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

Autor: Ben Krause-Kyora, Jørn Zeiler, Hiba Al-Jarah, Wijerathne Bohingamuwa, Becky Knight, Kinie Esser, Joan Ramon, Chris J. Conroy, Chris Hillman, Beate Böhlendorf-Arslan, Quintana Morales, Tarek Oueslati, Bouthéina Maraoui-Telmini, Jean-Denis Vigne, Nicole Boivin, Jude Perera, Silvia Radbauer, Ardern Hulme-Beaman, G. Adikari, Günther Karl Kunst, Heidi Eager, Sheila Hamilton-Dyer, Jeffrey Fleisher, Thomas Walker, Richard F. Helm, Thomas Cucchi, Terry O'Connor, Alison Crowther, Nimal Perera, Silvia Valenzuela-Lamas, Camilla Speller, Jeremy B. Searle, Arturo Morales-Muñiz, Pavel Gol'din, Anna Linderholm, Nabil Kallala, Alexandra Trinks, Zsófia E. Kovács, He Yu, Johannes Krause, Louisa Gidney, E. V. Gladilina, Wim Van Neer, David Orton, Eréndira M., Alexandra Jamieson, Edward R. Treasure, Joan Sanmartí Grego, Mariana Nabais, Greger Larson, Hanna Kivikero, Inge van der Jagt, Eve Rannamäe, Keith Dobney, Stephanie Wynne-Jones, Henriette Baron, Steven M. Goodman, Kerstin Pasda, René Kyselý
Přispěvatelé: Repositório da Universidade de Lisboa, Yu, He, Jamieson, Alexandra, Hulme-Beaman, Ardern, Conroy, Chris J., Speller, Camilla, Baron, Henriette, Crowther, Alison, Cucchi, Thomas, Fleisher, Jeffrey, Gladilina, Elena, Gol’din, Pavel, Goodman, Steven M., Kunst, Günther Karl, Linderholm, Anna, Morales-Muñiz, Arturo, Nabais, Mariana, Oueslati, Tarek, Quintana Morales, Eréndira M., Rannamäe, Eve, Sanmartí Grego, Joan, Valenzuela-Lamas, Silvia, Neer, Wim Van, Vigne, Jean-Denis, Wynne-Jones, Stephanie, Dobney, Keith, Boivin, Nicole, Searle, Jeremy B., Krause-Kyora, Ben, Krause, Johannes, Larson, Greger, Orton, David, Yu, He [0000-0003-1323-4730], Jamieson, Alexandra [0000-0003-0979-5762], Hulme-Beaman, Ardern [0000-0001-8130-9648], Conroy, Chris J. [0000-0001-7198-9651], Speller, Camilla [0000-0001-7128-9903], Baron, Henriette [0000-0003-4338-3681], Crowther, Alison [0000-0002-2394-1917], Cucchi, Thomas [0000-0001-6021-5001], Fleisher, Jeffrey [0000-0002-6505-9666], Gladilina, Elena [0000-0002-5114-7526], Gol’din, Pavel [0000-0001-6118-1384], Goodman, Steven M. [0000-0001-9318-0570], Kunst, Günther Karl [0000-0002-2175-8641], Linderholm, Anna [0000-0002-1613-9926], Morales-Muñiz, Arturo [0000-0002-9933-6836], Nabais, Mariana [0000-0001-5344-237X], Oueslati, Tarek [0000-0002-2886-085X], Quintana Morales, Eréndira M. [0000-0001-5927-5058], Rannamäe, Eve [0000-0003-1186-5512], Sanmartí Grego, Joan [0000-0002-6635-9249], Valenzuela-Lamas, Silvia [0000-0001-9886-0372], Neer, Wim Van [0000-0003-1710-3623], Vigne, Jean-Denis [0000-0002-7367-7552], Wynne-Jones, Stephanie [0000-0002-3005-8647], Dobney, Keith [0000-0001-9036-4681], Boivin, Nicole [0000-0002-7783-4199], Searle, Jeremy B. [0000-0001-7710-5204], Krause-Kyora, Ben [0000-0001-9435-2872], Krause, Johannes [0000-0001-9144-3920], Larson, Greger [0000-0002-4092-0392], Orton, David [0000-0003-4069-8004], Department of Cultures, Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, Research Laboratory for Archaeology and the History of Art [Oxford], School of Archaeology [Oxford], University of Oxford-University of Oxford, University of Liverpool, Liverpool John Moores University (LJMU), Museum of Vertebrate Zoology [Berkeley], University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, 07745, Germany, School of Social Science, University of Queensland, University of Queensland [Brisbane], Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Rent a Peasant, National Academy of Sciences of Ukraine (NASU), Field Museum of Natural History [Chicago, USA], Histoire, Archéologie et Littérature des Mondes Anciens - UMR 8164 (HALMA), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Open Access funding enabled and organized by Projekt DEAL
Jazyk: angličtina
Rok vydání: 2022
Předmět:
0106 biological sciences
Population genetics
[SDV]Life Sciences [q-bio]
General Physics and Astronomy
01 natural sciences
615 History and Archaeology
