Fine-scale genetic structure of brook trout in a dendritic stream network

Abstract

Conservation management of threatened species requires identifying the landscape features that shape population structure. Within river ecosystems, the dendritic nature of river networks and physical barriers, such as waterfalls, can strongly shape population structure. We examined population structure of native brook trout in a river network in northern New Hampshire, USA, including above and below waterfalls. We genotyped fish at 12 microsatellite loci including samples from six tributaries, mobile adults from three mainstem rivers, and fish from the hatchery broodstock that had been earlier stocked in the study region. We found that two subpopulations in tributaries above waterfalls were distinguished as unique genetic clusters with high levels of among population genetic diversity (average pairwise FST = 0.20) and low levels of within population genetic diversity (average allelic richness AR = 3.55), including one sub-population above a waterfall. With only one exception, subpopulations below waterfalls exhibited patterns of genetic diversity within and among populations consistent with contemporary gene flow among these subpopulations (average FST = 0.03; AR = 5.83). Most mobile adult fish caught in the mainstem rivers were genetically similar to those found in tributaries without waterfalls, suggesting that mobile individuals are likely connecting below-barrier subpopulations. Despite recent hatchery stocking in this system, we did not observe evidence of hatchery introgression with wild-caught fish. The complex metapopulation of naturally isolated and connected subpopulations of brook trout described in this study highlights the importance of considering fine scale genetic structure in conservation management.