Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple european introductions associated with human economic history
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10451/56903 |
Resumo: | 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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Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple european introductions associated with human economic historyArchaeologyPopulation geneticsThe 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.SpringerRepositório da Universidade de LisboaYu, HeJamieson, AlexandraHulme-Beaman, ArdernConroy, Chris J.Knight, BeckySpeller, CamillaAl-Jarah, HibaEager, HeidiTrinks, AlexandraAdikari, GaminiBaron, HenrietteBöhlendorf-Arslan, BeateBohingamuwa, WijerathneCrowther, AlisonCucchi, ThomasEsser, KinieFleisher, JeffreyGidney, LouisaGladilina, ElenaGol’din, PavelGoodman, Steven M.Hamilton-Dyer, SheilaHelm, RichardHillman, Jesse C.Kallala, NabilKivikero, HannaKovács, Zsófia E.Kunst, Günther KarlKyselý, RenéLinderholm, AnnaMaraoui-Telmini, BouthéinaMarković, NemanjaMorales-Muñiz, ArturoNabais, MarianaO’Connor, TerryOueslati, TarekQuintana Morales, Eréndira M.Pasda, KerstinPerera, JudePerera, NimalRadbauer, SilviaRamon, JoanRannamäe, EveSanmartí Grego, JoanTreasure, EdwardValenzuela-Lamas, Silviavan der Jagt, IngeVan Neer, WimVigne, Jean-DenisWalker, ThomasWynne-Jones, StephanieZeiler, JørnDobney, KeithBoivin, NicoleSearle, Jeremy B.Krause-Kyora, BenKrause, JohannesLarson, GregerOrton, David2023-03-29T13:44:11Z20222022-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10451/56903engYu, H., Jamieson, A., Hulme-Beaman, A., Conroy, C. J., Knight, B., Speller, C., Al-Jarah, H., Eager, H., Trinks, A., Adikari, G., Baron, H., Bohlendorf-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., Kovacs, Z. E., Kunst, G. K., Kysely, R., Linderholm, A., Maraoui-Telmini, B., Markovic, N., Morales-Muniz, A., Nabais, M., O'Connor, T., Oueslati, T., Quintana Morales, E. M., Pasda, K., Perera, J., Perera, N., Radbauer, S., Ramon, J., Rannamae, 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, 13(1) 2399. doi: 10.1038/s41467-022-30009-zhttps://doi.org/10.1038/s41467-022-30009-z2041-1723info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-08T17:04:39Zoai:repositorio.ul.pt:10451/56903Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T22:07:17.478788Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple european introductions associated with human economic history |
title |
Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple european introductions associated with human economic history |
spellingShingle |
Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple european introductions associated with human economic history Yu, He Archaeology Population genetics |
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 |
author |
Yu, He |
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, 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 |
author_role |
author |
author2 |
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, 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 |
author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Repositório da Universidade de Lisboa |
dc.contributor.author.fl_str_mv |
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, 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 |
dc.subject.por.fl_str_mv |
Archaeology Population genetics |
topic |
Archaeology Population genetics |
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. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022 2022-01-01T00:00:00Z 2023-03-29T13:44:11Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10451/56903 |
url |
http://hdl.handle.net/10451/56903 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
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., Bohlendorf-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., Kovacs, Z. E., Kunst, G. K., Kysely, R., Linderholm, A., Maraoui-Telmini, B., Markovic, N., Morales-Muniz, A., Nabais, M., O'Connor, T., Oueslati, T., Quintana Morales, E. M., Pasda, K., Perera, J., Perera, N., Radbauer, S., Ramon, J., Rannamae, 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, 13(1) 2399. doi: 10.1038/s41467-022-30009-z https://doi.org/10.1038/s41467-022-30009-z 2041-1723 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Springer |
publisher.none.fl_str_mv |
Springer |
dc.source.none.fl_str_mv |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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