Data and scripts for "The historical patterns that have shaped contemporary genetic differentiation across populations of Arctic charr in Scotland" by Sam Fenton, Colin W. Bean, Kathryn R. Elmer & Colin E. Adams

-Sample_list provides a list of all individuals across the dataset and the Accession numbers for raw ddRADseq data on NCBI short read archive and ND1 sequences on Genbank.

-Filtered.snps.vcf is the VCF file for the filtered SNP data (N=24,878 SNPs and 410 individuals).

-No_missing_data.snps.vcf is the VCF only containing the SNPs used for phylogenetic analysis i.e. no missing data and no non-neutral SNPs (N=5949 SNPs and 410 individuals).

S_alpinus_ND1_sequence.fa is the multiple sequence alignment of ND1 sequences generated for this paper (N=155).

-Neutral_SNPs.newick is the Newick tree used for the Treemix analysis. Code for these analysis was originally published as part of Dahms et al. (2022) Cast away in the Adriatic: Low degree of parallel genetic differentiation in three-spined sticklebacks. Molecular Ecology

-Pairwise_FST_geographic_distance.xlsx provides the pairwise FST values and the geographic distances used to calculate Isolation-by-distance. The type of comparison (e.g. within Hydrometric area, across Hydrometric Area, and within lake) is also indicated. 

-British_Isles_bathy.nc is the bathymetric data used to determine least-cost distance across the marine environment. Data was collected from GEBCO database.

-outlet_coordinates.csv is the latitude and longitude coordinates from each marine outlet point for river catchments to calculate least cost distance across the marine environment. Note theat populations in the same river system will have the same outlet point.

-marine_distances_between_outlets_km is the calculated least-cost distance between marine outlet points. These values are combined with distances within river systems to marine outlets calculated in QGIS to give total distances across river catchments.

-genetic_geographic.R contains the script used to calculate least-cost distance across marine environment and the comparisons of Isolation-by-distance.