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

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 Böhlendorf-Arslan, Wijerathne Bohingamuwa, Alison Crowther, Thomas Cucchi, Kinie Esser, Jeffrey Fleisher, Louisa Gidney, Elena Gladilina, Pavel Gol’din, Steven M. Goodman, Sheila Hamilton-Dyer, Richard Helm, Jesse C. Hillman, Nabil Kallala, Hanna Kivikero, Zsófia E. Kovács, Günther Karl Kunst, René Kyselý, Anna Linderholm, Bouthéina Maraoui-Telmini, Nemanja Marković, Arturo Morales-Muñiz, Mariana Nabais, Terry O’Connor, Tarek Oueslati, Eréndira M. Quintana Morales, Kerstin Pasda, Jude Perera, Nimal Perera, Silvia Radbauer, Joan Ramon, Eve Rannamäe, Joan Sanmartí Grego, Edward Treasure, Silvia Valenzuela-Lamas, Inge Jagt, Wim Neer, Jean-Denis Vigne, Thomas Walker, Stephanie Wynne-Jones, Jørn Zeiler, Keith Dobney, Nicole Boivin, Jeremy B. Searle, Ben Krause-Kyora, Johannes Krause (), Greger Larson () and David Orton ()
Additional contact information
He Yu: Max Planck Institute for Evolutionary Anthropology
Alexandra Jamieson: University of Oxford
Ardern Hulme-Beaman: University of Liverpool
Chris J. Conroy: University of California, Berkeley
Becky Knight: University of York
Camilla Speller: University of York
Hiba Al-Jarah: University of York
Heidi Eager: Cornell University
Alexandra Trinks: University of Oxford
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
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
Hanna Kivikero: University of Helsinki
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
Bouthéina Maraoui-Telmini: Institut National de Patrimoine
Nemanja Marković: Institute of Archaeology
Arturo Morales-Muñiz: Universidad Autónoma de Madrid
Mariana Nabais: University College London
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
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
Nicole Boivin: Max Planck Institute for the Science of Human History
Jeremy B. Searle: Cornell University
Ben Krause-Kyora: Kiel University
Johannes Krause: Max Planck Institute for Evolutionary Anthropology
Greger Larson: University of Oxford
David Orton: University of York

Nature Communications, 2022, vol. 13, issue 1, 1-13

Abstract: 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.

Date: 2022
References: View references in EconPapers View complete reference list from CitEc
Citations: View citations in EconPapers (1)

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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30009-z

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DOI: 10.1038/s41467-022-30009-z

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