The data analysis indicated that travel distance, user age, and user income level are important determinants of use of trout streams. These variables were incorporated into regression analysis to develop a use-prediction model. This use-prediction model was used to determine predicted use levels of sample streams. The predicted use levels combined with travel costs and expenditures on new fishing equipment were used to derive a statistical estimate of the demand schedules for the sample streams. These statistical demand curves were subjected to consumer surplus procedures to determine the values of the sample streams.

Habitats of Chesapeake Bay have been altered due to anthropogenic impacts and climate change. Due to these human disturbances, seagrasses have been extirpated from many areas in lower Chesapeake Bay and persisting beds face future losses as water temperatures continue to rise. Further loss of seagrass habitat will negatively impact juvenile blue crabs (Callinectes sapidus) that use seagrass beds as nursery grounds. Habitat degradation allows for more successful introductions of exotic species, and the communities formed from the mixing of native and exotic species are known as emerging ecosystems. Gracilaria vermiculophylla, an exotic macroalga, may be an emerging nursery habitat for juvenile blue crabs in Chesapeake Bay; however the extent to which the alga is present and used as a nursery by juvenile blue crabs are largely unknown. I investigated algal distribution in the shallow littoral areas of the York River, a subestuary of Chesapeake Bay, over two years (2013 – 2014) and found that G. vermiculophylla presence correlated with salinity and that algal presence and biomass increased with seagrass presence, although biomass was generally low. The alga was present in areas where seagrasses have been lost, and is therefore likely providing nursery habitat in these areas of high megalopal recruitment. Benthic epifaunal communities had lower species richness and were less abundant in G. vermiculophylla relative to seagrass, while benthic infaunal communities had lower species richness but similar abundance in the alga relative to seagrass. Juvenile blue crab densities were similar in the alga and seagrass, although seagrass supported about 3 times as many first and second instar crabs than G. vermiculophylla. Young juvenile blue crabs preferred seagrass, which may be due to epifaunal prey preference, and G. vermiculophylla likely represents a secondary nursery habitat. Juvenile blue crab growth rates of crabs 15 – 50 mm carapace width were similar in the alga, native seagrass, and unvegetated habitat, indicating that growth does not drive ontogenetic shifts in habitat use by larger (20 – 30 mm carapace width) juveniles. Similar growth rates also suggest that G. vermiculophylla performs similarly to seagrass as a nursery habitat in terms of providing resources for growth. Simulations of density-dependent migration of young juvenile blue crabs between habitat types suggest that G. vermiculophylla may mediate continued seagrass loss, at least in part. Together, these results increase our understanding of an emerging Chesapeake Bay ecosystem and the impacts that changes to nursery habitats have on the juvenile component of the blue crab population.

Batoid fishes are among the most threatened and least understood chondrichthyan species worldwide due to their large body size, conservative life-history characteristics, and predominantly coastal distributions where fishing and habitat degradation threaten the stability of populations. A lack of empirical life history data is widespread across batoid taxa — nearly half of all species are considered data deficient, thus hindering species assessments and the development of effective management strategies. Furthermore, many batoid taxa are in need of taxonomic re-examination. Increasing our understanding of life history traits that determine population productivity, such as age and size at maturity, growth rate, and fecundity is prerequisite to examining the potential for populations to increase or stabilize in response to fishing mortality. The Butterfly Rays (Myliobatiformes: Gymnuridae) are comprised of 10 globally distributed species that inhabit shallow coastal regions and are commonly caught in benthic fishing gears targeting commercially valuable species. Two species are recognized in the western Atlantic: the Spiny Butterfly ray, Gymnura altavela (Linnaeus 1758), and the Smooth Butterfly Ray, G. micrura (Bloch & Schneider 1801). Previous life history studies on U.S. Butterfly Rays were often spatially and temporally limited, which may bias conclusions due to underrepresentation of some life stages, and lead to inaccurate biological characterizations. Furthermore, sexual dimorphism and ontogenetic variability in body shape, and inter- and intraspecific inconsistencies in taxonomic characters (e.g., disk coloration, tail banding patterns) have contributed to substantial taxonomic confusion in the Gymnuridae. To address knowledge gaps in the life history and taxonomy of western Atlantic Butterfly Rays, this dissertation describes the age and growth of G. altavela, the reproductive biology of G. altavela and G. micrura, and the taxonomic status of G. micrura. The largest male and female G. altavela were estimated to be 11 and 18 yrs old, respectively. Disk width at maturity was 1278 mm and 946 mm for male and female G. altavela, respectively, and was significantly greater in Atlantic G. micrura (male: 390 mm; female: 551 mm) than Gulf of Mexico G. micrura (male: 298 mm; female: 448 mm). Maximum fecundity was seven in G. altavela, and ranged from six to 12 in G. micrura from the Atlantic and Gulf of Mexico, respectively. Based on geographical variation in life history parameters, morphology, and genetics, a re-description and proposed neotype for G. micrura is presented, and two new species and holotypes are described from the Atlantic (Gymnura n. sp. A) and Gulf of Mexico (Gymnura n. sp. B). In U.S. waters, Gymnura n. sp. A may be more vulnerable than Gymnura n. sp. B to indirect fishing mortality due to its larger size, potential later age at sexual maturity, and lower fecundity, since the probability of an individual encountering fishing gear before successfully reproducing is likely greater. This disseratation provides empirical support for the conservation and sustainable management of Atlantic Butterfly Rays. Careful consideration of species-specific taxonomy and biology is required to accurately assess the vulnerability of contemporary populations to extinction risk, and to document and maintain the true biodiversity of this taxon.

