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
<8, missing data >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.