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

He Yu 1 Alexandra Jamieson 2 Ardern Hulme-Beaman 3, 4 Chris Conroy 5 Becky Knight Camilla Speller Hiba Al-Jarah Heidi Eager Alexandra Trinks Gamini Adikari Henriette Baron Beate Böhlendorf-Arslan Wijerathne Bohingamuwa Alison Crowther 6, 7 Thomas Cucchi 8 Kinie Esser Jeffrey Fleisher Louisa Gidney 9 Elena Gladilina Pavel Gol’din 10 Steven Goodman 11 Sheila Hamilton-Dyer Richard Helm Jesse Hillman Nabil Kallala Hanna Kivikero Zsófia Kovács Günther Karl Kunst René Kyselý Anna Linderholm Bouthéina Maraoui-Telmini Nemanja Marković Arturo Morales-Muñiz Mariana Nabais Terry O’connor Tarek Oueslati 12 Eréndira Quintana Morales Kerstin Pasda Jude Perera Nimal Perera Silvia Radbauer Joan Ramon Eve Rannamäe Joan Sanmartí Grego Edward Treasure Silvia Valenzuela-Lamas Inge van der Jagt Wim van Neer Jean-Denis Vigne 8 Thomas Walker Stephanie Wynne-Jones Jørn Zeiler Keith Dobney Nicole Boivin Jeremy Searle Ben Krause-Kyora Johannes Krause Greger Larson David Orton 
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.
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Submitted on : Thursday, November 24, 2022 - 2:13:44 PM
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He Yu, Alexandra Jamieson, Ardern Hulme-Beaman, Chris Conroy, Becky Knight, et al.. Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history. Nature Communications, 2022, 13 (1), pp.2399. ⟨10.1038/s41467-022-30009-z⟩. ⟨hal-03659617⟩



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