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

He Yu; Alexandra Jamieson; Ardern Hulme-Beaman; Chris J. Conroy; Becky Knight; Camilla Speller; Hiba Al-Jarah; Heidi Eager; Alexandra Trinks; Gamini Adikari; Henriette Baron; Beate Böhlendorf-Arslan; Wijerathne Bohingamuwa; Alison Crowther; Thomas Cucchi; Kinie Esser; Jeffrey Fleisher; Louisa Gidney; Elena Gladilina; Pavel Gol’din; Steven M. Goodman; Sheila Hamilton-Dyer; Richard Helm; Jesse C. Hillman; Nabil Kallala; Hanna Kivikero; Zsófia E. Kovács; Günther Karl Kunst; René Kyselý; Anna Linderholm; Bouthéina Maraoui-Telmini; Nemanja Marković; Arturo Morales-Muñiz; Mariana Nabais; Terry O’Connor; Tarek Oueslati; Eréndira M. 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; Thomas Walker; Stephanie Wynne-Jones; Jørn Zeiler; Keith Dobney; Nicole Boivin; Jeremy B. Searle; Ben Krause-Kyora; Johannes Krause; Greger Larson; David Orton

doi:10.1038/s41467-022-30009-z

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

He Yu, Alexandra Jamieson, Ardern Hulme-Beaman, Chris J. Conroy, Becky Knight, Camilla Speller, Hiba Al-Jarah, Heidi Eager, Alexandra Trinks, Gamini Adikari, Henriette Baron, Beate Böhlendorf-Arslan, Wijerathne Bohingamuwa, Alison Crowther, Thomas Cucchi, Kinie Esser, Jeffrey Fleisher, Louisa Gidney, Elena Gladilina, Pavel Gol’dinSteven M. Goodman, Sheila Hamilton-Dyer, Richard Helm, Jesse C. Hillman, Nabil Kallala, Hanna Kivikero, Zsófia E. Kovács, Günther Karl Kunst, René Kyselý, Anna Linderholm, Bouthéina Maraoui-Telmini, Nemanja Marković, Arturo Morales-Muñiz, Mariana Nabais, Terry O’Connor, Tarek Oueslati, Eréndira M. 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, Thomas Walker, Stephanie Wynne-Jones, Jørn Zeiler, Keith Dobney, Nicole Boivin, Jeremy B. Searle, Ben Krause-Kyora, Johannes Krause^*, Greger Larson, David Orton

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	2399
Number of pages	13
Journal	Nature Communications
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41467-022-30009-z
Publication status	Published - 3 May 2022

Bibliographical note

Funding Information:
We thank the wet laboratory teams at MPI-SHH, the PalaeoBARN at the University of Oxford and BioArch at 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 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 (?lands 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 and the ?anakkale Museum, Jan Frol?k and Iva Herichov? (Institute of Archaeology of the Czech Academy of Sciences, Prague), Franz Humer and Eduard Pollhammer (Archaeological Park Carnuntum), Dorottya B. Ny?khelyi and L?szl? Dar?czi-Szab? (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 (programme of archaeological excavations abroad 2009); Spanish Agency of International Cooperation for the Development (2009), Catalan Institute of Classical Archaeology (ICAC), Vila Franca Municipal Museum and N?Zinga Oliveira (University of the Azores), Vujadin Ivanisevi? and Ivan Bugarski (Institute of Archaeology, Belgrade), Martin Nadler, M.A. and Dr. Silvia Codreanu-Windauer (N?rnberg and Regensburg respectively, Bavarian State Office for the Preservation of Monuments), the Field Museum of Natural History Chicago, The Natural History Museum London, and the American Museum of Natural History for providing materials and support. Funding was provided by the European Research Council (ERC-StG-337574-UNDEAD to G.L.; ERC-StG-206148 to N.B.; ERC-StG-716298 to S.V.-L.), the Natural Environment Research Council Doctoral Training Programme (A.J.), Wellcome (Small Grant in Humanities and Social Science 209817/Z to D.O.), the British Academy/Leverhulme Trust (SG170938 to D.O.), Estonian Research Council (PRG29 to E.R.), Czech Academy of Sciences (RVO:67985912 to R.K.), and Leverhulme Trust (ECF-2017-315 to A.H.B.), National Science Foundation (BCS 1123091 to J.F./S.W.-J.), Arts and Humanities Research Council (AH/J502716/1 to S.W.-J./J.F.). The de novo genome assembly, population genomics study, and radiocarbon dating were funded by the Max Planck Society.

