Coastal fishes of the western North Atlantic, such as sciaenids and their competitors, support substantial commercial and recreational fisheries in waters that may vary widely in temperature, salinity, light intensity and spectral distrubution, and dissolved oxygen levels, yet their ecophysiological abilities to cope with such variability have received little attention. I therefore applied multidisciplinary comparative techniques to investigate aspects of the sensory and energetic ecophysiology of several sciaenid fishes and non-sciaenid competitors common in the western North Atlantic. Auditory brainstem response experiments demonstrated that sciaenid fishes have greatest auditory sensitivity at low frequencies that match their vocalizations. Based upon both anatomy and auditory bandwidths, most sciaenids appear to be hearing generalists that are likely sensitive to the particle motion components of aquatic sounds. Electroretinographic experiments revealed that the luminous sensitivities, temporal properties, and chromatic characteristics of the visual systems of phylogenetically-similar sciaenid fishes from different microhabitats, and those of phylogenetically-dissimilar piscivores from similar microhabitats, all correlated with lifestyle and ecology. The eyes of benthic and nocturnal fishes were typified by high luminous sensitivity, slow temporal resolution, and relative diel-invariance, consistent with foraging in dim photoclimates. By contrast, the eyes of pelagic diurnal piscivores had comparatively lower luminous sensitivity, higher temporal resolution, and exhibited higher diel variation, consistent with specific diurnal light niches. Accordingly, visually-foraging diurnal piscivores may be disadvantaged in eutrophied, turbid waters characteristic of many modern estuaries. Intermittent-flow respirometry experiments revealed that the majority of sciaenid fishes had resting and active metabolic rates similar to those of most teleost fishes but significantly lower than high-demand species such as tunas. However, the metabolic rates of kingfishes (Menticirrhus sp.) were significantly higher than other sciaenids, but significantly lower than those of tunalike fishes. Estimates of standard metabolic rate from power performance curves fitted to active metabolic rate data did not differ significantly from experimentally-derived measurements in static chambers, validating the experimental approach. Data from these chapters were analyzed with linear repeated measures and nonlinear mixed effects models that considered repeated measurement of subjects, modeled within-individual correlations, and the included random factors that improved the scope of inference. Although not novel approaches, these methods demonstrate quantitative advancements for future analyses of physiological data comprised of multiple measurements taken from individual experimental subjects. Collectively, the results of this dissertation underscore the potential power and utility of physiological techniques to provide a wide variety of information that may complement more traditional techniques used in fisheries science, particularly when coupled with appropriate analytical strategies. Sciaenid fishes are model organisms for investigations of the links between form, function, and the environment in coastal ecosystems.

Meiotic recombination plays a fundamental role in many sexually reproducing species. Recombination shuffles the genetic material during the first meiotic cell division resulting in new combinations of alleles within each chromosome. In many organisms, the rate of recombination is not uniform across the genome but consists of so called hotspots where the recombination rate is remarkably higher than the genome average. In mammals, the regulation and location of recombination hotspots is regulated by a gene called PRDM9. Many nonmammalian animals, like birds, lack this gene and the precise mechanism for recombination rate regulation is still unknown. Previous findings in passerine birds have observed an association between recombination rate and a genomic feature known as CpG islands (CGIs). CGIs are often located in promoter regions of genes and depending on their methylation status constitute accessible chromatin regions. It has therefore been suggested that the proteins involved in the regulation of recombination have better access to less condense chromatin regions. In this study, I tested if the association between recombination rate and CGIs found in passerine birds is also true in chicken. I also tested if methylation levels of CGIs play a role in recombination rate regulation in chicken. To this end, I used previously published data for CGI locations and a methylation map in chicken, and unpublished data of recombination rate estimates. I found that the association between recombination rate and CGIs observed in passerine birds extends to chicken, suggesting that this is an ancestral trait in birds. I did not, however, find a negative association between methylation levels and recombination rate as hypothesised based on a relationship between methylation level and chromatin accessibility. This suggests that DNA methylation level at CGIs is not a strong determinant of recombination in chicken, although there may be some workflow artefacts or unknown factors remaining in my analysis obscuring the relationship between these two variables.

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We applied the Floristic Quality Index (FQI) to vegetation data collected across a chronosequence of created wetland (CW) sites in Virginia ranging in age from one to 15 years post-construction. at each site, we also applied FQI to a nearby forested reference wetland (REF), for a total of 30 sites (15 created, 15 reference). We tested the performance of the index against a selection of community metrics (species richness, diversity, evenness, percent native species) and site attributes (age, soil physiochemical variables). The relationship between FQI and community and environmental variables was analyzed with Spearman's rank order correlation coefficient and Canonical Correspondence Analysis (CCA). Calculation of FQI with all species (including non-natives) did not increase the number of significant correlations (p<0.05) with community attributes and/or environmental parameters when compared with FQI based on native species alone. Further, vegetation layer-based FQI calculations improved the sensitivity of the index to differences in floristic quality between sites when compared with an "overall" index calculated across layers, and a modified, abundance-weighted FQI showed a unique correspondence with community and environmental variables in the CW herbaceous layer and REF herbaceous and shrub-sapling layers. These results suggest that a "natives only", layer-based version of the index should be used in wetland assessment in Virginia, and an abundance-weighted FQI may be a useful tool for assessing floristic quality in certain layers. An abundance-weighted format is perhaps desirable because such an index preserves the "heritage" aspect of the species conservatism concept inherent in floristic quality assessment, and also entrains the "ecology" aspect of site assessment based on relative abundances of the inhabiting species. FQI did not successfully relate CW sites to REF sites, bringing into question the applicability of the FQI concept in comparing created wetlands to reference wetlands, and the use of forested reference wetlands in general to assess vegetation development in created sites. Based on correlations with soil nutrient variables and ordination results, we propose a conceptual model of vegetation development in created wetlands described as the "Initial Conditions" model, which is expressed in terms of initial site conditions, soil chemistry, species diversity, and floristic quality.

