Coverage-based SNP filtering
As we used previously sequenced genomes as well as new ones, sequencing coverage in the dataset varied from 7X to 25X. To remove coverage bias in our analysis we only used positions that are covered in all individuals within a population to calculate site frequency spectrum and population genetic statistics. To calculate genetic differentiation (FST ) and absolute divergence (DXY ) we used positions covered in all individuals considered in the comparison. Filtering was done equally on polymorphic and non-polymorphic sites. We calculated nucleotide diversity for different coverage filters for all individuals (1X to 7X) to verify that the genome-wide nucleotide diversities are unbiased to coverage (Fig. S2).