A study was undertaken to investigate the application of tissue culture and histochemical banding techniques normally used in mammalian studies to fish cells and to examine the mechanisms of chromosome evolution and speciation in salmonids by comparing the chromosomes of the hybrid to those of the parental types. The application of banding techniques was generally unsuccessful in revealing bands, though quinacrine staining did reveal the presence of two fluorescent spots in the vicinity of the centromere. These were thought to be heterochromatic blocks, possibly related to the high incidence of centric fusion or fission in salmonids. Results of chromosome analysis showerd a higher incidence of acrocentric chromosomes in the hybrid than in either parental type which together with evidence for tetraploidization in salmonids is consistant with some of the requirements for species diversification. Conditions of divergence in chromosome evolution and changes which would have to occur in the hybrid for divergence from the parental types to take place are discussed. The results of a preliminary electrophoretic examination of LDH and esterase activity tended to confirm hybridization.

Age and growth were determined from otoliths for 181 juvenile bluefish, Pomatomus saltatrix, collected using a variety of gear in northeast Florida during 2003 and 2005. Three distinct cohorts were identified recruiting to the near shore waters during spring, summer and fall. Growth rates were high regardless of cohort or season. To compare pre- and post-recruitment growth rates, models were fit to individual growth trajectories using change point analysis. Post-estuarine growth rates were generally higher. Growth rates and hatching times were within the range of those obtained in other bluefish studies conducted at higher latitudes. As this is the only area where winter recruitment of bluefish has been observed, coastal Florida habitats may be essential for the bluefish stock and will need to be carefully monitored in future studies. A technique to estimate the lipid content of bluefish was developed using fat stage (subjectively assigned based on mesenteric fat around the stomach), fish length, and fish weight. A highly significant relationship was observed between fat stage and lipid content in a generalized linear model. The visual lipid content technique provides rapid results, is inexpensive and could be easily implemented into current fisheries sampling methods. Total lipids were also extracted from potential bluefish prey species collected during sampling. Prey lipids ranged from 0.88% to 19.52%. Regular prey species from the MAB; Atlantic silverside and bay anchovy contained 3.49% and 3.19% mean lipids respectively. Highest lipid content was observed in mullet (Mugil spp.) (19.52%) and was significantly higher than other available prey species. A previous study indentified a decline in bluefish lipids as winter progressed as well as a prey preference for mullet. We propose mullet are the preferred prey choice due to their high lipid content.

The Assabet River located in eastern Massachusetts receives treated wastewater discharges from four major municipal wastewater treatment plants (WWTPs): Westborough, Marlborough, Hudson and Maynard. In periods of low flow, up to 95% of the Assabet River is wastewater effluent. Chemical analyses have shown that municipal wastewaters can contain estrogenic and dioxin-like compounds. Estrogenic compounds such as the natural estrogen 17β-estradiol (E2), the synthetic estrogen 17α-ethinyl estradiol (EE2), and the industrial compound nonylphenol (NP) can induce vitellogenin (VTG) and lead to feminization in male fish. CYP1A1-inducing compounds such as the polycyclic aromatic hydrocarbons (PAHs) and polybrominated diphenyl ethers (PBDEs) can produce both overt toxicity and alter reproductive function through the metabolism of natural estrogens. The purpose of the present research is to analyze the estrogenic and CYP1A1-inducing compounds in the Assabet River and their physiological effects on Japanese Medaka (Oryzias latipes). I used a bioassay that measures the induction of VTG and CYP1A1 in the livers of male Medaka and report results obtained by the USGS and EPA on analytical measurements of selected compounds. In the summers of 2010 and 2011 water samples were collected from the Assabet River, its tributaries and the four WWTPs. Male Medaka were exposed to the treatment samples as well as negative and positive controls. VTG and CYP1A1 induction were measured using real time RT-PCR. Concurrently collected samples from 2010 were analyzed by the USGS for more than 80 organic wastewater contaminants including several estrogenic EDCs and CYP1A1-inducing compounds. The USEPA also analyzed treated wastewater effluent samples collected from the four WWTPs for pharmaceuticals, hormones, nonylphenols and perfluorinated compounds. The bioassay from 2010 and 2011 reveal no statistically significant induction of VTG expression and only one significant induction of CYP1A1 expression. Few compounds were detected by the 2010 USGS and USEPA chemical analyses and the concentrations were low. Taken together the results indicate that VTG and CYP1A1 inducing compounds in the effluent-dominated Assabet River are present at low levels, which may be below the level of detection of the bioassays. In addition to the biological assay and chemical analysis Geographic Information Systems (GIS) was used to analyze land use/land cover (LU/LC) data in the Assabet River Watershed. Much of the land surrounding the Assabet River is forested but there are several LU/LC types that could negatively impact the water quality. High impact and low impact LU/LC types were differentiated in buffers around the Assabet River and six GIS sites. The composition of each site varies widely in its proportions of high and low impact land cover. The GIS analysis established locations on the Assabet River where water quality is more susceptible to degradation due to the distribution of high impact land use types.

