Data from: Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci

Moore J, Bourret V, Dionne M, Bradbury I, O’Reilly P, Kent M, Chaput G, Bernatchez L

Date Published: October 23, 2014

DOI: http://dx.doi.org/10.5061/dryad.sb601

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Microsatellite genotypes
Downloaded 28 times
Description Genotypes for the 15 microsatellite loci for all 153 sampling locations listed in table S1.
Download Ssalar_usat_genepop_23Sep2014.txt (1.072 Mb)
Details View File Details
Title SNP genotypes
Downloaded 28 times
Description Genotype data for all 3,192 SNP loci (i.e., SNPs after filters, see manuscript for details) and all 50 sampling locations listed in table S2 in Genepop format.
Download Ssalar_SNPall_genepop_28Apr2014.txt (24.17 Mb)
Details View File Details
Title Genotypes for loci under balancing selection inferred from Bayescan
Downloaded 8 times
Description In genepop format with loci names
Download Ssalar_SNP_Bayescan_Regions_neutral_genep...14.txt (812.1 Kb)
Details View File Details
Title Genotypes for loci under positive selection inferred from Bayescan
Downloaded 9 times
Description In genepop format with loci names
Download Ssalar_SNP_Bayescan_Regions_positive_gene...14.txt (812.1 Kb)
Details View File Details
Title Genotypes for outlier loci inferred from Hierarchical FDist
Downloaded 9 times
Description In genepop formal with loci names
Download Ssalar_SNP_ArlequinHier_Fct0.01_genepop_2...14.txt (471.1 Kb)
Details View File Details
Title Genotypes for outlier loci inferred using the nested FDist approach
Downloaded 11 times
Description In genepop format with loci names
Download Ssalar_SNP_nested_hierFdist_29Apr2014.txt (2.229 Mb)
Details View File Details
Title Example mainparam STRUCTURE file
Downloaded 41 times
Description These are the specs for performing the hierarchical population structure analyses on the regional groupings. Identical analyses were performed independently for each regional groupings as detailed in the manuscript.
Download mainparams (1.206 Kb)
Details View File Details
Title Details of the Bayescan run
Downloaded 7 times
Description The .verif file from the Bayescan analysis provides details of the parameters used for the run identifying outlier loci and putatively neutral loci in Bayescan. Note that the analysis was performed on regional groups, not on populations and that the genepop file would need to be modified accordingly.
Download Ssalar_SNP_bayescan_REGIONS_8Apr2014_Verif.txt (640.6 Kb)
Details View File Details
Title Genetic map data
Downloaded 6 times
Description Position of all loci used in the present study on the (female) genetic map of Atlantic salmon. Distance units for the locations are in centimorgan, 'lg' refers to linkage groups and the 'totalPos' column refers to distance from the beginning of lg 1. Other distances are for each linkage group separately.
Download MapData_JSM_9May2014.csv (172.3 Kb)
Details View File Details
Title R code to generate random loci
Downloaded 14 times
Description This R code was used to generate the random loci in figure 6.
Download Generate_random_loci.R (8.138 Kb)
Details View File Details
Title Neighbour-joining tree outfile
Downloaded 2 times
Description Output from Phylip program 'Neighbour' for the neighbour-joining of Cavalli-Sforza genetic distances in figure 2
Download ssalar_outtree.tre (3.809 Kb)
Details View File Details
Title PHYLIP infile for NJ tree
Downloaded 5 times
Description PHYLIP infile associated with the NJ tree in fig 2. Note that the Moisie River is removed from this analysis because it is missing all data at one loci.
Download Ssalar_usat_PHYLIP_MOIrem_17Mar2014.inf (644.9 Kb)
Details View File Details

When using this data, please cite the original publication:

Moore J, Bourret V, Dionne M, Bradbury I, O’Reilly P, Kent M, Chaput G, Bernatchez L (2014) Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci. Molecular Ecology 23(23): 5680-5697. http://dx.doi.org/10.1111/mec.12972

Additionally, please cite the Dryad data package:

Moore J, Bourret V, Dionne M, Bradbury I, O’Reilly P, Kent M, Chaput G, Bernatchez L (2014) Data from: Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.sb601
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: