The file contains all of the SNP data used in our article. The files named HapMap.fas.txt, HapMap.hmc.txt and HapMap.hmp.txt were obtained with the de novo UNEAK pipeline and respectively contains sequence of the SNP tag/read, the tag/read counts of each allele of the SNPs in each individual and eventually the genotypes. These files were obtained with the following default parameter settings: minimum tag count c = 5, error tolerance rate in the network filter e = 0.03 and minimum minor allele frequency mnMAF = 0.05. The last file named LymantriaD_Picq_et_al_80%_coverage_MafHeHw_LD_20170920.vcf present the 2327 SNPs obtained after the different SNP filtering steps (see Table 2 in our article). The 133 outlier SNPs are present in this file.