Predator populations can have significant impacts on prey recruitment success and prey population dynamics through consumption. Young, inexperienced prey are often most vulnerable to predation due to their small size and limited evasion capabilities. to reduce the risk of predation, new recruits and young juveniles typically settle in structured nursery habitats, such as seagrass beds, which promote higher survival by acting as refuges from predators. Thus, successful recruitment to the adult portion of the population is often dependent on the availability of suitable nursery habitat. In this thesis, I used field tethering experiments and gut content analyses to assess the role of habitat, body size, finfish predation, and cannibalism on the survival of one of the most ecologically and economically important species in Chesapeake Bay: the blue crab Callinectes sapidus. In field tethering experiments, survival probability of juvenile blue crabs in York River nursery habitats (i.e. seagrass beds, sand flats) increased significantly and additively with crab size and SAV cover. Images of predation events during tethering experiments revealed cannibalism by adult blue crabs to be a major source of juvenile mortality. Gut content analyses from three field studies identified seven predators of juvenile blue crabs in lower Chesapeake Bay nursery habitats: adult blue crabs, striped bass Morone saxatilis, red drum Sciaenops ocellatus, silver perch Bairdiella chrysoura, weakfish Cynoscion regalis, Atlantic croaker Micropogonias undulatus, and oyster toadfish Opsanus tau. Using frequency of consumption and diet proportion metrics, I determined striped bass, red drum, and silver perch to be the most impactful finfish predators on juvenile mortality, in addition to cannibalism. Atlantic croaker and oyster toadfish play minor roles in juvenile mortality in Chesapeake Bay nursery habitats. The probability of juvenile crabs being present in a predator’s gut was also significantly higher in seagrass beds than in unvegetated sand flats. Food web dynamics are an important aspect of ecosystem-based fisheries management. Understanding the ecological interactions between populations, and their environment, can provide insight into natural population fluctuations of valuable fishery species such as the blue crab. This thesis demonstrated the positive effects of body size and SAV cover on juvenile crab survival, indicating the importance of seagrass nursery habitat for blue crab population dynamics in Chesapeake Bay. However, despite the predator refuge offered by SAV, high densities of predators and prey in seagrass beds resulted in greater consumption of juveniles in those habitats. Key predators of juvenile blue crabs were also identified and their relative impacts were estimated. The predator-prey relationships revealed in this thesis were integrated into a revised food web for blue crabs in Chesapeake Bay, in the hopes of informing future ecosystem-based management efforts.

