Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history
Authors
Yu, HeJamieson, Alexandra
Hulme-Beaman, Ardern
Conroy, Chris J.
Knight, Becky
Speller, Camilla
Al-Jarah, Hiba
Eager, Heidi
Trinks, Alexandra
Adikari, Gamini
Baron, Henriette

Böhlendorf-Arslan, Beate
Bohingamuwa, Wijerathne
Crowther, Alison
Cucchi, Thomas
Esser, Kinie
Fleisher, Jeffrey
Gidney, Louisa
Gladilina, Elena
Gol’din, Pavel
Goodman, Steven M.
Hamilton-Dyer, Sheila
Helm, Richard
Hillman, Jesse C.
Kallala, Nabil
Kivikero, Hanna
Kovács, Zsófia E.
Kunst, Günther Karl
Kyselý, René
Linderholm, Anna
Maraoui-Telmini, Bouthéina
Marković, Nemanja

Morales-Muñiz, Arturo
Nabais, Mariana
O’Connor, Terry
Oueslati, Tarek
Quintana Morales, Eréndira M.
Pasda, Kerstin
Perera, Jude
Perera, Nimal
Radbauer, Silvia
Ramon, Joan
Rannamäe, Eve
Sanmartí Grego, Joan
Treasure, Edward
Valenzuela-Lamas, Silvia
van der Jagt, Inge
Van Neer, Wim
Vigne, Jean-Denis
Walker, Thomas
Wynne-Jones, Stephanie
Zeiler, Jørn
Dobney, Keith
Boivin, Nicole
Searle, Jeremy B.
Krause-Kyora, Ben
Krause, Johannes
Larson, Greger
Orton, David
article (publishedVersion)
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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 a...ttested 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.