Funding Information:
We thank the wet laboratory teams at MPI-SHH, the PalaeoBARN at the University of Oxford and BioArch at 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 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 and the Çanakkale Museum, 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 (programme of archaeological excavations abroad 2009); Spanish Agency of International Cooperation for the Development (2009), Catalan Institute of Classical Archaeology (ICAC), Vila Franca Municipal Museum and N’Zinga Oliveira (University of the Azores), Vujadin Ivanisević and Ivan Bugarski (Institute of Archaeology, Belgrade), Martin Nadler, M.A. and Dr. Silvia Codreanu-Windauer (Nürnberg and Regensburg respectively, Bavarian State Office for the Preservation of Monuments), the Field Museum of Natural History Chicago, The Natural History Museum London, and the American Museum of Natural History for providing materials and support. Funding was provided by the European Research Council (ERC-StG-337574-UNDEAD to G.L.; ERC-StG-206148 to N.B.; ERC-StG-716298 to S.V.-L.), the Natural Environment Research Council Doctoral Training Programme (A.J.), Wellcome (Small Grant in Humanities and Social Science 209817/Z to D.O.), the British Academy/Leverhulme Trust (SG170938 to D.O.), Estonian Research Council (PRG29 to E.R.), Czech Academy of Sciences (RVO:67985912 to R.K.), and Leverhulme Trust (ECF-2017-315 to A.H.B.), National Science Foundation (BCS 1123091 to J.F./S.W.-J.), Arts and Humanities Research Council (AH/J502716/1 to S.W.-J./J.F.). The de novo genome assembly, population genomics study, and radiocarbon dating were funded by the Max Planck Society.

Publisher Copyright:
© 2022, The Author(s).

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Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history
© The Author(s) 2022
Final published version, 2.12 MBLicence: CC BY

Cite this

Yu, H., Jamieson, A., Hulme-Beaman, A., Conroy, C. J., Knight, B., Speller, C., Al-Jarah, H., Eager, H., Trinks, A., Adikari, G., Baron, H., Böhlendorf-Arslan, B., Bohingamuwa, W., Crowther, A., Cucchi, T., Esser, K., Fleisher, J., Gidney, L., Gladilina, E., ... Orton, D. (2022). Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history. Nature Communications, 13(1), Article 2399. https://doi.org/10.1038/s41467-022-30009-z

@article{c5ddeb400a464f6cbac09dff8ba9f894,

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

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.",

author = "He Yu and Alexandra Jamieson and Ardern Hulme-Beaman and Conroy, {Chris J.} and Becky Knight and Camilla Speller and Hiba Al-Jarah and Heidi Eager and Alexandra Trinks and Gamini Adikari and Henriette Baron and Beate B{\"o}hlendorf-Arslan and Wijerathne Bohingamuwa and Alison Crowther and Thomas Cucchi and Kinie Esser and Jeffrey Fleisher and Louisa Gidney and Elena Gladilina and Pavel Gol{\textquoteright}din and Goodman, {Steven M.} and Sheila Hamilton-Dyer and Richard Helm and Hillman, {Jesse C.} and Nabil Kallala and Hanna Kivikero and Kov{\'a}cs, {Zs{\'o}fia E.} and Kunst, {G{\"u}nther Karl} and Ren{\'e} Kysel{\'y} and Anna Linderholm and Bouth{\'e}ina Maraoui-Telmini and Nemanja Markovi{\'c} and Arturo Morales-Mu{\~n}iz and Mariana Nabais and Terry O{\textquoteright}Connor and Tarek Oueslati and {Quintana Morales}, {Er{\'e}ndira M.} and Kerstin Pasda and Jude Perera and Nimal Perera and Silvia Radbauer and Joan Ramon and Eve Rannam{\"a}e and {Sanmart{\'i} Grego}, Joan and Edward Treasure and Silvia Valenzuela-Lamas and {van der Jagt}, Inge and {Van Neer}, Wim and Vigne, {Jean Denis} and Thomas Walker and Stephanie Wynne-Jones and J{\o}rn Zeiler and Keith Dobney and Nicole Boivin and Searle, {Jeremy B.} and Ben Krause-Kyora and Johannes Krause and Greger Larson and David Orton",