Oyster shell for native oyster reef restoration is scarce in Chesapeake Bay and other estuaries (Chapter 1). Consequently, alternative substrates merit consideration in oyster restoration. This dissertation examines the suitability of shell alternatives, including granite, concrete, limestone marl, concrete modules and reefballs with reef surveys and experiments in the Rappahannock and Lynnhaven Rivers of Chesapeake Bay. Oyster recruitment, growth, survival, density, biomass, condition, and disease stress, as well as reef accretion and persistence, were measured. In the Lynnhaven River, intertidal riprap had a mean density of 978 oysters m-2 (165 g AFDM m-2) and peak densities > 2000 oysters m-2 (Chapter 2), which are among the highest abundances on alternative reefs, shell or otherwise. Riprap reefs supported a robust population size structure, signifying consistent annual recruitment and reef sustainability. Riprap age (older > younger) and location influenced reef performance; granite and concrete both supported dense oyster-mussel assemblages. In 2005 and 2007, oyster and mussel population structure, density and biomass were quantified on a novel, subtidal concrete modular reef deployed in 2000 in the Rappahannock River (Chapter 3). The reef was not seeded or harvested. Densities (m-2 river bottom) were very high for oysters (2005: 991 m-2; 2007: 2191 m-2) and mussels (2005: 8433 m-2; 2007: 6984 m-2) and comparable to the highest densities on shell reefs. An adjoining 0.44 ha array of concrete reefs (Steamer Rock) was deployed in 1994 and sampled in 2006. These reefs contained > 4 million oysters and > 30 million mussels. Oysters from both reef systems had low disease prevalence and intensity. In a field experiment (Chapter 4), treatments simulating oyster habitat were placed at three intertidal sites in Long Creek of the Lynnhaven River. Granite had highest oyster recruitment and abundance (density > 1500 m-2 and biomass > 200 g AFDM m-2). Many reefs reached a mature state after two years. By Year 3, some reefs had accreted 15-20 L of shell m-2 river bottom, and contained three year classes; some treatments had > 30 % of live oysters growing on other oysters. Large oysters (> 95 mm shell height) had lower intensities of Dermo infection than smaller (60-90 mm) oysters. These patterns indicate that oyster disease tolerance has developed in these high-salinity waters, and highlight the importance of substrate type and reef location in ecological oyster reef restoration. In summer 2006, nine reefs were constructed at two shoreline sites in the Lynnhaven River (Chapter 5), three each of oyster shell (OS), riprap (RR), and concrete modules (CM). Six reefballs were placed at each site, half pre-seeded with hatchery-reared oysters. Finally, in situ setting of triploid oyster larvae on OS, RR and CM reefs was attempted. After 2.5 yrs, all reefs had high oyster density and biomass (unseeded: 150-1200 m -2, 150-600 g AFDM m-2; seeded: 30-1800 oysters m -2), and sustainable accretion rates (8-15 L m-2 yr -1); diploid and triploid oysters had light Dermo infections. Consequently, alternative substrates can serve as effective oyster reefs under diverse conditions in subtidal and intertidal environments of Chesapeake Bay.

The finfish communities using the intertidal surfaces of a bay-exposed marsh and a sheltered, channel marsh of the Goodwin Islands, York River, Virginia were studied from May to November 1994. Samples were taken approximately twice monthly using a flume weir at three stations in each marsh. Species composition, abundance and biomass were estimated, and growth patterns and production rates were described for the dominant species. A total of 3001 fish were collected from 11 species and 8 families. Fundulus heteroclitus dominated both marshes and accounted for 83.07% of the total number of fish caught, and 84.83% of the total biomass collected. Menidia menidia was the second most abundant species at 9.00% of the total number of fish, but F. majalis was second in the total biomass at 7.51 % of the total. Abundance first peaked in June, and a second peak occurred in November. Biomass had a small peak in the beginning of August, and a large peak in late September. Analysis of variance showed the number of species captured did not differ significantly between the marshes. However, both the number of individuals and biomass were significantly higher in the protected marsh. Correspondence analysis showed that species composition in the protected marsh was mostly cyprinodontids, but in the open marsh species composition varied more throughout the sampling season. Species densities were highest at 9.8 ± 3.3 fish/m2 for F. heteroclitus in the protected marsh. Production for F. heteroclitus over the summer in the protected marsh was high at 10.1 g dry wt.fm2 due to the large number of rapidly growing larval and juvenile fish.

