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
1
MPI-SHH -
Max Planck Institute for the Science of Human History
2 Research Laboratory for Archaeology and the History of Art [Oxford]
3 University of Liverpool
4 LJMU - Liverpool John Moores University
5 Museum of Vertebrate Zoology [Berkeley]
6 Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
7 School of Social Science, University of Queensland
8 AASPE - Archéozoologie, archéobotanique : sociétés, pratiques et environnements
9 Rent a Peasant
10 NASU - National Academy of Sciences of Ukraine
11 Field Museum of Natural History [Chicago, USA]
12 HALMA - Histoire, Archéologie et Littérature des Mondes Anciens - UMR 8164
2 Research Laboratory for Archaeology and the History of Art [Oxford]
3 University of Liverpool
4 LJMU - Liverpool John Moores University
5 Museum of Vertebrate Zoology [Berkeley]
6 Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
7 School of Social Science, University of Queensland
8 AASPE - Archéozoologie, archéobotanique : sociétés, pratiques et environnements
9 Rent a Peasant
10 NASU - National Academy of Sciences of Ukraine
11 Field Museum of Natural History [Chicago, USA]
12 HALMA - Histoire, Archéologie et Littérature des Mondes Anciens - UMR 8164
Alexandra Jamieson
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Ardern Hulme-Beaman
- Function : Author
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Chris Conroy
- Function : Author
- PersonId : 1193165
- ORCID : 0000-0001-7198-9651
Becky Knight
- Function : Author
Camilla Speller
- Function : Author
Hiba Al-Jarah
- Function : Author
Heidi Eager
- Function : Author
Alexandra Trinks
- Function : Author
Gamini Adikari
- Function : Author
Henriette Baron
- Function : Author
Beate Böhlendorf-Arslan
- Function : Author
Wijerathne Bohingamuwa
- Function : Author
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Thomas Cucchi
- Function : Author
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Kinie Esser
- Function : Author
Jeffrey Fleisher
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Elena Gladilina
- Function : Author
Pavel Gol’din
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Steven Goodman
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Sheila Hamilton-Dyer
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Richard Helm
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Jesse Hillman
- Function : Author
Nabil Kallala
- Function : Author
Hanna Kivikero
- Function : Author
Zsófia Kovács
- Function : Author
Günther Karl Kunst
- Function : Author
René Kyselý
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Anna Linderholm
- Function : Author
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Bouthéina Maraoui-Telmini
- Function : Author
Nemanja Marković
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Arturo Morales-Muñiz
- Function : Author
Mariana Nabais
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Terry O’connor
- Function : Author
Tarek Oueslati
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Eréndira Quintana Morales
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Kerstin Pasda
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Jude Perera
- Function : Author
Nimal Perera
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Silvia Radbauer
- Function : Author
Joan Ramon
- Function : Author
Eve Rannamäe
- Function : Author
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Joan Sanmartí Grego
- Function : Author
Edward Treasure
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Silvia Valenzuela-Lamas
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Inge van der Jagt
- Function : Author
Wim van Neer
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Jean-Denis Vigne
- Function : Author
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Thomas Walker
- Function : Author
Stephanie Wynne-Jones
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Jørn Zeiler
- Function : Author
Keith Dobney
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Nicole Boivin
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Jeremy Searle
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Ben Krause-Kyora
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Johannes Krause
- Function : Author
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Greger Larson
- Function : Author
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David Orton
- Function : Author
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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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