Genotype-by-sequencing data of Salmo trutta and Salmo salar

Genome wide genotypes from extracted DNA were obtained through the genotype-by-sequencing approach double-digest RAD. For these data digestion with the restriction enzymes PstI (cut site 5’-CTGCA|G-3’) and MSEI (cut site 5’-T|TAA-3’) was used in combination with size selection of the range 250-600bp. Each library, containing 60-90 individual fish, was added 5% PhiX and before 150bp paired-end sequencing in a single lane on a HiSeq X Ten platform (Illumina). Reads were then aligned to the S. trutta genome reference assembly (accession fSalTru1.1) for variant detection. R code for figures constructed from these data are also included. The file trout-salmon-genotypes.vcf.gz contains genotypes in vcf format.The file trout-salmon-individuals.txt relates genotypes to sampling site.The file Figures-code.r contain code for figures generated from the data.