Data from: SNPs to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees
Many wild Atlantic salmon (Salmo salar) populations are threatened by introgressive hybridization from domesticated fish that have escaped from aquaculture facilities. A detailed understanding of the hybridization dynamics between wild salmon and aquaculture escapees requires discrimination of diffe...
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Dryad Digital Repository
2016
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Online Access: | https://doi.org/10.5061/dryad.dg8f3 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::78daf3d4676d90ced54b5094a791dc79 2023-05-15T15:29:02+02:00 Data from: SNPs to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees Pritchard, Victoria L. Erkinaro, Jaakko Kent, Matthew P. Niemelä, Eero Orell, Panu Lien, Sigbjørn Primmer, Craig R. 2016-01-01 https://doi.org/10.5061/dryad.dg8f3 undefined unknown Dryad Digital Repository https://dx.doi.org/10.5061/dryad.dg8f3 http://dx.doi.org/10.5061/dryad.dg8f3 lic_creative-commons 10.5061/dryad.dg8f3 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:93517 oai:easy.dans.knaw.nl:easy-dataset:93517 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Atlantic salmon aquaculture escapee introgressive hybridization SNP array allelotyping North Atlantic Holocene Salmo salar Life sciences medicine and health care anthro-se hist Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2016 fttriple https://doi.org/10.5061/dryad.dg8f3 2023-01-22T17:41:57Z Many wild Atlantic salmon (Salmo salar) populations are threatened by introgressive hybridization from domesticated fish that have escaped from aquaculture facilities. A detailed understanding of the hybridization dynamics between wild salmon and aquaculture escapees requires discrimination of different hybrid classes, however markers currently available to discriminate the two types of parental genome have limited power to do this. Using a high-density Atlantic salmon SNP array in combination with pooled-sample allelotyping and an Fst outlier approach, we identified 200 SNPs that differentiated an important Atlantic salmon stock from the escapees potentially hybridizing with it. By simulating multiple generations of wild-escapee hybridization involving wild populations in two major phylogeographic lineages, and a genetically diverse set of escapees, we showed that both the complete set of SNPs and smaller sub-sets could reliably assign individuals to different hybrid classes up to the third hybrid (F3) generation. This set of markers will be a useful tool for investigating the genetic interactions between native wild fish and aquaculture escapes in many Atlantic salmon populations. Bayescan_Fdist2.tar.gzThis archive contains files used by Pritchard et al. (2016) for Fst outlier analyses: Index.txt - index of SNPs. Bayescan*.in - Bayescan input files, SNPs in index order. Fdist*.in -Fdist2 input files, SNPs in index order. datacal.c; fdist2.c; Original_README_fdist2 - Fdist2 source code & information. R_code_for_analysing_Fdist2_output.txt - modified R code from Lotterhos & Whitlock (2014). See README file in archive for further information.Genotyping_allelotyping.tar.gzThis archive contains the following data files for Pritchard et al. (2016): B_allele_freq_Naatamo_pools.csv: Uncorrected B allele frequencies for the Naatamo pools. B_allele_freq_New_Teno_pools.csv: Uncorrected B allele frequencies for the New Teno mainstem pools. B_allele_freq_Teno_Finnmark_pools.csv: Uncorrected B allele frequencies for ... Dataset Atlantic salmon North Atlantic Salmo salar Unknown Teno ENVELOPE(25.690,25.690,68.925,68.925) |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Atlantic salmon aquaculture escapee introgressive hybridization SNP array allelotyping North Atlantic Holocene Salmo salar Life sciences medicine and health care anthro-se hist |
spellingShingle |
Atlantic salmon aquaculture escapee introgressive hybridization SNP array allelotyping North Atlantic Holocene Salmo salar Life sciences medicine and health care anthro-se hist Pritchard, Victoria L. Erkinaro, Jaakko Kent, Matthew P. Niemelä, Eero Orell, Panu Lien, Sigbjørn Primmer, Craig R. Data from: SNPs to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees |
topic_facet |
Atlantic salmon aquaculture escapee introgressive hybridization SNP array allelotyping North Atlantic Holocene Salmo salar Life sciences medicine and health care anthro-se hist |
description |
Many wild Atlantic salmon (Salmo salar) populations are threatened by introgressive hybridization from domesticated fish that have escaped from aquaculture facilities. A detailed understanding of the hybridization dynamics between wild salmon and aquaculture escapees requires discrimination of different hybrid classes, however markers currently available to discriminate the two types of parental genome have limited power to do this. Using a high-density Atlantic salmon SNP array in combination with pooled-sample allelotyping and an Fst outlier approach, we identified 200 SNPs that differentiated an important Atlantic salmon stock from the escapees potentially hybridizing with it. By simulating multiple generations of wild-escapee hybridization involving wild populations in two major phylogeographic lineages, and a genetically diverse set of escapees, we showed that both the complete set of SNPs and smaller sub-sets could reliably assign individuals to different hybrid classes up to the third hybrid (F3) generation. This set of markers will be a useful tool for investigating the genetic interactions between native wild fish and aquaculture escapes in many Atlantic salmon populations. Bayescan_Fdist2.tar.gzThis archive contains files used by Pritchard et al. (2016) for Fst outlier analyses: Index.txt - index of SNPs. Bayescan*.in - Bayescan input files, SNPs in index order. Fdist*.in -Fdist2 input files, SNPs in index order. datacal.c; fdist2.c; Original_README_fdist2 - Fdist2 source code & information. R_code_for_analysing_Fdist2_output.txt - modified R code from Lotterhos & Whitlock (2014). See README file in archive for further information.Genotyping_allelotyping.tar.gzThis archive contains the following data files for Pritchard et al. (2016): B_allele_freq_Naatamo_pools.csv: Uncorrected B allele frequencies for the Naatamo pools. B_allele_freq_New_Teno_pools.csv: Uncorrected B allele frequencies for the New Teno mainstem pools. B_allele_freq_Teno_Finnmark_pools.csv: Uncorrected B allele frequencies for ... |
format |
Dataset |
author |
Pritchard, Victoria L. Erkinaro, Jaakko Kent, Matthew P. Niemelä, Eero Orell, Panu Lien, Sigbjørn Primmer, Craig R. |
author_facet |
Pritchard, Victoria L. Erkinaro, Jaakko Kent, Matthew P. Niemelä, Eero Orell, Panu Lien, Sigbjørn Primmer, Craig R. |
author_sort |
Pritchard, Victoria L. |
title |
Data from: SNPs to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees |
title_short |
Data from: SNPs to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees |
title_full |
Data from: SNPs to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees |
title_fullStr |
Data from: SNPs to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees |
title_full_unstemmed |
Data from: SNPs to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees |
title_sort |
data from: snps to discriminate different classes of hybrid between wild atlantic salmon and aquaculture escapees |
publisher |
Dryad Digital Repository |
publishDate |
2016 |
url |
https://doi.org/10.5061/dryad.dg8f3 |
long_lat |
ENVELOPE(25.690,25.690,68.925,68.925) |
geographic |
Teno |
geographic_facet |
Teno |
genre |
Atlantic salmon North Atlantic Salmo salar |
genre_facet |
Atlantic salmon North Atlantic Salmo salar |
op_source |
10.5061/dryad.dg8f3 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:93517 oai:easy.dans.knaw.nl:easy-dataset:93517 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
https://dx.doi.org/10.5061/dryad.dg8f3 http://dx.doi.org/10.5061/dryad.dg8f3 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.dg8f3 |
_version_ |
1766359397724848128 |