note = "Funding Information: We thank the wet laboratory teams at MPI-SHH, the PalaeoBARN at the University of Oxford and BioArch at 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 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 (?lands 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 and the ?anakkale Museum, Jan Frol?k and Iva Herichov? (Institute of Archaeology of the Czech Academy of Sciences, Prague), Franz Humer and Eduard Pollhammer (Archaeological Park Carnuntum), Dorottya B. Ny?khelyi and L?szl? Dar?czi-Szab? (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 (programme of archaeological excavations abroad 2009); Spanish Agency of International Cooperation for the Development (2009), Catalan Institute of Classical Archaeology (ICAC), Vila Franca Municipal Museum and N?Zinga Oliveira (University of the Azores), Vujadin Ivanisevi? and Ivan Bugarski (Institute of Archaeology, Belgrade), Martin Nadler, M.A. and Dr. Silvia Codreanu-Windauer (N?rnberg and Regensburg respectively, Bavarian State Office for the Preservation of Monuments), the Field Museum of Natural History Chicago, The Natural History Museum London, and the American Museum of Natural History for providing materials and support. Funding was provided by the European Research Council (ERC-StG-337574-UNDEAD to G.L.; ERC-StG-206148 to N.B.; ERC-StG-716298 to S.V.-L.), the Natural Environment Research Council Doctoral Training Programme (A.J.), Wellcome (Small Grant in Humanities and Social Science 209817/Z to D.O.), the British Academy/Leverhulme Trust (SG170938 to D.O.), Estonian Research Council (PRG29 to E.R.), Czech Academy of Sciences (RVO:67985912 to R.K.), and Leverhulme Trust (ECF-2017-315 to A.H.B.), National Science Foundation (BCS 1123091 to J.F./S.W.-J.), Arts and Humanities Research Council (AH/J502716/1 to S.W.-J./J.F.). The de novo genome assembly, population genomics study, and radiocarbon dating were funded by the Max Planck Society. Funding Information: We thank the wet laboratory teams at MPI-SHH, the PalaeoBARN at the University of Oxford and BioArch at 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 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 ({\AA}lands 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 and the {\c C}anakkale Museum, Jan Frol{\'i}k and Iva Herichov{\'a} (Institute of Archaeology of the Czech Academy of Sciences, Prague), Franz Humer and Eduard Pollhammer (Archaeological Park Carnuntum), Dorottya B. Ny{\'e}khelyi and L{\'a}szl{\'o} Dar{\'o}czi-Szab{\'o} (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 (programme of archaeological excavations abroad 2009); Spanish Agency of International Cooperation for the Development (2009), Catalan Institute of Classical Archaeology (ICAC), Vila Franca Municipal Museum and N{\textquoteright}Zinga Oliveira (University of the Azores), Vujadin Ivanisevi{\'c} and Ivan Bugarski (Institute of Archaeology, Belgrade), Martin Nadler, M.A. and Dr. Silvia Codreanu-Windauer (N{\"u}rnberg and Regensburg respectively, Bavarian State Office for the Preservation of Monuments), the Field Museum of Natural History Chicago, The Natural History Museum London, and the American Museum of Natural History for providing materials and support. Funding was provided by the European Research Council (ERC-StG-337574-UNDEAD to G.L.; ERC-StG-206148 to N.B.; ERC-StG-716298 to S.V.-L.), the Natural Environment Research Council Doctoral Training Programme (A.J.), Wellcome (Small Grant in Humanities and Social Science 209817/Z to D.O.), the British Academy/Leverhulme Trust (SG170938 to D.O.), Estonian Research Council (PRG29 to E.R.), Czech Academy of Sciences (RVO:67985912 to R.K.), and Leverhulme Trust (ECF-2017-315 to A.H.B.), National Science Foundation (BCS 1123091 to J.F./S.W.-J.), Arts and Humanities Research Council (AH/J502716/1 to S.W.-J./J.F.). The de novo genome assembly, population genomics study, and radiocarbon dating were funded by the Max Planck Society. Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = may,