Derelict fishing gear, particularly pots or traps, occupy waters worldwide and cause negative ecological and economic impacts. Derelict pots persist throughout Chesapeake Bay, the largest estuary in the U.S., that supports a valuable commercial fishery for the blue crab Callinectes sapidus. Chesapeake Bay is responsible for 30-40% of U.S. commercial blue crab harvests. Yet, few studies have quantified the impacts of derelict pots on harvest or the perceptions of commercial fishers on derelict pot mitigation activities in this predominantly pot fishery. This thesis examined the impacts of derelict pots on harvest in a field experiment and worked with commercial fishers to develop and disseminate a mail survey that was used to quantify the preferences and decision-making of commercial fishers for addressing derelict pots. The field experiment simulated the presence of derelict pots near actively fished pots and found that derelict pots can reduce harvests by up to 30% during the summer, but not during the fall. Female capture rates were consistently lower when derelict pots were present, but male capture rates were not negatively affected. To better understand the perceptions of commercial fishers and their preferences for derelict pot mitigation actions (e.g., location and removal program, installation of identification tags on pots), a stated preference survey with a discrete choice experiment was distributed to all commercial fishers licensed to deploy hard pots in Virginia. There was a 42% response rate (430 of 1,032 fishers returned the survey packet), and most mitigation activities included in the survey were too costly for commercial fishers to willingly participate in. Management incentives (e.g., bushel limit increase, pot limit increase, season extension) alone were not enough to offset costs and encourage participation in activities that were disliked by commercial fishers. However, there was strong heterogeneity observed across the population, thus some segments of the population would be far more willing to participate in mitigation efforts than others. For instance, participants that perceived derelict pots to cause only negative impacts were 37% more willing to participate in any mitigation activity on average. Results from this study can be used to better inform resource managers and policymakers responsible for addressing the issue of derelict pots and other types of derelict fishing gear plaguing fisheries around the world.

American eels are infected by the introduced parasitic nematode, Anguillicoloides crassus, which can cause significant damage to their swimbladders. Despite the high prevalence and severe damage caused by A. crassus, the population level effects on American eels are not well understood. The prevalence and swimbladder damage in young glass eels and elvers are relatively unstudied, despite the potential for this parasite to cause tissue damage. Additionally, the effects of environmental, temporal, and spatial variables have been debated in previous studies without consensus. Also, the potential for eels to recover from infection and tissue damage has been speculated but not definitively shown. Therefore this Master’s thesis sought to answer these questions through field and laboratory studies. Glass and elvers stage American eels were collected during the spring and summer of 2015 and dissected to enumerate infection intensity and estimate swimbladder condition using the swimbladder degenerative index (SDI). Data were then combined with a larger dataset for yellow eels and analyzed using zero-inflated and ordinal logistic regressions to determine the effects of season, site, and eel length on infection intensity and swimbladder condition. The relationship between infection intensity and swimbladder condition was evaluated. This dataset was then used to investigate if the force-of-infection (i.e. rate of uninfected eels becoming infected) varied by host age and if there was evidence of disease associated mortality. to investigate recovery from parasite-induced swimbladder damage, 270 wild caught (presumably infected), individually tagged yellow eels were held in a freshwater recirculating system and fed a parasite-free diet for six months. Each month eels were x-rayed, weighted, and measured. The length and area of the swimbladder of each individually tagged eel were measured on x-ray images for temporal comparisons. at the end of the experiment, all eels were euthanized and dissected to determine infection intensity, SDI, and dissected swimbladder length. The trends of average monthly length ratio index (LRI; length of swimbladder to eel total length) and area of swimbladders were determined, as well as the relationships to SDI and infection intensity. Our field study showed that glass eels have a very low prevalence compared to elvers and yellow eels. Infection intensities of elvers and yellow eels varied by season and site and increased with total length. Swimbladder damage also varied by season and increased with total length. Infection intensity and swimbladder damage were non-linearly related. Force-of-infection was highest for age 2 eels and also varied by season, with the highest values in the winter and lowest in the early spring. Parasite-associated mortality was observed, with infected eels having an annual survival rate of 0.76 that of uninfected eels. Results from our x-ray experiment showed that LRI and area increased slightly through time. SDI also increased slightly over the course of the experiment, and SDI, LRI, and swimbladder area all were in agreement of improvement in swimbladder condition, however full recovery was not observed. In conclusion, the health of American eels in the Chesapeake Bay is adversely impacted by A. crassus, though that effect varies by season, system, length of the eel and whether infection level is being measured by infection intensity or swimbladder condition. Also American eels may have the ability to recover from A. crassus infection, but more work is needed to determine if this occurs in the wild.

