Stocked‐Fish Introgression into Wild Brook Trout Populations Depends on Habitat

The genetic constitution of populations is affected by myriad factors, including both natural and anthropogenic habitat transformations. Previous work on the population structure of Brook Trout Salvelinus fontinalishas suggested that supplemental stocking for fishery enhancement has transformed natural genetic diversity. We utilized microsatellite analysis of 11 loci to examine the genetic structure of over 950 Brook Trout sampled across 50 locations, including hatcheries; holding ponds; wild, unstocked waters; and repeatedly stocked waterbodies across Adirondack lakes and ponds in New York State, USA. From these data, we estimated the degree of introgressive hybridization, tested for associations with landscape and stocking variables, and tested predicted patterns of genetic diversity, effective population size, and genetic population structure. Widespread repeated stocking of a single hybrid strain has led to the dramatic genetic homogenization of Brook Trout across the sampled lakes and ponds. Model selection indicated that environmental factors were more important than stocking intensity for determining the extent of stocked‐fish introgression, and certain environmental circumstances may make some populations relatively resilient to repeated stocking activities. Known, protected heritage strains were confirmed as mostly unadmixed, but holding ponds with heritage brood populations used for supplemental stocking had become differentiated from the natal strains in two of the three cases tested. In addition to the importance of these results for understanding the effects of stocking activities on the genetic integrity of Brook Trout populations, our findings illustrate how current genetic techniques can aid in the development of management practices that are related to the conservation of species supporting economically important freshwater fisheries.