I examined the effects of temperature (25, 30, and 35°C) on growth, standard metabolic rate (SMR), and lower dissolved oxygen tolerance (LDOT) of juvenile Speckled Peacock Bass Cichla temensis. Fish were acclimated to 150-L aquaria for 7 weeks before the growth, SMR, and LDOT experiments. The growth study lasted 58 days and fish acclimated to 25 and 30°C displayed similar growth rates, while fish acclimated to 35°C had very poor growth rates. The SMR and LDOT experiments were performed using intermittent respirometers. Fish acclimated to 25°C had the lowest SMR, followed by 30°C, and finally 35°C. The highest LDOT was observed at 25°C, followed by 30°C, and finally 35°C. Collectively, these results suggest that 25-30°C is within the thermal optima of Speckled Peacock Bass for grow-out and survival in an aquaculture setting. Further, I recommend maintaining dissolved oxygen concentrations at or near saturation.

The primary purpose of this study was to evaluate the feasibility of controlling oyster drills in Tomales Bay, particularly Urosalpinx cinerea and Ocenebra Japonica (astropods, Muricidae), with chemicals which have been succesfully tested on a number of oyster pests, Including urosalpinx, in Long Island Sound (Loosanoff , 1956- 1961). The problem was polo to provide information. en the present status of drills alle is the bay, a basic preliminary in evaluating others of pest control.

The persistence of predator-prey systems in evolutionar time is a function of the efficiency with which the predator obtains its food, and the ability of the prey to avoid ex- tinction. One of the important components of survival of the system is environmental heterogeneity (Huffaker 1958). Along rocky intertidal regions of the northern Pacific coast of North America, a major predator, the starfish Pisast ochraceus has a dominant effect upon patterns of distribution of many intertidal organisms (Paine 1966). Likewise, the distribution of intertidal fauna exert an effect upon the activities of Pisaster. Other biological interactions such an grazing activities of limpets and predatory behavior of emails also affect the intertidal distribution of species (Connell 1961, 1970, Dayton 1971).

In the Chesapeake Bay, < 1% of the historic oyster population remains, and efforts have been increasing to restore oysters and the services they provide. Building reefs that successfully provide ecosystem services–especially habitat and foraging grounds–may require different restoration techniques than those previously used, and success may depend on reef morphology (complexity), location, and environmental conditions. Salinity and habitat complexity are two important factors that may interact to effect benthic communities and predator-prey interactions on restored reefs. The goals of this project were: (1) Characterize the benthic communities on restored oyster reefs in lower Chesapeake Bay, and (2) examine the effects of structural complexity and salinity on benthic communities and predator-prey interactions. A two-year field survey of restored reefs was carried out in four rivers in lower Chesapeake Bay to characterize faunal communities on restored reefs and to quantify the effect of reef complexity on faunal communities. A laboratory mesocosm experiment was conducted to examine the effect of reef complexity on predator foraging. In total, 61 macrofaunal species were identified among all samples, and restored reefs supported on average, 6,169 org/m2 and 67.88 g-AFDW/m2. There were significant differences in the community composition and diversity among the rivers, and salinity was the environmental factor that best explained the observed differences in species composition across the rivers. Salinity and rugosity (i.e., structural complexity) both positively affected diversity, while salinity negatively affected macrofaunal abundance and biomass. Oyster density and rugosity positively affected macrofaunal biomass, and oyster density positively affected mud crab, polychaete, and mussel densities. In the mesocosm experiment, predator foraging, measured by proportion and number of prey consumed, was significantly reduced in the presence of oyster shell structure. However, predators were able to consume more prey when prey density was increased, even in the presence of oyster shell structure. These results combine to enhance our understanding of the benefits of increased habitat complexity for both prey and predators on restored oyster reefs. Increasing complexity worked to increase the abundance, biomass, and diversity of organisms inhabiting restored reefs, and even though predator consumption was reduced in the presence of structure compared to non-structured habitat, predators were able to consume more prey individuals when prey density was increased. Therefore, increasing the structure of oyster reef habitat may benefit prey species by providing refuge habitat, and benefit predators by providing an increased abundance of available prey items.

