Atlantic horseshoe crabs (Limulus polyphemus) have endured decades of intense harvest pressure. Genetics studies have shown evidence of distinct sub-groups spanning the coast, although few fine-scale studies have been done to delineate these groups on a local level. Massachusetts lies directly between two of these sub-groups. With documented differences in prosomal widths of horseshoe crabs from either side of Cape Cod, it is possible that Cape Cod is a barrier to gene flow and that there are two distinct genetic groups within Massachusetts. Regulations currently consider all horseshoe crabs to be of one stock. I examined 6 microsatellite loci from 193 horseshoe crabs collected from 7 locations across Massachusetts between 5 May and 24 June 2010. I also analyzed the prosomal widths of 324 horseshoe crabs from 8 locations across Massachusetts. Data analysis revealed low divergence with a G′ST of 0.005 (95% CI −0.004–0.013) and a G″ST of 0.015 (95% CI −0.014–0.045). Wellfleet Bay showed evidence of divergence from all other sites except Buzzards Bay. Isolation by distance is apparent via the Atlantic Ocean. Phenotypic variation in the prosomal widths of horseshoe crabs shows greater divergence among sites than neutral markers and indicates the presence of additive genetic effects. Low divergence and high heterozygosity indicate that although documented population declines have occurred, effective population size (Ne) is still large enough to maintain allele frequencies. With isolation by distance, divergence is likely to increase over time if populations remain low. Phenotypic divergence shows the possibility of local adaptation and that the implementation of management units (MUs) to the north and south of Cape Cod would be recommended as a conservative measure.

Hypoxia inducible factors (HIFs) are transcription factors and the master regulators of oxygen-dependent gene expression in animals. The focus of this thesis is the distribution of HIF protein in tissues of the fish Fundulus heteroclitus and F. grandis, two widespread species that occur in naturally hypoxic waters. Polyclonal antibodies against HIF-1α, HIF-2α, and HIF-3α were tested on proteins made in vitro and on extracts made from several tissues of normoxic and hypoxic fish. Antibodies against HIF-1α and 3α bound specifically to full length protein made in vitro, and produced bands on western blots of nuclear extracts of near the expected molecular weights for these proteins. Hypoxic exposure did not markedly increase the intensity of these bands, and mass spectrometry failed to identify HIF-1α and 3α peptides in excised gel bands. Thus, further tests of antibody specificity are needed before the tissue distribution of HIF in these fish can be confidently assessed.

The fresh-water mussel industry of the Tennessee River is nearing an end. Overharvesting, habitat alterations, and pollution are the major contributors to the depletion of the mussel resource, upon which the shell industry is based. A history of unconcern by shell harvesters and weak conservation enforcement by governmental agencies, has left the major waterways of the United States nearly void of commercial clams. The lower Tennessee River presently supplies the mussel industry with nearly all the important species of mollusks. If this industry is to be maintained in the United States, ways to preserve and propagate the mussel population must be sought. A number of recommendations have been submitted in this work that could aid in the protection of the mussel fauna. Limitations or harvesting methods, more stringent enforcement of existing laws, and extended research on propagation possibilities are suggested as aids in the preservation of this valuable natural resource.

Small scale protected zones are valuable for helping the health and productivity of fisheries at Lake Tanganyika (East Africa). Spatial placement of protected areas relies on accurate maps of benthic habitats, consisting of detailed bathymetry data and information on lake-floor substrates. This information is unknown for most of Lake Tanganyika. Fish diversity is known to correlate with rocky substrates in ≤ 30 m water depth, which provide spawning grounds for littoral and pelagic species. These benthic habitats form important targets for protected areas, if they can be precisely located. At the NMVA, echosounding defined the position of the 30-m isobath and side-scan sonar successfully discriminated among crystalline basement, CaCO3-cemented sandstones, mixed sediment, and shell bed substrates. Total area encompassed from the shoreline to 30 m water depth is ~21 km2 and the distance to the 30-m isobath varies with proximity to deltas and rift-related faults. Total benthic area defined by crystalline basement is ~1.6 km2, whereas the total area of CaCO3-cemented sandstone is 0.2 km2. Crystalline basement was present in all water depths (0-30 m), whereas CaCO3-cemented sandstones were usually encountered in water ≤ 5 m deep. Spatial organization of rocky substrates is chiefly controlled by basin structure and lake level history.

