This package includes the following : A matrix of 5,111 SNPs genotyped in the subgenus Alytes (Ao_complex_5111loci.str) A matrix of 3,535 SNPs genotyped in A. o. lusitanicus, A. o. pertinax and A. cisternasii (OC_3535loci.str) A matrix of 15,211 SNPs genotyped in A. o. pertinax and A. dickhilleni (OD_15211loci.str) SNP matrices (.str), Q estimates and environemental suitability estimates (Q_transect_xxx.txt), distances along transects (dist_transect_xxx.txt), hzar inputs (Input_HZ_xxx.csv), lists of diagnostic loci (HZ_xxx_diag_loci.csv) and R commands (HZ_xxx.r), as used to analyze the hybrid zones coded as CAN, HUE, POR, MAD, GAL, PYR Locus-by-locus cline parameters for the eight hybrid zones considered (Clines_HZ_xxx.csv) and R commands used for vizualization (Clines.Display.r) Occurrence records of Alytes (Occurence_dataset.csv) Bioacoustic dataset (Bioacoustic_dataset.csv), and the R commands used for analyses (Bioacoustics.r) Morphometric dataset, including raw measurements (Morphometric_dataset.csv), the input file for GroupStruct (Morphometric_dataset_naked.csv), the size-corrected measurements (Morphometric_dataset_corrected.csv), and the R commands used for analyses (Morphometrics.r) Environemental dataset (Environemental_dataset.csv), and the R commands used for analyses (Environmental.r)