Podarcis bocagei vs P. carbonelli hybrid zone SNP datasets from ddRADseq

We used double digestion restriction site associated DNA (ddRAD)
sequencing to discover SNPs in samples across a transect including a
hybrid zone between Podarcis carbonelli and Podarcis carbonelli.
We used P. bocagei and P. carbonelli samples from the locations
at the extremes of the transect as references. We obtained a SNP dataset
including all SNPs after removing loci with depth coverage <8,
missing data >20%, removing loci containing more than five SNPs,
and with more than 70% heterozygosity (complete dataset; 6905 SNPs, 329
individuals). Additionally, we obtained from the complete dataset two
other datasets, prior to apply a missing data filter. One dataset
contained loci with allele frequencies higher than 0.8 in the reference
population containing only parental individuals of one species and lower
than 0.2 in the reference population of the other species
("80/20" dataset; 2300 SNPs, 329 individuals); the other dataset
comprised diagnostic SNPs between reference populations (diagnostic
dataset; 1241 SNPs, 236 individuals) but excluding private alleles from
references, i.e. excluding alleles that are not present in the populations
of contact. Individuals with missing data >35% were removed from
all datasets (the number of individuals reported for each dataset is after
applying this filter, but note that the 80/20 and the diagnostic datasets
were obtained before applying this filter to the complete dataset). Across
datasets, average depth of coverage by individuals was 28 (median = 26.8,
min = 12.5, max = 85.8) and by loci was 29 (median = 28.8; min = 15.6; max
= 48.6). The analysis of replicate samples (four samples were replicated
twice, i.e. were amplified and sequenced in independent libraries and SNP
calling was performed independently) showed high levels (99.87%) of
multilocus genotype replicability.