Genomic data reveals cryptic diversity and suggests five putative species in the Broad-snouted caiman in South America

This dataset contains genotyping-by-sequencing (GBS) data generated to investigate genetic diversity and population structure in the crocodylian Caiman latirostris across its range in Brazil. Tissue samples were obtained through field surveys conducted between 2018 and 2020, complemented with specimens from herpetological collections at UFES, UFRPE, and PUC-MINAS to ensure representation of all major hydrographic basins where the species occurs. Tissue samples were preserved in ethanol and genomic DNA was extracted using a saline protocol and quantified with Qubit.GBS libraries for 96 individuals were prepared using the restriction enzyme PstI and sequenced on an Illumina HiSeq 2500 platform (single-end reads, up to 110 bp). These data support analyses of population structure, phylogeography, and genetic diversity in C. latirostris and are made available to facilitate reproducibility and future comparative studies.