SNP dataset
We obtained 592.4 million reads from the two runs of sequencing. After filtering for low quality reads and assigning individuals to barcodes, on average 1,62 Mio reads per individual aligned to our improved reference genome, resulting in between 0.96 Mio (Site NE1) and 2.61 Mio (C1) reads per population. Across all individuals, high quality reads covered an average of 17.99 Mio nucleotides of the genome (~0.71%). Average number of sites for each individual ranged from 3.1 Mio to 15.5 Mio, with an average of 8.6 Mio per individual. Using this data, a total of 21,892 SNPs present on 7,679 RAD-tags passed filtering and were used in the genotype-environment analyses. The dataset used to examine population structure consisted of 2,476 variable sites with data for all individuals.