(1) Three alternative ddRAD datasets of concatenated SNPs used in ML phylogenetic analyses: (i) Complete data of 71341 SNPs/loci. (ii) Reduced data of 13 184 SNPs/loci present at least in 30% of individuals. (iii) Reduced data of 699 SNPs/loci present at least in 90% of individuals. (2) Alternative ddRAD datasets used for sNMF analysis (in two formats - geno and nexus): (i) 13 586 loci present in 30% of genotyped ingroup individuals. (ii) 787 loci present in 90% of genotyped ingroup individuals. The data are used and analysed in Komarova et al., submitted to Molecular Ecology. [(1) Three alternative ddRAD datasets of concatenated SNPs used in ML phylogenetic analyses: (i) Complete data of 71341 SNPs/loci. (ii) Reduced data of 13 184 SNPs/loci present at least in 30% of individuals. (iii) Reduced data of 699 SNPs/loci present at least in 90% of individuals. (2) Alternative ddRAD datasets used for sNMF analysis (in two formats - geno and nexus): (i) 13 586 loci present in 30% of genotyped ingroup individuals. (ii) 787 loci present in 90% of genotyped ingroup individuals. The data are used and analysed in Komarova et al., submitted to Molecular Ecology.]