Data from: AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague-mediated selection
The black rat (Rattus rattus) is the main reservoir of plague (Yersinia pestis infection) in Madagascar's rural zones. Black rats are highly resistant to plague within the plague focus (central highland), whereas they are susceptible where the disease is absent (low altitude zone). To better un...
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ftdryad:oai:v1.datadryad.org:10255/dryad.1346 2023-05-15T18:05:07+02:00 Data from: AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague-mediated selection Tollenaere, Charlotte Duplantier, Jean-Marc Rahalison, Lila Ranjalahy, Michel Brouat, Carine Madagascar 100-1000 years BP 2010-03-12T07:37:02Z http://hdl.handle.net/10255/dryad.1346 https://doi.org/10.5061/dryad.1346 unknown Molecular Ecology 0962-1083 doi:10.5061/dryad.1346/1 doi:10.5061/dryad.1346/2 doi:10.1111/j.1365-294X.2010.04633.x PMID:20444082 doi:10.5061/dryad.1346 Tollenaere C, Duplantier J-M, Rahalison L, Ranjalahy M, Brouat C (2010) AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague-mediated selection. Molecular Ecology 20(5): 1026-1038. http://hdl.handle.net/10255/dryad.1346 Adaptation genetics Association study Disease resistance Pathogen-mediated selection Population genomics Yersinia pestis Article 2010 ftdryad https://doi.org/10.5061/dryad.1346 https://doi.org/10.5061/dryad.1346/1 https://doi.org/10.5061/dryad.1346/2 https://doi.org/10.1111/j.1365-294X.2010.04633.x 2020-01-01T14:14:26Z The black rat (Rattus rattus) is the main reservoir of plague (Yersinia pestis infection) in Madagascar's rural zones. Black rats are highly resistant to plague within the plague focus (central highland), whereas they are susceptible where the disease is absent (low altitude zone). To better understand plague wildlife circulation and host evolution in response to a highly virulent pathogen, we attempted to determine genetic markers associated with plague resistance in this species. To this purpose, we combined a population genomics approach and an association study, both performed on 249 AFLP markers, in Malagasy R. rattus. Simulated distributions of genetic differentiation were compared to observed data in four independent pairs, each consisting of one population from the plague focus and one from the plague-free zone. We found 22 loci (9% of 249) with higher differentiation in at least two independent population pairs or with combining p-values over the four pairs significant. Among the 22 outlier loci, 16 presented significant association with plague zone (plague focus vs. plague-free zone). Population genetic structure inferred from outlier loci was structured by plague zone, whereas the neutral loci dataset revealed structure by geography (eastern vs. western populations). A phenotype association study revealed that two of the 22 loci were significantly associated with differentiation between dying and surviving rats following experimental plague challenge. The 22 outlier loci identified in this study may undergo plague selective pressure either directly or more probably indirectly due to hitchhiking with selected loci. Article in Journal/Newspaper Rattus rattus Dryad Digital Repository (Duke University) |
institution |
Open Polar |
collection |
Dryad Digital Repository (Duke University) |
op_collection_id |
ftdryad |
language |
unknown |
topic |
Adaptation genetics Association study Disease resistance Pathogen-mediated selection Population genomics Yersinia pestis |
spellingShingle |
Adaptation genetics Association study Disease resistance Pathogen-mediated selection Population genomics Yersinia pestis Tollenaere, Charlotte Duplantier, Jean-Marc Rahalison, Lila Ranjalahy, Michel Brouat, Carine Data from: AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague-mediated selection |
topic_facet |
Adaptation genetics Association study Disease resistance Pathogen-mediated selection Population genomics Yersinia pestis |
description |
The black rat (Rattus rattus) is the main reservoir of plague (Yersinia pestis infection) in Madagascar's rural zones. Black rats are highly resistant to plague within the plague focus (central highland), whereas they are susceptible where the disease is absent (low altitude zone). To better understand plague wildlife circulation and host evolution in response to a highly virulent pathogen, we attempted to determine genetic markers associated with plague resistance in this species. To this purpose, we combined a population genomics approach and an association study, both performed on 249 AFLP markers, in Malagasy R. rattus. Simulated distributions of genetic differentiation were compared to observed data in four independent pairs, each consisting of one population from the plague focus and one from the plague-free zone. We found 22 loci (9% of 249) with higher differentiation in at least two independent population pairs or with combining p-values over the four pairs significant. Among the 22 outlier loci, 16 presented significant association with plague zone (plague focus vs. plague-free zone). Population genetic structure inferred from outlier loci was structured by plague zone, whereas the neutral loci dataset revealed structure by geography (eastern vs. western populations). A phenotype association study revealed that two of the 22 loci were significantly associated with differentiation between dying and surviving rats following experimental plague challenge. The 22 outlier loci identified in this study may undergo plague selective pressure either directly or more probably indirectly due to hitchhiking with selected loci. |
format |
Article in Journal/Newspaper |
author |
Tollenaere, Charlotte Duplantier, Jean-Marc Rahalison, Lila Ranjalahy, Michel Brouat, Carine |
author_facet |
Tollenaere, Charlotte Duplantier, Jean-Marc Rahalison, Lila Ranjalahy, Michel Brouat, Carine |
author_sort |
Tollenaere, Charlotte |
title |
Data from: AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague-mediated selection |
title_short |
Data from: AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague-mediated selection |
title_full |
Data from: AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague-mediated selection |
title_fullStr |
Data from: AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague-mediated selection |
title_full_unstemmed |
Data from: AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague-mediated selection |
title_sort |
data from: aflp genome scan in the black rat (rattus rattus) from madagascar: detecting genetic markers undergoing plague-mediated selection |
publishDate |
2010 |
url |
http://hdl.handle.net/10255/dryad.1346 https://doi.org/10.5061/dryad.1346 |
op_coverage |
Madagascar 100-1000 years BP |
genre |
Rattus rattus |
genre_facet |
Rattus rattus |
op_relation |
Molecular Ecology 0962-1083 doi:10.5061/dryad.1346/1 doi:10.5061/dryad.1346/2 doi:10.1111/j.1365-294X.2010.04633.x PMID:20444082 doi:10.5061/dryad.1346 Tollenaere C, Duplantier J-M, Rahalison L, Ranjalahy M, Brouat C (2010) AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague-mediated selection. Molecular Ecology 20(5): 1026-1038. http://hdl.handle.net/10255/dryad.1346 |
op_doi |
https://doi.org/10.5061/dryad.1346 https://doi.org/10.5061/dryad.1346/1 https://doi.org/10.5061/dryad.1346/2 https://doi.org/10.1111/j.1365-294X.2010.04633.x |
_version_ |
1766176570402144256 |