SNP datasets obtained with ddRADseq from four contact zones between Podarcis carbonelli and four other Podarcis species

We used double digestion restriction site associated DNA (ddRAD) sequencing to discover SNPs in samples from four contact zones between Podarcis carbonelli and four other Podarcis species. We obtained a panel of SNPs for each for each contact zone and reference populations and a dataset of diagnostic SNPs between reference populations for each contact zone but excluding private alleles from references, i.e. excluding alleles that are not present in the populations of contact. The final datasets (complete and diagnostic) were obtained after removing loci with depth coverage 20% and removing individuals with more than 35% of missing data. Across complete and diagnostic datasets, mean coverage by individuals ranged from 28 to 47 and by loci from 28 to 44. The analysis of replicate samples (about 6% of samples were replicated, i.e. were amplified and sequenced in independent libraries and SNP calling was performed independently) showed high levels (>99%) of multilocus genotype replicability.