The eastern oyster Crassostrea virginica is an ecologically and commercially important species whose natural populations have been devastated by overharvesting, habitat destruction, and disease, but the rapid growth of oyster aquaculture has shown potential to restore the economic significance of this species. A key threat to the growth and sustainability of oyster aquaculture is the association of human-pathogenic Vibrio bacteria with product marketed for raw consumption. Two Vibrio species, Vibrio vulnificus and Vibrio parahaemolyticus, are the causes of the highest rates of seafood consumption-related mortality and gastrointestinal illness, respectively. Identification of the factors influencing V. vulnificus and V. parahaemolyticus prevalence and intensity in oysters is fundamental to better risk management. Within the oyster, these bacterial species interact with the same tissues as the prevalent oyster parasite, Perkinsus marinus, yet little is known about the effect of P. marinus infection on bacterial levels. Answering the fundamental question of whether P. marinus correlates with V. vulnificus and V. parahaemolyticus levels in oysters was the focus of this research. Oysters were deployed in the York River, Gloucester Point, VA, where both Vibrio species and P. marinus are endemic, and were sampled at five time points when levels of both P. marinus and Vibrio spp. were expected to be high in oysters. Abundance of all three organisms and pathogenic strains of V. parahaemolyticus were determined in individual oysters using molecular methods to investigate potential correlations between parasite and bacterial abundance. Additionally, the levels of V. vulnificus and V. parahaemolyticus in relation to histopathology associated with P. marinus infection and other conditions were determined. The following year, manipulation of P. marinus disease progression, which is slowed by lower salinities and favored by higher salinities, was attempted by deploying oysters at two additional sites of different salinities to gain insight into whether the timing of P. marinus infection emergence directly influences Vibrio levels. No correlation was observed between total abundance of P. marinus and either V. vulnificus or V. parahaemolyticus. Manipulation of P. marinus disease progression produced no effect on P. marinus emergence, so this yielded no insight into P. marinus-Vibrio interactions. Histopathological analyses did not reveal any correlations between P. marinus ranking, distribution, or associated tissue damage and Vibrio spp. levels. Though few in number, oysters infected by Haplosporidium nelsoni were characterized by higher levels of V. vulnificus, and oysters of peak gametogenic development had significantly higher levels of pathogenic strains of V. parahaemolyticus. The results with regard to H. nelsoni and gametogenic state warrant further study. The primary conclusion of this study is that oyster health has little influence on levels of human-pathogenic Vibrio species in oysters, inter-host variability in Vibrio levels is likely explained by other factors.