From 2008 to 2012, the total U.S. commercial landings of blue crabs (Callinectes sapidus Rathbun, 1896) averaged over 173 million lbs. Chesapeake Bay and its tributaries are important contributors to this fishery, providing greater than 30% of national commercial landings annually. In Chesapeake Bay, C. sapidus exhibits a complex life cycle in which mated females migrate to the saline waters of the Bay mouth to spawn. During migration, females can traverse multiple management jurisdictions, complicating effective management of this important fishery. Sustained declines in harvest have led to management strategies focused on protecting the female spawning stock in an attempt to enhance recruitment back into the Bay. This study presents the results of a broad scale mark-recapture study (n=7,072) in 11 Chesapeake Bay subestuaries and one coastal embayment, designed to track female migration and quantify spatial variation in exploitation rates of mature female blue crabs. Tagging was conducted in fall 2014 (September and October), when most females have matured and begin to migrate to the spawning grounds, and in summer 2015 (July), when additional females mature and migrate to the spawning grounds. Approximately 8.1% of tagged females were recaptured within one year of release. Overall, the exploitation rate of the 2015 blue crab spawning stock in Chesapeake Bay was 10.5%; however exploitation varied widely among systems (4.0-28.5%). This estimate is below both the management target and threshold exploitation rates and the population grew in subsequent years, suggesting recruitment overfishing of blue crabs was not occurring in Chesapeake Bay at this time.

The Louisiana oyster industry is greatly impacted by freshwater and sediment diversions that are part of the effort to restore the state’s coastline. A habitat suitability index (HSI) proposes species-habitat relationships that can be instrumental in creating impact assessments and suitability predictions for management as new diversions are implemented. An oyster (Crassostrea virginica) HSI was developed using three variables crucial to oyster sustainability: average annual salinity, minimum monthly salinity, and average salinity during the spawning season. These Legacy HSI visualizations show annual fluctuations in the distribution of zones suitable for oyster cultivation prior to proposed diversions in Pontchartrain and Barataria Basins from 1967 to 2016. Modeling suitability based upon these variables can provide crucial information for timing the use of diversions to lessen harmful effects upon the oyster industry as well as indicate new potentially suitable areas that the diversions may create.

Snapping turtles (Chelydra serpentina) are being harvested in unprecedented numbers in the United States (US) to meet the needs of international markets. Over three million live snapping turtles from farm and wild caught stock were exported from the US to Asia in 2012-14 alone. In the Commonwealth of Virginia, records indicate that 29,860 snapping turtles were commercially harvested between 2000 and 2015. Size limits are often used to regulate harvest pressure in snapping turtles and other game species. I analyzed the historic harvest of eleven US states to test the efficacy of minimum-size limit regulations at reducing commercial harvest pressure. Further, I conducted a four-year mark-recapture study on three Virginia waterways that have each experienced a different level of historic commercial harvest. As part of the larger mark/recapture project, I conducted radio telemetry on 23 turtles to examine seasonal, body size, and sex-specific effects on home range size of snapping turtles in a lotic system. I incorporated survival and growth rates from this study, demographic rates from the literature, and state-collected harvest rates into a hybrid age/stage population matrix model to estimate the population growth rate at three harvest levels (0%, 21%, 58%) that were estimated based on annual commercial landing reports on file with the Virginia Department of Game and Inland Fisheries. I used the model to test population viability under multiple size limit regulations, and used sensitivity analyses to identify adult stages most critical to the overall population growth rate. Based on model estimates, size-limits were effective at reducing harvest by 30-87% in years with high harvest pressure. However, most size limit regulations result in the removal of larger breeding adults, which has been shown to be detrimental to long term population viability. Based on radio-telemetry data, I found evidence that snapping turtles utilize lotic and lentic habitats differently, which can have implications for management of this iconic species. Matrix population modelling predicted that population densities at the moderate and high harvest site were reduced by 47% and 62%, respectively, when compared to the no harvest site. Model results indicate that, while an increase to the minimum-size limit in 2012 protected a larger portion of the population, that the commercial harvest of snapping turtles in the Commonwealth of Virginia is not sustainable under current state regulations. Our analysis suggests that minimum-size limits of 35.6 cm curved carapace length or greater will maintain viable populations by protecting a larger portion of reproducing snapping turtles within a population.

