Freshwater ecosystems face increasing threats from habitat fragmentation, driven by shifting precipitation patterns and increasing human activities, including water abstraction and damming. Fish, which play a critical role in maintaining riverine biodiversity, functioning and ecosystem services, are particularly impacted. Understanding the genetic consequences of fragmentation at the river network scale is thus crucial for assessing populations and species conservation status and for developing effective management measures.
We analysed the effects of river fragmentation caused by drying and physical barriers on populations of two endemic fish species, Squalius laietanus and Parachondrostoma miegii, within the Siurana basin (Ebro Basin, Spain). This 600 km²-wide Mediterranean basin is heavily impacted by water abstraction, numerous barriers, and worsening droughts in recent years. Utilising sequenced-based microsatellite data, we analysed spatial patterns of genetic variation, including testing for correlations between among-population genetic differentiation, distance, and fragmentation metrics.
We revealed highly structured populations with limited genetic exchange, some being strongly isolated and genetically depauperated, particularly those located upstream. For Squalius laietanus, upstream populations exhibited the lowest allelic richness (AR: 1.4) and private allelic richness (PA: 0.037), with moderate differentiation across the network (Fst: 0.102–0.232). Parachondrostoma miegii populations showed similarly degraded upstream diversity (AR: 2.78; PA: 0.01) and overall lower genetic differentiation (Fst: 0.038–0.154). Mantel tests and multiple regressions on distance matrices (MRMs) revealed that physical and hydrological fragmentation significantly structured fish populations, increasing the risk of genetic degradation and local extinction, particularly in upstream areas. Overall, our study highlights how riverscape population genetics can reveal patterns of isolation and vulnerability that might otherwise remain unnoticed. Since lack of connectivity hinders population recovery and reduces the adaptive potential to environmental change, this information is essential for designing conservation strategies addressing population-level diversity and mitigating fragmentation impacts. Restoring or maintaining connectivity means not only preserving fish species but also safeguarding river ecosystems' resilience.