Data from: Global population divergence and admixture of the brown rat (Rattus norvegicus)
Native to China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution. While black rats and the house mouse tracked the regional development of human agricultural settlements, brown rats did not appear in Europe until the 1500s, suggesting their range expansion was a re...
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Data Archiving and Networked Services (DANS)
2016
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Online Access: | https://doi.org/10.5061/dryad.jb3tc http://library.wur.nl/WebQuery/wurpubs/523507 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::838f9a9aaaceeb50178534854cd19499 2023-05-15T18:05:10+02:00 Data from: Global population divergence and admixture of the brown rat (Rattus norvegicus) Puckett, Emily E. Park, Jane Combs, Matthew Blum, Michael J. Bryant, Juliet E. Caccone, Adalgisa Costa, Federico Deinum, Eva E. Esther, Alexandra Himsworth, Chelsea G. Keightley, Peter D. Ko, Albert Lundkvist, Ake McElhinney, Lorraine M. Morand, Serge Robins, Judith Russell, James Strand, Tanja M. Suarez, Olga Yon, Lisa Munshi-South, Jason 2016-01-01 https://doi.org/10.5061/dryad.jb3tc http://library.wur.nl/WebQuery/wurpubs/523507 undefined unknown Data Archiving and Networked Services (DANS) http://dx.doi.org/10.5061/dryad.jb3tc http://library.wur.nl/WebQuery/wurpubs/523507 https://dx.doi.org/10.5061/dryad.jb3tc lic_creative-commons oai:easy.dans.knaw.nl:easy-dataset:95614 wurdata:oai:library.wur.nl:wurpubs/523507 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:95614 10.5061/dryad.jb3tc 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::fdb035c8b3e0540a8d9a561a6c44f4de 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Life sciences medicine and health care commensal invasive species population genomics cityscapes phylogeography RAD-seq Rattus norvegicus Rattus rattus 2007-2015 Global envir demo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2016 fttriple https://doi.org/10.5061/dryad.jb3tc 2023-01-22T17:41:32Z Native to China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution. While black rats and the house mouse tracked the regional development of human agricultural settlements, brown rats did not appear in Europe until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade. We inferred the global phylogeography of brown rats using 32 k SNPs, and detected 13 evolutionary clusters within five expansion routes. One cluster arose following a southward expansion into Southeast Asia. Three additional clusters arose from two independent eastward expansions: one expansion from Russia to the Aleutian Archipelago, and a second to western North America. Westward expansion resulted in the colonization of Europe from which subsequent rapid colonization of Africa, the Americas and Australasia occurred, and multiple evolutionary clusters were detected. An astonishing degree of fine-grained clustering between and within sampling sites underscored the extent to which urban heterogeneity shaped genetic structure of commensal rodents. Surprisingly, few individuals were recent migrants, suggesting that recruitment into established populations is limited. Understanding the global population structure of R. norvegicus offers novel perspectives on the forces driving the spread of zoonotic disease, and aids in development of rat eradication programmes. Puckett_etal_RatPhylogeog_SNPs.tarSNPs (l=32,127) discovered from a ddRAD-Seq project with Rattus norvegicus (n=314) and Rattus rattus (n=33) samples from around the world. SNPs are aligned to the Rattus norvegicus Rnor_6.0 genome and provided as binary PLINK files (.bed, .bim, .fam). See Tables S1 and S2 of the manuscript for locations for each sample name.Puckett_etal-RatPhylogeog-MitoHaplotypesMitochondrial SNP haplotypes produced from ddRAD-Seq data. We identified 104 haplotypes in 144 brown rat (Rattus norvegicus) samples, that group into 10 clades. SNP positions found in Table S3 of the manuscript. ... Dataset Rattus rattus Unknown |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care commensal invasive species population genomics cityscapes phylogeography RAD-seq Rattus norvegicus Rattus rattus 2007-2015 Global envir demo |
spellingShingle |
Life sciences medicine and health care commensal invasive species population genomics cityscapes phylogeography RAD-seq Rattus norvegicus Rattus rattus 2007-2015 Global envir demo Puckett, Emily E. Park, Jane Combs, Matthew Blum, Michael J. Bryant, Juliet E. Caccone, Adalgisa Costa, Federico Deinum, Eva E. Esther, Alexandra Himsworth, Chelsea G. Keightley, Peter D. Ko, Albert Lundkvist, Ake McElhinney, Lorraine M. Morand, Serge Robins, Judith Russell, James Strand, Tanja M. Suarez, Olga Yon, Lisa Munshi-South, Jason Data from: Global population divergence and admixture of the brown rat (Rattus norvegicus) |
