Data from: Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins
Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication wa...
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ftzenodo:oai:zenodo.org:5007156 2023-06-06T11:52:00+02:00 Data from: Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins Lopez, Maria E. Benestan, Laura Moore, Jean-Sebastien Perrier, Charles Gilbey, John Di Genova, Alex Maass, Alejandro Díaz, Diego Lhorente, Jean-Paul Correa, Katharina Neira, Roberto Bernatchez, Louis Yáñez, José M. 2018-08-02 https://zenodo.org/record/5007156 https://doi.org/10.5061/dryad.60b9p56 unknown doi:10.1111/eva.12689 https://zenodo.org/communities/dryad https://zenodo.org/record/5007156 https://doi.org/10.5061/dryad.60b9p56 oai:zenodo.org:5007156 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode Salmo salar selective sweeps single nucleotide polymorphisms info:eu-repo/semantics/other dataset 2018 ftzenodo https://doi.org/10.5061/dryad.60b9p5610.1111/eva.12689 2023-04-13T21:31:05Z Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In the present study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population-specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point towards a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps. Genotypes_CAN-W-D_SCT-W-DThis VCF file includes the genotypes of four ... Dataset Atlantic salmon Salmo salar Zenodo |
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Open Polar |
collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
unknown |
topic |
Salmo salar selective sweeps single nucleotide polymorphisms |
spellingShingle |
Salmo salar selective sweeps single nucleotide polymorphisms Lopez, Maria E. Benestan, Laura Moore, Jean-Sebastien Perrier, Charles Gilbey, John Di Genova, Alex Maass, Alejandro Díaz, Diego Lhorente, Jean-Paul Correa, Katharina Neira, Roberto Bernatchez, Louis Yáñez, José M. Data from: Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins |
topic_facet |
Salmo salar selective sweeps single nucleotide polymorphisms |
description |
Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In the present study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population-specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point towards a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps. Genotypes_CAN-W-D_SCT-W-DThis VCF file includes the genotypes of four ... |
format |
Dataset |
author |
Lopez, Maria E. Benestan, Laura Moore, Jean-Sebastien Perrier, Charles Gilbey, John Di Genova, Alex Maass, Alejandro Díaz, Diego Lhorente, Jean-Paul Correa, Katharina Neira, Roberto Bernatchez, Louis Yáñez, José M. |
author_facet |
Lopez, Maria E. Benestan, Laura Moore, Jean-Sebastien Perrier, Charles Gilbey, John Di Genova, Alex Maass, Alejandro Díaz, Diego Lhorente, Jean-Paul Correa, Katharina Neira, Roberto Bernatchez, Louis Yáñez, José M. |
author_sort |
Lopez, Maria E. |
title |
Data from: Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins |
title_short |
Data from: Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins |
title_full |
Data from: Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins |
title_fullStr |
Data from: Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins |
title_full_unstemmed |
Data from: Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins |
title_sort |
data from: comparing genomic signatures of domestication in two atlantic salmon (salmo salar l.) populations with different geographical origins |
publishDate |
2018 |
url |
https://zenodo.org/record/5007156 https://doi.org/10.5061/dryad.60b9p56 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
doi:10.1111/eva.12689 https://zenodo.org/communities/dryad https://zenodo.org/record/5007156 https://doi.org/10.5061/dryad.60b9p56 oai:zenodo.org:5007156 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.60b9p5610.1111/eva.12689 |
_version_ |
1767957834974101504 |