    (University of York)

  • Jørn Zeiler

    (ArchaeoBone)

  • Keith Dobney

    (University of Liverpool
    University of Sydney
    University of Aberdeen
    Simon Fraser University)

  • Nicole Boivin

    (Max Planck Institute for the Science of Human History
    The University of Queensland)

  • Jeremy B. Searle

    (Cornell University)

  • Ben Krause-Kyora

    (Kiel University)

  • Johannes Krause

    (Max Planck Institute for Evolutionary Anthropology
    Max Planck Institute for the Science of Human History)

  • Greger Larson

    (University of Oxford)

  • David Orton

    (University of York)

Abstract

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.

Suggested Citation

  • He Yu & Alexandra Jamieson & Ardern Hulme-Beaman & Chris J. Conroy & Becky Knight & Camilla Speller & Hiba Al-Jarah & Heidi Eager & Alexandra Trinks & Gamini Adikari & Henriette Baron & Beate Böhlendo, 2022. "Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30009-z
    DOI: 10.1038/s41467-022-30009-z
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    References listed on IDEAS

    as
    1. Joseph K Pickrell & Jonathan K Pritchard, 2012. "Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data," PLOS Genetics, Public Library of Science, vol. 8(11), pages 1-17, November.
    2. Heng Li & Richard Durbin, 2011. "Inference of human population history from individual whole-genome sequences," Nature, Nature, vol. 475(7357), pages 493-496, July.
    3. Wickham, Chris, 2005. "Framing the Early Middle Ages: Europe and the Mediterranean, 400-800," OUP Catalogue, Oxford University Press, number 9780199264490, Decembrie.
    4. Thomas Walker & Janet Ridout Sharpe & Hazel Williams, 2021. "Barn Owls and Black Rats from a Rural Roman Villa at Gatehampton, South Oxfordshire," Environmental Archaeology, Taylor & Francis Journals, vol. 26(5), pages 487-496, September.
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