Multispecies genomic assessment and monitoring of fish biodiversity in response to a major hydroelectric development

Hydroelectric developments can impact connectivity of migratory fishes in rivers. To assess population structure and to inform an upstream fish passage program designed to mitigate impacts of Site C, a new hydroelectric dam on the Peace River, northeastern British Columbia (Canada), we collected single nucleotide polymorphism (SNP) data for six freshwater fish species from the river and seven of its tributaries. Bull trout, Arctic grayling, and rainbow trout (Salmonidae) showed strong differentiation between spawning populations upstream and downstream of the dam. Slimy sculpin (Cottidae), redside shiner, and longnose dace (Leuciscidae) showed variable differentiation between an upstream tributary and Peace River sites, but little differentiation among Peace River sites. Applying SNP assays (6-11 loci) to the salmonids sampled in the Peace River from 2016 to 2024 assigned most bull trout and Arctic grayling to tributaries upstream of the dam (93.8% and 92.2%, respectively). Rainbow trout assignments were more evenly distributed between upstream (53.5%) and downstream tributaries (29.0%). Our results highlight the value of a multispecies approach to understand habitat use and connectivity across species, and suggest that upstream fish passage is vital to maintain connectivity between habitats upstream and downstream of the dam.