Data from: Genetic population structure in prickly sculpin (Cottus asper) reflects isolation by environment between two life history ecotypes

Life-history transitions have evolved repeatedly in numerous taxa, although the ecological and evolutionary conditions favouring such transitions in the presence of gene flow remain poorly understood. The present study aimed to disentangle the effects of isolation-by-distance and isolation-by-environment on genetic differentiation between two sympatric life-history ecotypes. Using 14 microsatellite loci, we first characterized amphidromous and freshwater groups of Cottus asper in a high gene flow setting in the Lower Fraser River system (south-western British Columbia, Canada) to test for the effects of habitat and geographical distance on the distribution of life-history ecotypes. Within the main river channel, no genetic differentiation was found, whereas tributaries even close to the estuary were genetically differentiated. Partial mantel tests confirmed that genetic differentiation between river tributaries and the main channel was independent from geographical distance, with distance-scaled migration rates indicating reduced gene flow from the main channel into the tributaries. Our results suggest that isolation-by-environment can play an important role for the early stage of life-history transitions, and may promote differentiation among life-history ecotypes despite the presence of gene flow.