day = "3",

doi = "10.1038/s41467-022-30009-z",

language = "English",

volume = "13",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

number = "1",

}

Yu, H, Jamieson, A, Hulme-Beaman, A, Conroy, CJ, Knight, B, Speller, C, Al-Jarah, H, Eager, H, Trinks, A, Adikari, G, Baron, H, Böhlendorf-Arslan, B, Bohingamuwa, W, Crowther, A, Cucchi, T, Esser, K, Fleisher, J, Gidney, L, Gladilina, E, Gol’din, P, Goodman, SM, Hamilton-Dyer, S, Helm, R, Hillman, JC, Kallala, N, Kivikero, H, Kovács, ZE, Kunst, GK, Kyselý, R, Linderholm, A, Maraoui-Telmini, B, Marković, N, Morales-Muñiz, A, Nabais, M, O’Connor, T, Oueslati, T, Quintana Morales, EM, Pasda, K, Perera, J, Perera, N, Radbauer, S, Ramon, J, Rannamäe, E, Sanmartí Grego, J, Treasure, E, Valenzuela-Lamas, S, van der Jagt, I, Van Neer, W, Vigne, JD, Walker, T, Wynne-Jones, S, Zeiler, J, Dobney, K, Boivin, N, Searle, JB, Krause-Kyora, B, Krause, J, Larson, G & Orton, D 2022, 'Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history', Nature Communications, vol. 13, no. 1, 2399. https://doi.org/10.1038/s41467-022-30009-z

TY - JOUR

T1 - Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

AU - Yu, He

AU - Jamieson, Alexandra

AU - Hulme-Beaman, Ardern

AU - Conroy, Chris J.

AU - Knight, Becky

AU - Speller, Camilla

AU - Al-Jarah, Hiba

AU - Eager, Heidi

AU - Trinks, Alexandra

AU - Adikari, Gamini

AU - Baron, Henriette

AU - Böhlendorf-Arslan, Beate

AU - Bohingamuwa, Wijerathne

AU - Crowther, Alison

AU - Cucchi, Thomas

AU - Esser, Kinie

AU - Fleisher, Jeffrey

AU - Gidney, Louisa

AU - Gladilina, Elena

AU - Gol’din, Pavel

AU - Goodman, Steven M.

AU - Hamilton-Dyer, Sheila

AU - Helm, Richard

AU - Hillman, Jesse C.

AU - Kallala, Nabil

AU - Kivikero, Hanna

AU - Kovács, Zsófia E.

AU - Kunst, Günther Karl

AU - Kyselý, René

AU - Linderholm, Anna

AU - Maraoui-Telmini, Bouthéina

AU - Marković, Nemanja

AU - Morales-Muñiz, Arturo

AU - Nabais, Mariana

AU - O’Connor, Terry

AU - Oueslati, Tarek

AU - Quintana Morales, Eréndira M.

AU - Pasda, Kerstin

AU - Perera, Jude

AU - Perera, Nimal

AU - Radbauer, Silvia

AU - Ramon, Joan

AU - Rannamäe, Eve

AU - Sanmartí Grego, Joan

AU - Treasure, Edward

AU - Valenzuela-Lamas, Silvia

AU - van der Jagt, Inge

AU - Van Neer, Wim

AU - Vigne, Jean Denis

AU - Walker, Thomas

AU - Wynne-Jones, Stephanie

AU - Zeiler, Jørn

AU - Dobney, Keith

AU - Boivin, Nicole

AU - Searle, Jeremy B.

