Data for paper: The making of a genetic cline: introgression of oceanic genes into coastal cod populations in the North East Atlantic
Files included in this data package includes data, scripts and a simulation program to replicate simulations of genetic divergence patterns and comparision with observations, as described in the paper. Filename: content coastalcoddata.csv: genotypes and metadata, described in detail below IBD.dat: d...
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ftzenodo:oai:zenodo.org:4586840 2024-09-15T17:52:28+00:00 Data for paper: The making of a genetic cline: introgression of oceanic genes into coastal cod populations in the North East Atlantic Jorde, Per Erik Huserbråten, Mats Seliussen, Bjørghild Myksvoll, Mari Vikebø, Frode Dahle, Geir Aglen, Asgeir Johansen, Torild 2021-03-05 https://doi.org/10.5061/dryad.zs7h44j7t unknown Zenodo https://doi.org/10.1139/cjfas-2020-0380 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.zs7h44j7t oai:zenodo.org:4586840 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode info:eu-repo/semantics/other 2021 ftzenodo https://doi.org/10.5061/dryad.zs7h44j7t10.1139/cjfas-2020-0380 2024-07-25T11:01:08Z Files included in this data package includes data, scripts and a simulation program to replicate simulations of genetic divergence patterns and comparision with observations, as described in the paper. Filename: content coastalcoddata.csv: genotypes and metadata, described in detail below IBD.dat: data, pairwise observed Fst among cod samples report_pairwise_Fst_Vikingbank.R: R-script to extract relevant data from IBD.dat connectivity_matrix.txt: output from oceanographic modelling, for simulations popfile.dat: population data, for simulations simmat: compiled simulation program (linux 64 bit, dynamically linked) simmat.c: C source code for simmat simulation program simloop.R: R-script for running simulations (R.scripts uses the R computing environment: https://www.r-project.org/) The coastalcoddata.csv file contains SNP genotypes and metadata for individual cod (one line per individual), coastal cod as well as reference samples: Column name: Explanation RefSamp: 0 = coastal cod sample, 1 = North Sea reference sample, 2 = NEAC reference sample Region: County (prior to 2020 county revision) Locality: Name of sample locality Year: Year of sampling Lat: Latitude of sample locality Long: Longitude of sample locality SampleID: Internal ID og sample locality and year IndividualID: Individual number Otype: Otolith type of individual (1 = certain CC/NS, 2 = uncertain CC/NS, 4 = uncertain NEAC, 5 = certain NEAC, where NS=North Sea cod, CC=coastalcod, NEAC=North East Arctic cod) Missing: Number of missing genotypes for individual cgpGmoS1026 (and so on): SNP genotype in Genepop 3-digit format (missing genotype =000000) Genotype and position data from coastalcoddata.csv are used to calculate pairwise genetic divergence (Fst) and geographic distances (Dist) among samples, including all individuals or after removal of suspect NEAC individuals (w/otolith types 4 or 5). The calculated values are reported in the IDB.dat file as Fst (all individuals) and Fst.NCC (excluding suspect NEAC), respectively, with lower (CL025) and ... Other/Unknown Material Arctic cod North East Atlantic Zenodo |
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Files included in this data package includes data, scripts and a simulation program to replicate simulations of genetic divergence patterns and comparision with observations, as described in the paper. Filename: content coastalcoddata.csv: genotypes and metadata, described in detail below IBD.dat: data, pairwise observed Fst among cod samples report_pairwise_Fst_Vikingbank.R: R-script to extract relevant data from IBD.dat connectivity_matrix.txt: output from oceanographic modelling, for simulations popfile.dat: population data, for simulations simmat: compiled simulation program (linux 64 bit, dynamically linked) simmat.c: C source code for simmat simulation program simloop.R: R-script for running simulations (R.scripts uses the R computing environment: https://www.r-project.org/) The coastalcoddata.csv file contains SNP genotypes and metadata for individual cod (one line per individual), coastal cod as well as reference samples: Column name: Explanation RefSamp: 0 = coastal cod sample, 1 = North Sea reference sample, 2 = NEAC reference sample Region: County (prior to 2020 county revision) Locality: Name of sample locality Year: Year of sampling Lat: Latitude of sample locality Long: Longitude of sample locality SampleID: Internal ID og sample locality and year IndividualID: Individual number Otype: Otolith type of individual (1 = certain CC/NS, 2 = uncertain CC/NS, 4 = uncertain NEAC, 5 = certain NEAC, where NS=North Sea cod, CC=coastalcod, NEAC=North East Arctic cod) Missing: Number of missing genotypes for individual cgpGmoS1026 (and so on): SNP genotype in Genepop 3-digit format (missing genotype =000000) Genotype and position data from coastalcoddata.csv are used to calculate pairwise genetic divergence (Fst) and geographic distances (Dist) among samples, including all individuals or after removal of suspect NEAC individuals (w/otolith types 4 or 5). The calculated values are reported in the IDB.dat file as Fst (all individuals) and Fst.NCC (excluding suspect NEAC), respectively, with lower (CL025) and ... |
format |
Other/Unknown Material |
author |
Jorde, Per Erik Huserbråten, Mats Seliussen, Bjørghild Myksvoll, Mari Vikebø, Frode Dahle, Geir Aglen, Asgeir Johansen, Torild |
spellingShingle |
Jorde, Per Erik Huserbråten, Mats Seliussen, Bjørghild Myksvoll, Mari Vikebø, Frode Dahle, Geir Aglen, Asgeir Johansen, Torild Data for paper: The making of a genetic cline: introgression of oceanic genes into coastal cod populations in the North East Atlantic |
author_facet |
Jorde, Per Erik Huserbråten, Mats Seliussen, Bjørghild Myksvoll, Mari Vikebø, Frode Dahle, Geir Aglen, Asgeir Johansen, Torild |
author_sort |
Jorde, Per Erik |
title |
Data for paper: The making of a genetic cline: introgression of oceanic genes into coastal cod populations in the North East Atlantic |
title_short |
Data for paper: The making of a genetic cline: introgression of oceanic genes into coastal cod populations in the North East Atlantic |
title_full |
Data for paper: The making of a genetic cline: introgression of oceanic genes into coastal cod populations in the North East Atlantic |
title_fullStr |
Data for paper: The making of a genetic cline: introgression of oceanic genes into coastal cod populations in the North East Atlantic |
title_full_unstemmed |
Data for paper: The making of a genetic cline: introgression of oceanic genes into coastal cod populations in the North East Atlantic |
title_sort |
data for paper: the making of a genetic cline: introgression of oceanic genes into coastal cod populations in the north east atlantic |
publisher |
Zenodo |
publishDate |
2021 |
url |
https://doi.org/10.5061/dryad.zs7h44j7t |
genre |
Arctic cod North East Atlantic |
genre_facet |
Arctic cod North East Atlantic |
op_relation |
https://doi.org/10.1139/cjfas-2020-0380 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.zs7h44j7t oai:zenodo.org:4586840 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.zs7h44j7t10.1139/cjfas-2020-0380 |
_version_ |
1810294496224608256 |