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, but the ecological and evolutionary conditions favoring such transitions in the presence of gene flow remain poorly understood. Here, we 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 (Southwestern British Columbia, Canada) to test for effects of habitat and geographic 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 geographic 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.