Age and growth rates for salmon sharks (Lamna ditropis) in the eastern North Pacific (ENP) were estimated from seasonally formed bands in the vertebrae, and compared to previously published life history parameters for this species from the western North Pacific (WNP). Results of this study show that salmon sharks in the ENP achieve their maximum length at a faster rate, reach sexual maturity at an earlier age and achieve a greater weight-at-length than those in the WNP. Additionally, this dissertation shows that adult salmon sharks maintain a specific body temperature independent of changes in ambient temperature through a combination of physical and physiological means, and essentially function as homeotherms. Due to uncertainty in previous life history parameter estimates for sand tiger sharks (Carcharias taurus) in the western North Atlantic, age and growth rates were re-estimated using a larger sample size and captive individuals injected with oxytetracycline (OTC), a fluorescent skeletal marker. The results support a hypothesis that this species forms one pair of growth bands annually in the vertebral centra, whereas previous growth rate estimates were based on the formation of two bands per year. as such, the growth rate of this species is considerably slower than previously predicted and the population more susceptible to fishing mortality. Demographic analyses were conducted for salmon sharks in the ENP and WNP, and for sand tiger sharks (based on new life history parameter estimates) with uncertainty in vital rates incorporated via Monte Carlo simulations. Density-dependent compensation was included in models where fishing mortality was imposed by increasing sub-adult survivorship from output values generated by a previously published "Intrinsic Rebound Potential" model. The results indicate that both species are extremely vulnerable to fishing mortality and that no fishery should be implemented for sand tiger sharks or salmon sharks in the WNP. Salmon sharks in the ENP were the only population examined that indicated the potential to tolerate any fishing mortality. A comparison of growth completion rates and other life history parameters of ectothermic and endothermic sharks did not indicate that endothermic sharks achieve their maximum length at a faster rate than ectothermic sharks.

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Theory and small-scale experiments predict that biodiversity losses can decrease the magnitude and stability of ecosystem services such as production and nutrient cycling. Most of this research, however, has been isolated from spatial processes, such as dispersal and disturbance, which create and maintain diversity in nature. Since common anthropogenic drivers of biodiversity change, such as habitat fragmentation, species introductions, and climate change, are mediated by these understudied processes, it is unclear how environmental degradation will affect ecosystem services. This dissertation examines how diversity interacts with spatial processes to affect the magnitude and stability of ecosystem functions, using seagrass communities as a model system. Diverse communities were more resistant to colonization, but the order of species arrivals affected competition outcomes. as predicted, grazer metacommunities assembled from diverse species pools were more diverse at all scales, had larger grazer populations, and usually kept their primary food resource, epiphytic algae, at lower abundances than metacommunities assembled from smaller species pools. Counter to theory, increasing the number of mobile grazer species in these metacommunities increased spatial and temporal variability of producers and grazers. Effects of diversity on stability also differed qualitatively between patch and metacommunity scales. Moreover, allowing grazers to move among patches reduced diversity effects on production and modified relationships between grazer diversity and stability. Finally, dispersal significantly increased resistance to and recovery from a mimicked macroalgal bloom. However, diversity did not. None of the existing theories for biodiversity-ecosystem function relationships or consumer-resource metacommunity dynamics completely explained patterns observed in these experiments. Effects of diversity and dispersal on ecosystem functions were complex, but seemed to be influenced by habitat choice and synchronization of grazer and epiphyte dynamics among patches. Overall, these results emphasize the importance of incorporating spatial processes and trophic interactions into the study of biodiversity-ecosystem function relationships. This information is critical for conserving diversity and managing ecosystem services in light of the ongoing changes to regional species pools caused by anthropogenic disturbance.

The spatially complex lower Chesapeake Bay estuary is characterized by a variety of bottom types and hydrodynamic regimes. to account for this physically-induced variability a benthic habitat delineation scheme was developed based on existing knowledge of physical and geological characteristics. Within the context of this scheme a series of studies were conducted to identify biotic response to and interactions with the physical, chemical and geological gradients that characterize the lower Chesapeake Bay. These studies characterized organism distribution and abundance patterns within the lower bay and identified processes controlling those patterns. The biological community of the polyhaline basin habitat, an area characterized by moderate tidal, but little wave-induced bottom disturbance was defined and described for the first time. This community is characterized by large tube and burrow builders, epifaunal and commensal organisms, shallowly-distributed, short-lived species and deeply-dwelling predators. The basin is also the preferred habitat of overwintering blue crabs and an area where biotic sediment reworking generally exceeds physical reworking. The results of these studies suggest that within the lower Chesapeake Bay estuarine system, the relative importance of biological versus physical processes in maintaining the structure and dynamics of estuarine benthic communities will be greatest in the basin habitat.

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