Minimal Introgression but Restricted Gene Flow: How Stocking and Dams Influence Wild Brook Trout (<scp><i>Salvelinus fontinalis</i></scp>) Genetics and Morphology

ABSTRACT Anthropogenic activities are increasingly influencing eco‐evolutionary processes across spatial, temporal, and biological scales. Freshwater ecosystems, harbouring species that are important for subsistence, recreational, and commercial fisheries, are particularly vulnerable. In North America, brook trout ( Salvelinus fontinalis ) populations have experienced widespread declines due to factors including habitat fragmentation and angling. To increase population densities and meet fishing demands, thousands of captive‐bred individuals are released annually. Stocking, however, could lead to introgression of maladaptive genes into the wild population and, in combination with the presence of dams restricting gene flow, may reduce their evolutionary potential. Here, we sampled 495 fish from 14 inland and two coastal sites in the state of Rhode Island, USA and from two hatchery strains. We used quaddRAD to develop single nucleotide polymorphism (SNP) markers and combined genetic and geometric‐morphometric analyses to evaluate intraspecific variation, the consequences of stocking, and test hypotheses, in a riverscape framework, on how dams influence gene flow. We found moderate genetic structure within streams with low levels of genetic diversity and effective population sizes but higher than the two hatchery strains. Importantly, we found no significant introgression from captive‐bred individuals. However, we did detect isolation‐by‐distance and ‐by‐resistance (due to dams) with evidence for upstream and downstream gene flow occurring mainly within catchments. Phenotypic differentiation also was apparent both between wild and hatchery brook trout and even among streams, correlating with genetic distances. Our findings highlight the importance of fine‐scale analyses in evaluating anthropogenic impacts and uncovering hidden intraspecific variation. Conservation efforts for wild brook trout populations, which harbour distinct genetic and phenotypic variation, will require careful attention, and our results will help inform management strategies across the species' range.