AU - Krause-Kyora, Ben

AU - Krause, Johannes

AU - Larson, Greger

AU - Orton, David

N1 - Funding Information: We thank the wet laboratory teams at MPI-SHH, the PalaeoBARN at the University of Oxford and BioArch at 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 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 (?lands 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 and the ?anakkale Museum, Jan Frol?k and Iva Herichov? (Institute of Archaeology of the Czech Academy of Sciences, Prague), Franz Humer and Eduard Pollhammer (Archaeological Park Carnuntum), Dorottya B. Ny?khelyi and L?szl? Dar?czi-Szab? (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 (programme of archaeological excavations abroad 2009); Spanish Agency of International Cooperation for the Development (2009), Catalan Institute of Classical Archaeology (ICAC), Vila Franca Municipal Museum and N?Zinga Oliveira (University of the Azores), Vujadin Ivanisevi? and Ivan Bugarski (Institute of Archaeology, Belgrade), Martin Nadler, M.A. and Dr. Silvia Codreanu-Windauer (N?rnberg and Regensburg respectively, Bavarian State Office for the Preservation of Monuments), the Field Museum of Natural History Chicago, The Natural History Museum London, and the American Museum of Natural History for providing materials and support. Funding was provided by the European Research Council (ERC-StG-337574-UNDEAD to G.L.; ERC-StG-206148 to N.B.; ERC-StG-716298 to S.V.-L.), the Natural Environment Research Council Doctoral Training Programme (A.J.), Wellcome (Small Grant in Humanities and Social Science 209817/Z to D.O.), the British Academy/Leverhulme Trust (SG170938 to D.O.), Estonian Research Council (PRG29 to E.R.), Czech Academy of Sciences (RVO:67985912 to R.K.), and Leverhulme Trust (ECF-2017-315 to A.H.B.), National Science Foundation (BCS 1123091 to J.F./S.W.-J.), Arts and Humanities Research Council (AH/J502716/1 to S.W.-J./J.F.). The de novo genome assembly, population genomics study, and radiocarbon dating were funded by the Max Planck Society. Funding Information: We thank the wet laboratory teams at MPI-SHH, the PalaeoBARN at the University of Oxford and BioArch at 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 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 and the Çanakkale Museum, 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 (programme of archaeological excavations abroad 2009); Spanish Agency of International Cooperation for the Development (2009), Catalan Institute of Classical Archaeology (ICAC), Vila Franca Municipal Museum and N’Zinga Oliveira (University of the Azores), Vujadin Ivanisević and Ivan Bugarski (Institute of Archaeology, Belgrade), Martin Nadler, M.A. and Dr. Silvia Codreanu-Windauer (Nürnberg and Regensburg respectively, Bavarian State Office for the Preservation of Monuments), the Field Museum of Natural History Chicago, The Natural History Museum London, and the American Museum of Natural History for providing materials and support. Funding was provided by the European Research Council (ERC-StG-337574-UNDEAD to G.L.; ERC-StG-206148 to N.B.; ERC-StG-716298 to S.V.-L.), the Natural Environment Research Council Doctoral Training Programme (A.J.), Wellcome (Small Grant in Humanities and Social Science 209817/Z to D.O.), the British Academy/Leverhulme Trust (SG170938 to D.O.), Estonian Research Council (PRG29 to E.R.), Czech Academy of Sciences (RVO:67985912 to R.K.), and Leverhulme Trust (ECF-2017-315 to A.H.B.), National Science Foundation (BCS 1123091 to J.F./S.W.-J.), Arts and Humanities Research Council (AH/J502716/1 to S.W.-J./J.F.). The de novo genome assembly, population genomics study, and radiocarbon dating were funded by the Max Planck Society. Publisher Copyright: © 2022, The Author(s).

PY - 2022/5/3

Y1 - 2022/5/3

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85129257221&partnerID=8YFLogxK

U2 - 10.1038/s41467-022-30009-z

DO - 10.1038/s41467-022-30009-z

M3 - Article

C2 - 35504912

AN - SCOPUS:85129257221

SN - 2041-1723

VL - 13

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 2399

ER -

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

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Bibliographical note

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The archaeology of a global disease vector

Rats as proxies for urbanism and communications in medieval northern Europe

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

Abstract

Bibliographical note

Access to Document

Other files and links

Projects

The archaeology of a global disease vector

Rats as proxies for urbanism and communications in medieval northern Europe

Cite this