Where Are We Going to Live? Population Genomics Emits Warning Signals about Endangered Amazonian Rheophilic Loricariids under Habitat Loss

Abstract The Araguaia-Tocantins basin is a hotspot of ichthyofaunal endemism within the Amazon biome but is increasingly threatened by habitat fragmentation and environmental degradation, mainly driven by hydroelectric development and waterways. These impacts pose severe risks to lotic habitats, such as rapids, which sustain specialized and range-restricted taxa. We conducted the first population genomic assessment of three rheophilic species of Baryancistrus (B. longipinnis, B. niveatus, and Baryancistrus sp. “Araguaia”) using thousands of genome-wide SNPs obtained through ddRADseq. Overall, analyses revealed weak neutral population structure across species, with limited genetic differentiation. However, subtle isolation by distance was detected in B. niveatus, along with short-distance relatedness in B. niveatus and B. longipinnis. Landscape genetic models (MLPE) indicated that environmental gradients, particularly turbidity, slope, and riparian condition, significantly shaped genetic patterns, especially in B. niveatus. Remarkably, B. longipinnis exhibited low genetic diversity (HO = 0.31 (0.28–0.35); HE = 0.356 (0.36–0.37)), elevated inbreeding (F = 0.12 (0.03–0.20)), and signs of genetic erosion. Tajima’s D values suggested population contraction across all species, likely associated with habitat loss. These findings highlight the vulnerability of rheophilic taxa and identify the Pedral do Lourenço rapids as a key refuge for B. longipinnis, supporting its immediate protection.