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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Online Access: | https://dx.doi.org/10.5061/dryad.dg8f3 https://datadryad.org/stash/dataset/doi:10.5061/dryad.dg8f3 |
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ftdatacite:10.5061/dryad.dg8f3 2024-02-04T09:58:53+01:00 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 https://dx.doi.org/10.5061/dryad.dg8f3 https://datadryad.org/stash/dataset/doi:10.5061/dryad.dg8f3 en eng Dryad https://dx.doi.org/10.1111/eva.12407 Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 allelotyping Salmo salar introgressive hybridization SNP array aquaculture escapee Holocene Dataset dataset 2016 ftdatacite https://doi.org/10.5061/dryad.dg8f310.1111/eva.12407 2024-01-05T01:14:15Z 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) ... : 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 the old Teno and Finnmark pools. B_allele_freqs_all_pops.csv: Corrected B allele frequencies for all populations. Individuals_and_pooling.csv: Details of genotyped individuals. ... Dataset Atlantic salmon Finnmark Salmo salar Finnmark DataCite Metadata Store (German National Library of Science and Technology) Teno ENVELOPE(25.690,25.690,68.925,68.925) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
allelotyping Salmo salar introgressive hybridization SNP array aquaculture escapee Holocene |
spellingShingle |
allelotyping Salmo salar introgressive hybridization SNP array aquaculture escapee Holocene 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 |
allelotyping Salmo salar introgressive hybridization SNP array aquaculture escapee Holocene |
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) ... : 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 the old Teno and Finnmark pools. B_allele_freqs_all_pops.csv: Corrected B allele frequencies for all populations. Individuals_and_pooling.csv: Details of genotyped individuals. ... |
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 |
publishDate |
2016 |
url |
https://dx.doi.org/10.5061/dryad.dg8f3 https://datadryad.org/stash/dataset/doi:10.5061/dryad.dg8f3 |
long_lat |
ENVELOPE(25.690,25.690,68.925,68.925) |
geographic |
Teno |
geographic_facet |
Teno |
genre |
Atlantic salmon Finnmark Salmo salar Finnmark |
genre_facet |
Atlantic salmon Finnmark Salmo salar Finnmark |
op_relation |
https://dx.doi.org/10.1111/eva.12407 |
op_rights |
Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 |
op_doi |
https://doi.org/10.5061/dryad.dg8f310.1111/eva.12407 |
_version_ |
1789963467717869568 |