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Climate change in the northeastern United States currently and in future decadal predictions is characterized by warmer average temperatures and more frequent and intense storm events. Many aquatic organisms that thrive below a certain temperature threshold, such as brook trout, are being pushed towards their upper thermal limits, ultimately lowering their probability of survival and resilience to disturbance. In late-August and early-September 2011, Hurricane Irene and Tropical Storm Lee created an extended flood in the Delaware Water Gap region of Pennsylvania and New Jersey, as well as much of the northeast. This dissertation examines the effects of this flood on a network of naturally fragmented tributaries in the Delaware Water Gap National Recreation Area. All study sites showed significant changes in mesohabitat and in-stream large woody debris. Because of the area geology, downstream reaches of tributaries were more disturbed, exhibited significant changes in substrate composition, and had a greater loss of species richness. Abundance of all species varied significantly between years, in some locations increasing 500% between 2011 before the flood and 2012 after the flood. Displaced adults and massive increases in young-of-year recruitment should indicate a substantial change in genetic diversity and differentiation over time and space. In fact, pairwise Fst (a comparative measure of genetic differentiation) showed significant differences in nearly all study populations before and after the flood. Of even greater concern was an increase in fixed monomorphic loci in multiple populations. A rich and well-conserved landscape provides the resources necessary to build resilient stream communities and populations after a large disturbance. However, fine scale examination of population genetics show a much graver trend in species health due to fewer reproducing adults and higher offspring survival the following year. Such genetic homogenization increases the likelihood of inbreeding and susceptibility to disease and other long-term environmental stressors. The electronic version of this dissertation is at OhioLink ETD Center, www.ohiolink,edu/etd

The brook trout Salvelinus fontinalis is the only salmonid native to the southern Appalachian Mountains, and is distributed across eastern North America from Canada to Georgia. This species was once abundant in coldwater lakes and streams throughout its range, but environmental disturbances and the introduction of non-native species have drastically reduced the number and sizes of wild populations. Genetic evidence suggests a division at the subspecies level between southern- and northern-derived brook trout populations, with the break between the two forms occurring roughly at the New River watershed. Before the subspecies structure was recognized, brook trout of northern origin were widely stocked throughout the Southeast. The primary objective of this study was to determine the phylogenetic origin of all wild brook trout populations in southwestern Virginia using allozyme markers. Seventy-eight streams believed to contain brook trout in the New, James, Holston, and Yadkin river drainages were sampled by backpack electrofishing. Muscle tissue samples were collected from 916 individuals from 56 populations using a non-lethal biopsy technique. The samples were analyzed by cellulose acetate gel electrophoresis and histochemical staining techniques. Variation at four polymorphic loci, including the diagnostic creatine kinase (CK-A2*) locus, was quantified in terms of genetic diversity and population genetic differentiation. Allele frequencies indicated that 19 populations were of putative southern origin, 5 of northern origin, and 32 of mixed genetic origin. The secondary objective was to determine the geographic distribution of southern- and northern-form brook trout populations throughout the native range using data compiled from all known genetic studies. A map of these data showed that the break between the southern and northern form is sharp, occurring at the New/Roanoke-James watershed divide. Populations from the New River drainage expressed the southern allele at a frequency of 85%, suggesting that their historic native character is southern, and that the presence of northern alleles is due to stocking or stream-capture events. The persistence of the southern form, despite the heavy stocking of northern-derived individuals, may be evidence of an adaptive advantage for the southern form of the species. Existence of adaptive genetic differentiation supports the case for conservation of the southern form of the species in future management of brook trout.