Food web models are one tool used by resource managers to evaluate changes in trophic interactions in response to changes in biotic and abiotic drivers in an ecosystem. Food web modeling provides a range of potential outcomes for managers to consider, to use in fisheries management. However, it is well known that food web models require large amounts of disparate data, which can amplify uncertainties in model output. Previous studies have leveraged stable isotope data to compare the trophodynamics between modeled trophic levels and in situ data. Here, we provide a new framework to aid users in evaluating the level of agreement between trophic levels generated from food web models and from stable isotope data using a Bayesian statistical approach. Using a previously developed food web model from coastal Louisiana as a case study, this paper presents an updated framework to use stable isotope analysis as a validation method for food web models. The validation process included Spearman-rank correlation analyses in addition to developing and using the first open-source food web model validation visualization tool, EcoTuneR, this webtool provides a more accessible way visualize the Bayesian derived trophic level probability curves with the food web model trophic levels. Reported correlation between the stable isotope trophic levels and the food web model trophic levels were comparable to previous studies (functional group Spearman-rank correlation, R=0.56, n=47, p > 0.001 | niche-aggregated R=0.77, n=17, p > 0.001 | age-aggregated R=0.53, n=34, p > 0.001). Results of the Bayesian model showed that 47% of the food web model species functional groups fell within the 95% credibility intervals of the Bayesian derived stable isotope trophic levels. Acknowledging that all modeling studies have limitations, this case study provides a framework and a new tool for researchers to better consider uncertainties in data and the inherent variability in coastal ecosystems.

The blue crab (Callinectes sapidus) is a commercially and ecologically importantspecies found along the Atlantic coast of North and South America. These crustaceans play a critical role in coastal ecosystems, serving as both predators and prey in the food web. The blue crab supports a major fishery in Chesapeake Bay, where the species is a cultural icon. Juvenile blue crabs, the smallest and most vulnerable size classes of individuals, are reliant upon structurally complex habitats. Population dynamics of this species are therefore influenced by spatiotemporally fluctuating environmental variables, such as habitat availability. Understanding blue crab ecology is essential for managing their populations sustainably and maintaining the health of their habitats. The primary aim of this dissertation was to quantitatively evaluate the contributions of several widely distributed habitats to blue crab population dynamics in Chesapeake Bay. Empirical valuation of nursery habitat effects on blue crab population dynamics can (i) estimate the optimal extent of habitat required for the long-term sustainability of blue crab fisheries, (ii) quantify how changes in habitat extent will affect blue crab populations, such as alterations due to climate change, and (iii) inform ecosystem-based fisheries management (EBFM) decisions, as a complement to stock assessments. Here, I present four separate but interrelated studies examining habitat-specific demographic rates at multiple spatial and temporal scales. These studies involved a combination of survey data, mensurative and manipulative field experiments, and complex population dynamics models. Chapter 1 evaluates nursery habitat contributions to blue crab population dynamics by examining relationships between juvenile blue crab distributions and multiple environmental variables in three tributaries—the York, James, and Rappahannock rivers—at broad spatial (regional) and temporal (decadal) scales using fisheries-independent survey data and digitized GIS maps of habitat distributions. Chapter 2 examines fine-scale spatiotemporal (i.e., 10s of km2 over biweekly intervals) variation and ontogenetic shifts in juvenile blue crab densities in salt marsh edge, seagrass, shallow detrital habitat, and unstructured habitat under a suite of physical and biological parameters in the York River. Chapter 3 expands on these findings to examine the mechanistic basis for ontogenetic habitat shifts by evaluating differential abundance and survival of juvenile blue crabs across three size classes in salt marsh edge, seagrass, and unstructured sand habitat, with specific attention to effects of refuge, turbidity, and postlarval supply. Finally, Chapter 4 integrates population-scale indices of abundance from two major fisheries-independent surveys with time-series of habitat data to assess the influence of seagrass species on blue crab population dynamics at the scale of Chesapeake Bay.

Sharks of the Atlantic coast of the United States have suffered increased fishing pressure in last three decades. Commercial and recreational catches jumped in the mid to late 1980's, leading to regulation by the National Marine Fisheries Service in the early 1990's. The Virginia Institute of Marine Sciences' shark long-line survey, begun in 1974, and continuing to the present day, is thus well positioned to look at the effects of this fishing mortality on sharks. Using GAM modelling, six of ten shark species analyzed, including the most common species, Carcharhinus plumbeus, suffered declines of from 98-99% of early abundances in the survey. Only two species showed no significant trends, and only one (C. obscurus) showed signs of recovery. Analysis of size changes showed that both C. plumbeus and C. obscurus have suffered declines in both mean and variance of their size distribution since 1974. Analyses of mass changes showed that five of thirteen species have shown biologically significant declines in mass per shark since 1974. Six of the remaining eight showed no trend in mass per shark. Habitat analyses showed that few species showed effects of climate scale variables such as the North Atlantic Oscillation index, Chesapeake Bay discharge, or the Palmer Drought Index. Many species showed significant changes in patterns in abundance with local environmental variables, such as temperature, salinity, and water depth. These patterns, when combined, revealed several groupings of species, including deep-water species, Bay-abundant species, and near-shore species. Another group consisted of species that occur in this area only as they move north and south en route to more northerly areas for summer months. One group was made up of two species (S. acanthias and M. canis) that occurred almost exclusively in cold water (April and May). Analysis of New Jersey long-line data from 1961-62 with a resample of many of the same sites revealed that abundances off New Jersey show a trend in both mass and abundance similar to that found in the VIMS survey data. Overall, this study demonstrated many trends in shark distribution and ecology not previously shown in any way other than anecdotally.