[SHS]Humanities and Social Sciences
PHYLOGEOGRAPHY
Max planck institute
PLAGUE
DISPERSAL
0303 health sciences
Multidisciplinary
humanities
Europe
Multidisciplinary Sciences
ALIGNMENT
Archaeology
1181 Ecology
evolutionary biology
language
Science & Technology - Other Topics
Christian ministry
Training program
YERSINIA-PESTIS
[SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory
European black rats
Library science
DNA
Mitochondrial
010603 evolutionary biology
Institutional support
SEQUENCE
General Biochemistry
Genetics and Molecular Biology
Middle East
03 medical and health sciences
Population history
Classical archaeology
Political science
Animals
Humans
030304 developmental biology
Plague
National history
Science & Technology
COVID-19
Excavation
General Chemistry
FRAMEWORK
language.human_language
Rats
Coronavirus
MICE
INDIAN-OCEAN
PATTERNS
Catalan
Zdroj: Digital.CSIC: Repositorio Institucional del CSIC
Consejo Superior de Investigaciones Científicas (CSIC)
Digital.CSIC. Repositorio Institucional del CSIC
instname
Nature Communications
Nature Communications, 2022, 13 (1), pp.2399. ⟨10.1038/s41467-022-30009-z⟩
bioRxiv
ISSN: 2006-0343
2041-1723
Popis: 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 generated a de novo genome assembly of the black rat, 67 ancient black rat mitogenomes and 36 ancient nuclear genomes from sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of mitochondrial DNA 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.
We thank the wet laboratory teams at MPI-SHH, the PalaeoBARN at the University of Oxford and the University of York. We thank David K. James and Lucia Hui of the Alameda County Vector Control Services District for procuring the rat used for the de novo genome. We are grateful to Sarah Nagel at Max Planck Institute for the Evolutionary Anthropology for the single-stranded library preparation, and Dovetail Genomics for the de novo genome assembly service. We thank Maria Spyrou for her suggestions and comments. We acknowledge Ewan Chipping and Helena England (University of York), Carl Phillips, Veronica Lindholm (Ålands Museum), Christine McDonnell and Nienke van Doorn (York Archaeological Trust), Emile Mittendorf (Gemeente Deventer), Inge Riemersma (Archaeological depot, Provincie Zuid-Holland), the Turkish Ministry of Culture & Tourism, Jan Frolík and Iva Herichová (Institute of Archaeology of the Czech Academy of Sciences, Prague), Franz Humer and Eduard Pollhammer (Archaeological Park Carnuntum), Dorottya B. Nyékhelyi and László Daróczi-Szabó (Budapest History Museum), Institut National du Patrimoine (Tunisia), University of Barcelona, Spanish Ministry of Science and Innovation (Project HUM2006-03432/HIST), Spanish Ministry of Culture (program of archaeological excavations abroad 2009); Spanish Agency of International Cooperation for the Development (2009), Catalan Institute of Classical Archaeology (ICAC), Vujadin Ivanisević, Nemanja Marković and Ivan Bugarski (Archaeological Institute 809 Belgrade), the Field Museum Chicago, the British National History Museum and the American Museum of Natural History for providing materials and support. G.L. and A.J. were supported by the ERC (grant ERC-2013-StG-337574-UNDEAD) and A.J. was supported by the Natural Environment Research Council Doctoral Training Program. D.O. was supported by Wellcome (Small Grant in Humanities and Social Science 209817/Z) and the British Academy / Leverhulme Trust (Small Research Grant SG170938). E.R. was supported by Estonian Research Council grant No PRG29. R.K. was supported by the Czech Academy of Sciences institutional support (RVO:67985912). S.V.-L. was supported by the ERC (grant ERC-StG- 716298 ZooMWest). H.E. was funded by an ERC grant (206148) through the Sealinks Project. A.H.B was funded by the Leverhulme Trust (ECF-2017-315). The de novo genome assembly, population genomics study, and radiocarbon dating were funded by the Max Planck Society.
Databáze: OpenAIRE
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