Data from: Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation
A species’ genetic diversity bears the marks of evolutionary processes that have occurred throughout its history. However, robust detection of selection in wild populations is difficult and often impeded by lack of replicate tests. Here, we investigate selection in pink salmon (Oncorhynchus gorbusch...
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fttriple:oai:gotriple.eu:50|dedup_wf_001::eb2ce0e43d5e20a42e16e86fb4f4ca2e 2023-05-15T17:52:50+02:00 Data from: Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation Limborg, Morten T. Waples, Ryan K. Seeb, James E. Seeb, Lisa W. 2014-09-17 https://doi.org/10.5061/dryad.pp43m undefined unknown http://dx.doi.org/10.5061/dryad.pp43m https://dx.doi.org/10.5061/dryad.pp43m lic_creative-commons oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:86834 oai:easy.dans.knaw.nl:easy-dataset:86834 10.5061/dryad.pp43m 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Life sciences medicine and health care parallel evolution life-history haploid linkage mapping Oncorhynchus gorbuscha Molecular adaptation and selection climate change North Pacific Ocean envir demo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2014 fttriple https://doi.org/10.5061/dryad.pp43m 2023-01-22T17:22:33Z A species’ genetic diversity bears the marks of evolutionary processes that have occurred throughout its history. However, robust detection of selection in wild populations is difficult and often impeded by lack of replicate tests. Here, we investigate selection in pink salmon (Oncorhynchus gorbuscha) using genome scans coupled with inference from a haploid-assisted linkage map. Pink salmon have a strict 2-year semelparous life history which has resulted in temporally isolated (allochronic) lineages that remain sympatric through sharing of spawning habitats in alternate years. The lineages differ in a range of adaptive traits, suggesting different genetic backgrounds. We used genotyping by sequencing of haploids to generate a high-density linkage map with 7035 loci and screened an existing panel of 8036 loci for signatures of selection. The linkage map enabled identification of novel genomic regions displaying signatures of parallel selection shared between lineages. Furthermore, 24 loci demonstrated divergent selection and differences in genetic diversity between lineages, suggesting that adaptation in the 2 lineages has arisen from different pools of standing genetic variation. Findings have implications for understanding asynchronous population abundances as well as predicting future ecosystem impacts from lineage-specific responses to climate change. Haploid genotypes for two pink salmon mapping families X01 and X05This file includes the raw haploid genotypes for each of two mapping families (X01 and X05) in the respective R/qtl input format. These genotypes represent the raw output from STACKS (see associated paper) and thus includes loci that were subsequently discarded during the mapping analyses. Dataset Oncorhynchus gorbuscha Pink salmon Unknown Pacific |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care parallel evolution life-history haploid linkage mapping Oncorhynchus gorbuscha Molecular adaptation and selection climate change North Pacific Ocean envir demo |
spellingShingle |
Life sciences medicine and health care parallel evolution life-history haploid linkage mapping Oncorhynchus gorbuscha Molecular adaptation and selection climate change North Pacific Ocean envir demo Limborg, Morten T. Waples, Ryan K. Seeb, James E. Seeb, Lisa W. Data from: Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation |
topic_facet |
Life sciences medicine and health care parallel evolution life-history haploid linkage mapping Oncorhynchus gorbuscha Molecular adaptation and selection climate change North Pacific Ocean envir demo |
description |
A species’ genetic diversity bears the marks of evolutionary processes that have occurred throughout its history. However, robust detection of selection in wild populations is difficult and often impeded by lack of replicate tests. Here, we investigate selection in pink salmon (Oncorhynchus gorbuscha) using genome scans coupled with inference from a haploid-assisted linkage map. Pink salmon have a strict 2-year semelparous life history which has resulted in temporally isolated (allochronic) lineages that remain sympatric through sharing of spawning habitats in alternate years. The lineages differ in a range of adaptive traits, suggesting different genetic backgrounds. We used genotyping by sequencing of haploids to generate a high-density linkage map with 7035 loci and screened an existing panel of 8036 loci for signatures of selection. The linkage map enabled identification of novel genomic regions displaying signatures of parallel selection shared between lineages. Furthermore, 24 loci demonstrated divergent selection and differences in genetic diversity between lineages, suggesting that adaptation in the 2 lineages has arisen from different pools of standing genetic variation. Findings have implications for understanding asynchronous population abundances as well as predicting future ecosystem impacts from lineage-specific responses to climate change. Haploid genotypes for two pink salmon mapping families X01 and X05This file includes the raw haploid genotypes for each of two mapping families (X01 and X05) in the respective R/qtl input format. These genotypes represent the raw output from STACKS (see associated paper) and thus includes loci that were subsequently discarded during the mapping analyses. |
format |
Dataset |
author |
Limborg, Morten T. Waples, Ryan K. Seeb, James E. Seeb, Lisa W. |
author_facet |
Limborg, Morten T. Waples, Ryan K. Seeb, James E. Seeb, Lisa W. |
author_sort |
Limborg, Morten T. |
title |
Data from: Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation |
title_short |
Data from: Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation |
title_full |
Data from: Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation |
title_fullStr |
Data from: Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation |
title_full_unstemmed |
Data from: Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation |
title_sort |
data from: temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation |
publishDate |
2014 |
url |
https://doi.org/10.5061/dryad.pp43m |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Oncorhynchus gorbuscha Pink salmon |
genre_facet |
Oncorhynchus gorbuscha Pink salmon |
op_source |
oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:86834 oai:easy.dans.knaw.nl:easy-dataset:86834 10.5061/dryad.pp43m 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.pp43m https://dx.doi.org/10.5061/dryad.pp43m |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.pp43m |
_version_ |
1766160574065934336 |