Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history
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 perio...
Published in: | Nature Communications |
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Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Format: | Article in Journal/Newspaper |
Language: | English |
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Nature Publishing Group
2023
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Online Access: | http://hdl.handle.net/10138/353515 |
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Open Polar |
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HELDA – University of Helsinki Open Repository |
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ftunivhelsihelda |
language |
English |
topic |
1181 Ecology evolutionary biology 615 History and Archaeology Population history European black rats |
spellingShingle |
1181 Ecology evolutionary biology 615 History and Archaeology Population history European black rats 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, Jesse C. Kallala, Nabil Kivikero, Hanna Kovács, Zsofia E. Kunst, Günther Karl Kyselý, René Linderholm, Anna Maraoui-Telmini, Bouthéina Markovic, 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 Sanmarti 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 Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history |
topic_facet |
1181 Ecology evolutionary biology 615 History and Archaeology Population history European black rats |
description |
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. Peer reviewed |
author2 |
Department of Cultures |
format |
Article in Journal/Newspaper |
author |
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, Jesse C. Kallala, Nabil Kivikero, Hanna Kovács, Zsofia E. Kunst, Günther Karl Kyselý, René Linderholm, Anna Maraoui-Telmini, Bouthéina Markovic, 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 Sanmarti 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 |
author_facet |
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, Jesse C. Kallala, Nabil Kivikero, Hanna Kovács, Zsofia E. Kunst, Günther Karl Kyselý, René Linderholm, Anna Maraoui-Telmini, Bouthéina Markovic, 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 Sanmarti 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 |
author_sort |
Yu, He |
title |
Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history |
title_short |
Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history |
title_full |
Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history |
title_fullStr |
Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history |
title_full_unstemmed |
Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history |
title_sort |
palaeogenomic analysis of black rat (rattus rattus) reveals multiple european introductions associated with human economic history |
publisher |
Nature Publishing Group |
publishDate |
2023 |
url |
http://hdl.handle.net/10138/353515 |
genre |
Rattus rattus |
genre_facet |
Rattus rattus |
op_relation |
10.1038/s41467-022-30009-z 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 , Gol'din , P , Goodman , S M , Hamilton-Dyer , S , Helm , R , Hillman , J C , Kallala , N , Kivikero , H , Kovács , Z E , Kunst , G K , Kyselý , R , Linderholm , A , Maraoui-Telmini , B , Markovic , N , Morales-Muñiz , A , Nabais , M , O'Connor , T , Oueslati , T , Quintana Morales , E M , Pasda , K , Perera , J , Perera , N , Radbauer , S , Ramon , J , Rannamäe , E , Sanmarti Grego , J , Treasure , E , Valenzuela-Lamas , S , van der Jagt , I , Van Neer , W , Vigne , J-D , Walker , T , Wynne-Jones , S , Zeiler , J , Dobney , K , Boivin , N , Searle , J B , 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 , 2399 . https://doi.org/10.1038/s41467-022-30009-z 003e985b-469c-4929-bd7f-4d69f9094810 http://hdl.handle.net/10138/353515 |
op_rights |
cc_by openAccess info:eu-repo/semantics/openAccess |
container_title |
Nature Communications |
container_volume |
13 |
container_issue |
1 |
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1787427932649553920 |
spelling |
ftunivhelsihelda:oai:helda.helsinki.fi:10138/353515 2024-01-07T09:46:12+01:00 Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history 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, Jesse C. Kallala, Nabil Kivikero, Hanna Kovács, Zsofia E. Kunst, Günther Karl Kyselý, René Linderholm, Anna Maraoui-Telmini, Bouthéina Markovic, 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 Sanmarti 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 Department of Cultures 2023-01-24T09:46:03Z 13 application/pdf http://hdl.handle.net/10138/353515 eng eng Nature Publishing Group 10.1038/s41467-022-30009-z 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 , Gol'din , P , Goodman , S M , Hamilton-Dyer , S , Helm , R , Hillman , J C , Kallala , N , Kivikero , H , Kovács , Z E , Kunst , G K , Kyselý , R , Linderholm , A , Maraoui-Telmini , B , Markovic , N , Morales-Muñiz , A , Nabais , M , O'Connor , T , Oueslati , T , Quintana Morales , E M , Pasda , K , Perera , J , Perera , N , Radbauer , S , Ramon , J , Rannamäe , E , Sanmarti Grego , J , Treasure , E , Valenzuela-Lamas , S , van der Jagt , I , Van Neer , W , Vigne , J-D , Walker , T , Wynne-Jones , S , Zeiler , J , Dobney , K , Boivin , N , Searle , J B , 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 , 2399 . https://doi.org/10.1038/s41467-022-30009-z 003e985b-469c-4929-bd7f-4d69f9094810 http://hdl.handle.net/10138/353515 cc_by openAccess info:eu-repo/semantics/openAccess 1181 Ecology evolutionary biology 615 History and Archaeology Population history European black rats Article publishedVersion 2023 ftunivhelsihelda 2023-12-14T00:06:37Z 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. Peer reviewed Article in Journal/Newspaper Rattus rattus HELDA – University of Helsinki Open Repository Nature Communications 13 1 |