SNPS dataset of the Baryancistrus species of the Tocantins river

This dataset contains Variant Call Format (VCF) files with SNPs derived from double-digest RADseq (ddRADseq) for three rheophilic armored catfish species (Baryancistrus longipinnis, Baryancistrus niveatus, and Baryancistrus sp. “Araguaia”) sampled in the Tocantins River basin, Brazil. Raw sequence data were processed with Stacks, following quality control (Q20 trimming, head cropping, length filtering), and loci were assembled de novo. SNPs were subsequently filtered to build neutral SNP datasets, using thresholds for minimum allele frequency (MAF ≥ 0.025), Hardy–Weinberg equilibrium, depth, missing data, and linkage disequilibrium pruning. Outlier loci (putative under selection) were removed. Final datasets retained: B. longipinnis: 2,758 neutral SNPs (24 individuals) B. niveatus: 5,040 neutral SNPs (15 individuals) Baryancistrus sp. “Araguaia”: 3,508 neutral SNPs (6 individuals) The VCFs can be used to replicate analyses of genetic diversity, population structure, isolation by distance (IBD), and landscape genomics presented in the associated study: Where are we going to live? Population genomics emits warning signal about endangered Amazonian rheophilic loricariids under habitat loss.