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

• Main Authors: Yu, He, Jamieson, 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, Chris, Kallala, Nabil, Kivikero, Hanna, Kovács, Zsófia E., Kunst, Günther Karl, Kyselý, René, Linderholm, Anna, Maraoui-Telmini, Bouthéina, Morales-Muñiz, Arturo, Nabais, Mariana, O’Connor, Terry, Oueslati, Tarek, Quintana Morales, Eréndira M., Pasda, Kerstin, Jude Perera, Perera, Nimal, Radbauer, Silvia, Ramon, Joan, Rannamäe, Eve, Sanmartí Grego, Joan, Treasure, Edward, Valenzuela-Lamas, Silvia, Jagt, Inge van der, Neer, Wim Van, 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
• Format: Report
• Language: English
• Published: BioRxiv 2021
• Subjects: Rattus rattus
• Online Access: http://hdl.handle.net/10261/245808; https://doi.org/10.1101/2021.04.14.439553

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, ...