topic_facet |
Life sciences medicine and health care commensal invasive species population genomics cityscapes phylogeography RAD-seq Rattus norvegicus Rattus rattus 2007-2015 Global envir demo |
description |
Native to China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution. While black rats and the house mouse tracked the regional development of human agricultural settlements, brown rats did not appear in Europe until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade. We inferred the global phylogeography of brown rats using 32 k SNPs, and detected 13 evolutionary clusters within five expansion routes. One cluster arose following a southward expansion into Southeast Asia. Three additional clusters arose from two independent eastward expansions: one expansion from Russia to the Aleutian Archipelago, and a second to western North America. Westward expansion resulted in the colonization of Europe from which subsequent rapid colonization of Africa, the Americas and Australasia occurred, and multiple evolutionary clusters were detected. An astonishing degree of fine-grained clustering between and within sampling sites underscored the extent to which urban heterogeneity shaped genetic structure of commensal rodents. Surprisingly, few individuals were recent migrants, suggesting that recruitment into established populations is limited. Understanding the global population structure of R. norvegicus offers novel perspectives on the forces driving the spread of zoonotic disease, and aids in development of rat eradication programmes. Puckett_etal_RatPhylogeog_SNPs.tarSNPs (l=32,127) discovered from a ddRAD-Seq project with Rattus norvegicus (n=314) and Rattus rattus (n=33) samples from around the world. SNPs are aligned to the Rattus norvegicus Rnor_6.0 genome and provided as binary PLINK files (.bed, .bim, .fam). See Tables S1 and S2 of the manuscript for locations for each sample name.Puckett_etal-RatPhylogeog-MitoHaplotypesMitochondrial SNP haplotypes produced from ddRAD-Seq data. We identified 104 haplotypes in 144 brown rat (Rattus norvegicus) samples, that group into 10 clades. SNP positions found in Table S3 of the manuscript. ... |
format |
Dataset |
author |
Puckett, Emily E. Park, Jane Combs, Matthew Blum, Michael J. Bryant, Juliet E. Caccone, Adalgisa Costa, Federico Deinum, Eva E. Esther, Alexandra Himsworth, Chelsea G. Keightley, Peter D. Ko, Albert Lundkvist, Ake McElhinney, Lorraine M. Morand, Serge Robins, Judith Russell, James Strand, Tanja M. Suarez, Olga Yon, Lisa Munshi-South, Jason |
author_facet |
Puckett, Emily E. Park, Jane Combs, Matthew Blum, Michael J. Bryant, Juliet E. Caccone, Adalgisa Costa, Federico Deinum, Eva E. Esther, Alexandra Himsworth, Chelsea G. Keightley, Peter D. Ko, Albert Lundkvist, Ake McElhinney, Lorraine M. Morand, Serge Robins, Judith Russell, James Strand, Tanja M. Suarez, Olga Yon, Lisa Munshi-South, Jason |
author_sort |
Puckett, Emily E. |
title |
Data from: Global population divergence and admixture of the brown rat (Rattus norvegicus) |
title_short |
Data from: Global population divergence and admixture of the brown rat (Rattus norvegicus) |
title_full |
Data from: Global population divergence and admixture of the brown rat (Rattus norvegicus) |
title_fullStr |
Data from: Global population divergence and admixture of the brown rat (Rattus norvegicus) |
title_full_unstemmed |
Data from: Global population divergence and admixture of the brown rat (Rattus norvegicus) |
title_sort |
data from: global population divergence and admixture of the brown rat (rattus norvegicus) |
publisher |
Data Archiving and Networked Services (DANS) |
publishDate |
2016 |
url |
https://doi.org/10.5061/dryad.jb3tc http://library.wur.nl/WebQuery/wurpubs/523507 |
genre |
Rattus rattus |
genre_facet |
Rattus rattus |
op_source |
oai:easy.dans.knaw.nl:easy-dataset:95614 wurdata:oai:library.wur.nl:wurpubs/523507 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:95614 10.5061/dryad.jb3tc 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::fdb035c8b3e0540a8d9a561a6c44f4de 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.jb3tc http://library.wur.nl/WebQuery/wurpubs/523507 https://dx.doi.org/10.5061/dryad.jb3tc |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.jb3tc |
_version_ |
1766176618738352128 |