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Extensive investigations have been made of the oxygen end carbon dioxide content of water in which fishes live. A review of the literature, however, shows that these studies have not been made under controlled laboratory conditions dealing with the species studied in this investigation. It was the purpose of this study to determine the lowest concentration of dissolved oxygen that will support certain species of fishes and, also, the lethal effects resulting from increased carbon dioxide tension as determined under carefully controlled laboratory conditions.

The objectives of this study were to determine naturally occurring concentrations of vitamin A1 and A2 in selected native fishes and, under laboratory conditions, to determine the possible role of beta-carotene and lutein in the synthesis of vitamin A by goldfish. The native fishes were selected to exhibit different feeding habits and were taken from different habitats (stream vs. lake) during different seasons of the year. In the laboratory, two possible precursors, beta-carotene and lutein, were incorporated into the diet to determine the role of these substances in the synthesis of vitamin A. Species of fish differed in amounts of vitamin A1 and A2 by their ability to metabolize vitamin A from their environment. Seasonally, vitamin A1 and A2 were in highest concentration during the fall. Drake's Creek fishes had a higher concentration of vitamin A1 and A2 than did those from Rough River Lake; however, no significant difference was observed. Goldfish readily converted beta-carotene and lutein to vitamin A1 but only lutein conversion to vitamin A2 was suggested. Vitamin A1 conversion to A2 was also observed in this study.

Larval fish were studied on the Middle Fork of Drake's Creek from 18 March 1982 to 9 September 1982. A total of 6,057 individuals representing 28 species and six unidentified cyprinids was collected. Micropterus sp. was the dominant species representing 33% of the total. Most of the remaining taxa were,generally,equally represented. Juvenile banded sculpins were the first larvae observed -- followed by darters, suckers, minnows, and sunfishes. The percid species, logperch, greenside darter, and Etheostoma (Ulocentra), illustrated the longest spawning periods, their larvae being taken from 24 March to 8 July. Maximum species occurrence was observed from 7 July to 15 July when over 20 species of larvae were collected. Larvae avoided the stream current, selecting for low-flow shoreline habitat areas, with few larvae being taken in stream drift. Two-way analyses of variance showed significant differences in habitat selection by nine species of larvae. The two habitats having the highest larval abundance were an emergent vegetation shoreline area and a limestone rock outcrop.

A dependable source of quality fish spawn is a fundamental prerequisite for fish culture development. This is especially important inasmuch as most of the cultivable species do not breed in confined waters. Also, sport fisheries are gaining greater popularity, and subsequently the fish supply is being taxed. Still another need for fish spawn is in the ever increasing demand for bait minnows. Also, the construction of more and more dams has resulted in insurmountable obstacles for ascending and descending fish, which may ultimately result in complete destruction of some fisheries. Thus some measure of artificial propagation will have to be taken to safegaurd our valuable fishery resources. A partial solution to this problem of supplementing natural propagation is that of inducing the fish to spawn artificially in the hatchery. A method of doing this is by stimulating fish to breed by the use of pituitary hormones. Those pituitary hormone-containing glands are often collected under a variety of field conditions which may involve considerable effort, time, and money. Therefore,, it was my objective in this study to develop a practical refined assay on hormones using as small an amount as possible of the crude extract of pituitary suspension, and to make it simple enough that every lay fisheries man ,dll be able to apply it, thus meeting his demand for quality fish eggs in his own hatchery when he needs it most.

The toxin-producing harmful algal bloom (HAB) species Alexandrium monilatum has long been associated with finfish and shellfish mortalities in the Gulf of Mexico. In the summer of 2007, A. monilatum re-emerged as a bloom-forming species in the Chesapeake Bay. Over the last decade, late summer blooms of A. monilatum have been expanding in range in the lower Chesapeake Bay and have reached record-high densities, particularly in the lower York River. This dinoflagellate species overwinters in the sediments as a resting cyst, and upon excystment under suitable environmental conditions produces blooms the following summer. The research presented here includes the first mapping and quantification of resting cysts of A. monilatum in surface sediments in the Chesapeake Bay using quantitative real-time polymerase chain reaction (qPCR) assays. A systematic grid sampling design was employed to collect pre-bloom sediments in the southwestern portion of the Chesapeake Bay each year from 2014-2016. Cysts were widespread in the bottom sediments and sediment cyst density increased from 2014-2016, reaching as high as 90,000 cysts/cc in the York River channel. A multiple linear regression was used to model cyst density using environmental parameters. Sediment type was a strong predictor of cyst density, with higher cyst densities found at sites with more fine sediments (silts and clays). Laboratory HAB toxicity bioassay methods were used to investigate potential adverse health impacts of A. monilatum on adult triploid eastern oysters, Crassostrea virginica. Oyster behavior and mortality were monitored and routine paraffin histology was performed to analyze tissue damage. Oysters did not exhibit mortality or tissue damage in a 48-hour fed toxicity bioassay. However, a 96-hour unfed toxicity bioassay led to 67% mortality, and erosion of the gill and mantle epithelial tissues in 94% of oysters exposed to A. monilatum (live cell or lysate). In the summer of 2015, oysters were deployed in the lower York River to assess effects of exposure before, during, and after a natural A. monilatum bloom. A subsample of six live oysters was collected weekly for two months and processed for histology. There was no mortality of deployed oysters, but minor epithelial erosion of the mantle was seen in half of the oysters sampled during the peak of the A. monilatum bloom from early to mid-August. Field and laboratory results showed that C. virginica did occasionally consume A. monilatum, and exposure of C. virginica to live A. monilatum or lysate could lead to epithelial erosion of external tissues and mortality. It is clear from the findings of this research that A. monilatum has established itself in the York River region of the Chesapeake Bay and that at least under laboratory conditions, persistent exposure to A. monilatum (live or lysate) can have serious potential health impacts on adult oysters.