Climate change and increasing anthropogenic activities are causing rapid changes to environmental and ecological processes in the Arctic Ocean. To better understand these changes, scientists have increased research efforts in these regions, but to date the number of studies on Arctic nearshore habitats are lacking. My dissertation responds to the paucity of information and investigates patterns in Arctic nearshore fish communities and food webs to gain insight to how these ecosystems may shift as these changes continue. I used multivariate statistical analysis to examine patterns in community structure and composition to determine that Arctic nearshore fish communities are largely driven by prey availability, salinity and temperature; and that species that are more abundant in warmer conditions are likely to increase in abundance as climatic conditions in the Arctic continue to warm. I improved the ability to apply stable isotope methods to Arctic food web studies by determining more appropriate model parameters using a laboratory-based isotope study on a common Arctic nearshore fish, and discuss its potential as a biological monitor species. These new parameters are used to confirm that a shift in prey resource dependence occurs across the seasonal shift from ice-covered winter to open-water summer conditions. Changes in basal resource dependence also occur later in the season across a latitudinal gradient where a shift to dependence on allochtonous inputs from nearby rivers increased trophic diversity. Using isotopic niche space theory, it was determined that the Arctic nearshore has a diverse prey base but that niche spaces of Arctic warm-water and cold-water species do overlap, and if numbers of warm-water fish continue to increase it will likely increase competition for resources for potentially less-adaptable, well-established, cold-water forage fish. On the other hand, if pelagic productivity is expected to increase and support larger fish biomasses, then there will be more than enough resources for warm-water and cold-water species to coexist, thus creating a more diverse prey base for piscivores in the Arctic.

Populations of largemouth bass, Micropterus salmoides, and bluegill, Lepomis macrochirus, were evaluated from five pit-lakes in Muhlenberg County, Kentucky, to determine if accurate proportional stock density (PSD) data can be obtained from a mandatory creel survey. It was hypothesized that the proportion of stock-to-quality (300-400mm) and quality (+400mm) largemouth bass from four years (2007-2010) of creel survey data would be statistically similar to those generated through on-site sampling in 2011. Fish were collected via a combination of gill netting, seining, hook-and-line fishing, and boat-mounted electro-fishing. In two of the pit-lakes, the sampling-generated length frequency data was not significantly different from the creel survey data (Pump Gadj[1]=0.03, P=0.8629, Goose Gadj[1]=0.76, P=0.3850). There were significant differences between creel and sampling data for the other pit-lakes (Big Reno Gadj[1]=5.74 P=0.0166, Airstrip Gadj[1]=14.3 P=0.0002, Lime Gadj[1]=9.81 P=0.0017). At least one of the lakes likely demonstrated significances because of low sample size (Airstrip and/or Lime). Changes in population structure due to modified harvest regulations may be responsible for the significant differences (Big Reno and Lime). Population structures were verified with relative weight, length-at-age, and an assessment of five years of largemouth bass and bluegill PSD data. It appears that creel survey data does accurately reflect that of simple sampling techniques and can help guide management decisions.

This study examines spatially continuous sampling data in order to investigate patterns of abundance and distribution of three recreationally important sunfish species (bluegill, redear, and spotted sunfish) along the main-stem of the Peace River, a large softwater river located in southwest Florida. A total of 467 electrofishing transects were sampled biannually from spring 2008 to spring 2010. Sampling sites ranged from the headwaters of the Peace River in Polk County, FL to the oligohaline waters located in Charlotte County, FL. All fish were collected with boat mounted electrofishing gear, and aquatic habitat and physiochemical water quality measurements were recorded at each transect. Pearson's correlation coefficient and conical correspondence analysis were used to interpret relationships between sunfish abundance and associated environmental variables. Results showed that relative abundance of sunfish varied significantly between the upper, middle, and lower basins of the river. Distance from headwaters, conductivity and macrophyte coverage were all significant predictors of relative species abundance. Spotted sunfish were found closer to the headwaters and were positively associated with higher amounts of aquatic vegetation. Redear were most common in the middle basin and were most associated with changes in conductivity. Bluegill were relatively more abundant further downriver where conductivities were higher. Woody debris was strongly associated with fish abundance for all species but did not significantly explain the variance in species composition between locations in the river. The result of this study can be used by fisheries professionals to better manage sunfish populations in the Peace River and other lotic systems.