This thesis developed from the VIMS Larval Fish Monitoring Program, which began in 2007 as part of a study comparing the larval fish assemblages of Chesapeake and Delaware Bays. Ribeiro et al. (2015) analyzed data from the first three years of this time series to describe the temporal variation in the larval fish assemblages. After this initial study was completed (three years in duration), the sampling continued at the fixed station near the mouth of the York River, which was used to represent the Chesapeake Bay. For this thesis, therefore, eight years of data (2007-2015) were available to investigate temporal changes in the larval fish assemblage, and to better evaluate intra-annual variation of the larval fish assemblage. Further, larval fish indexes of five target species of commercial and recreational importance in the Chesapeake Bay, were examined, including Anchovy (Anchoa spp.), Atlantic Menhaden (Brevoortia tyrannus), American Eel (Anguilla rostrata), Summer Flounder (Paralichthys dentatus), and Atlantic Croaker (Micropogonias undulatus). Regression models were used to evaluate the effect of different environmental and temporal variables on the larval fish density from the York River system. Results show a stable assemblage in the York River since 2007, with marked seasonal patterns in terms of composition and abundance of larval fishes. The assemblage from May to August is formed by estuarine species with high number of larval fishes (e.g., Anchovy, Green Goby, Naked Goby); the assemblage from September to April is characterized by a lower number of species, mainly coastal spawners such as Atlantic Croaker, Summer Flounder, and Atlantic Menhaden. at the species level, slight annual variations were found, although in general abundances were stable across the time series. Because the larval fish monitoring program sampled at a single fixed station located in the lower portion of the York River system, it is limited spatially even though it has good temporal resolution (eight years). One fixed station may capture only localized patterns and it is unclear if this is comparable to the larval fish assemblage in southern portion of the Chesapeake Bay generally. The second chapter of this thesis addresses the question of spatial variation of the larval fish assemblage, principally between the York River system and the mouth of the Chesapeake Bay. Samples taken in three locations were compared to determine if the assemblage varied among the sampling locations. Larval stages of two coastal spawners, Atlantic Menhaden and Atlantic Croaker, were the two most abundant at both all locations. Results indicate species specific differences among the locations, for example, Atlantic Croaker larvae were more abundant in the York River mouth (YRM) than in the Chesapeake Bay mouth (CBM), indicating significant spatial variation in larval fish assemblage composition over a distance of approximately 40 km, the distance between the YRM and CBM. This variation should be taken into account when generalizing the structure of the larval fish assemblage of the York River spatially.

Thousands of floating objects, known as drifting fish aggregating devices (dFADs), are released every year by commercial tropical tuna purse seine vessels in the three equatorial oceans to aggregate tuna and increase catch. The escalation in the number of dFADs deployed over the last three decades has caused changes in fishing effort that are poorly reflected in traditional indices of purse seine effort and catch per unit of effort (CPUE). In addition, concerns have been raised regarding the impacts of such high numbers of dFADs being deployed on both catch and bycatch species. I studied two aspects of dFAD deployments in order to clarify how dFADs are used by purse seiners and how they affect the magnitude of bycatch. My specific goals were to determine how often purse seine vessels fish on the dFADs they deploy and how regional dFAD density affects the magnitude of bycatch and catch. I analyzed commercial data, independent observer data, satellite buoy trajectories, and estimated floating object densities from the French tropical tuna purse seine fisheries in the Atlantic and Indian Oceans to examine these relationships. My results indicate that only 2.7-20.6% of dFAD fishing sets were on the dFADs that French purse seiners deployed over the period 2007-2013. Although this percentage increased over time, such a low percentage suggests that French vessels do not primarily increase CPUE by using the dFADs they deploy for directed fishing. If French purse seiners are not mainly using their own dFADs in this manner, then using a metric of nominal effort based on individual vessel activity is unlikely to produce reliable CPUE estimates for the fishery. While information about how often purse seiners fish on their own dFADs could be incorporated into indices of fishing effort, it may be just as important, if not more so, to quantify the collective component of dFAD releases for overall fishing effort. The results for the second objective showed that average dFAD density had a relatively weak relationship with total bycatch biomass. There was no statistically significant effect on mean total bycatch biomass, but dFAD density was related to heteroscedasticity in bycatch biomass. In particular, there was a significant negative relationship between dFAD density and the upper quantiles of the bycatch biomass distribution, suggesting that dFAD density determines the upper bound for bycatch biomass caught per set. These relationships were not constant across species, however, as the five most prevalent bycatch species (i.e., those caught in the greatest number of sets) showed a mix of positive, negative, or no relationships to dFAD density. The total biomass of catch increased significantly as average dFAD density increased both at the mean and throughout the majority of the distribution, although this effect only explained a small fraction of the total variance in catch biomass. at this time, the low amount of variance explained and the inconsistent impact of average dFAD density on bycatch and target species indicate that it would be ineffective to mitigate bycatch levels in these fisheries by attempting to control regional dFAD densities.