Salinity-associated differential gene expression in natural populations of the euryhaline killifish Aphanius iberus

Background Salinity is a major ecological driver in aquatic environments and strongly influences the physiology, distribution, and survival of fish species. While many fishes are restricted to narrow salinity ranges, euryhaline species can tolerate large osmotic fluctuations despite the substantial physiological adjustments required. The Spanish toothcarp, Aphanius iberus , an endemic Mediterranean killifish, is one of such exceptional species capable of inhabiting environments ranging from freshwater to hypersaline systems. However, despite this remarkable resilience, the molecular mechanisms underlying salinity tolerance and osmoregulatory plasticity in this species remain poorly understood. Results We analyzed using RNA sequencing transcriptomes from the gills and gastrointestinal tract of individuals from four wild populations spanning a natural salinity gradient from freshwater (0.75 PSU) to brackish (5-10 PSU) and hypersaline (~50 PSU) habitats. Differential gene expression analyses revealed strong tissue-specific patterns and environment-dependent responses. A substantially higher number of differentially expressed genes was detected in the gills, where genes associated with ion transport, cytoskeletal remodeling, and energetic metabolism varied across salinity conditions, reflecting their central role in osmoregulation. In the gastrointestinal tract, pathways related to lipid and carbohydrate metabolism were enriched, particularly in brackish populations. In addition, several genes associated with osmotic stress responses, including ATPases, histones, and transposable elements, showed significant expression differences across populations. Conclusions These findings offer novel insights into the molecular architecture of salinity tolerance in euryhaline fishes, highlighting coordinated transcriptional responses across tissues involved in ion regulation and metabolic adjustment and improving our understanding of how euryhaline fishes cope with extreme and fluctuating osmotic environments. From a conservation perspective, identifying the molecular basis of this physiological plasticity contributes to the management of this highly threatened endemic species and the dynamic coastal habitats it inhabits.