For data-limited fisheries, length-based mortality estimators are attractive as alternatives to age-structured models due to the simpler data requirements and ease of use of the former. This dissertation develops new extensions of mean length-based mortality estimators and applies them to federally-managed stocks in the southeastern U.S. and U.S. Caribbean. Chapter 1 presents a review of length-based methods from the literature. Common themes regarding the methodology, assumptions, and diagnostics in these length-based methods are discussed. In Chapter 2, a simulation study evaluates the performance of the length-converted catch curve (LCCC), Beverton-Holt equation (BHE), and Length Based-Spawner Potential Ratio (LB-SPR) over a range of scenarios. Although the LCCC and BHE are older methods than LB-SPR, the former outperformed LB-SPR in many scenarios in the simulation. Overall, it was found that the three length-based mortality estimators are less likely to perform well for low M/K stocks (M/K is the ratio of the natural mortality rate and the von Bertalanffy growth parameter; this ratio describes different life history strategies of exploited fish and invertebrate populations), while various decision rules for truncating the length data for the LCCC and BHE were less influential. In Chapter 3, a multi-stock model is developed for the non-equilibrium mean length-based mortality estimator and then applied to the deepwater snapper complex in Puerto Rico. The multispecies estimator evaluates synchrony in changes to the mean length of multiple species in a complex. Synchrony in mortality can reduce the number of estimated parameters and borrows information from more informative species to lesser sampled species in the model. In Chapter 4, a new method is developed to estimate mortality from both mean lengths and catch rates (MLCR), which is an extension of the mean length-only (ML) model. to do so, the corresponding behavior for the catch rate following step-wise changes in mortality is derived. Application of both models to Puerto Rico mutton snapper shows that the MLCR model can provide more information to support a more complex mortality history with the two data types compared to the ML model. In Chapter 5, a suite of mean length-based mortality estimators is applied to six stocks (four in the Gulf of Mexico and two in the U.S. Atlantic) recently assessed with age-structured models. There was general agreement in historical mortality trends between the age-structured models and the mean length-based methods, although there were some discrepancies which are discussed. All models also agreed on the overfishing status in the terminal year of the assessment of the six stocks considered here when the mortality rates were compared relative to reference points. This dissertation develops new length-based assessment methods which consider multiple sources of data. The review guides prospective users on potential choices for assessment with length-based methods. Issues and diagnostics associated with the methods are also discussed in the review and highlighted in the example applications.

A changing climate has been identified as a major driver of changes in marine species’ distribution, phenology, and habitat selection in recent decades and is expected to continue to influence these traits. These changes are not only happening in our oceans, but within coastal habitats as well, where waters are susceptible to sudden changes in temperature and oxygen levels are influenced by nutrient inputs. These changes which will likely impact fish species that utilize these areas as nurseries, spawning habitat, or foraging grounds. In this dissertation I consider climate impacts on two important predators, the sandbar shark (Carcharhinus plumbeus) and cobia (Rachycentron canadum), both of which rely on coastal habitats like Chesapeake Bay for their survival. I used a series of physiological, survey, tagging, and modeling studies to estimate the current and future impacts of climate change on these two species. Sandbar sharks are unable to handle temperatures as warm as 32°C physiology, but in the wild prefer temperatures between 22-26°C. As a result, I estimate bottom habitat losses in Chesapeake Bay by end-of-century for juvenile sandbar sharks. Although they are relatively intolerant of hypoxia (critical oxygen concentration = 3.5 mg l-1), juvenile sandbar shark appear to prefer areas on the fringes of hypoxic zones to avoid larger sharks and find more abundant prey. Therefore, the continued reduction in oxygen levels throughout the entire water column actually improves juvenile sandbar shark suitable habitat. Being a bottom dwelling species, sandbar shark in Chesapeake Bay may be forced to remain in non-preferred bottom habitat, move up in the water column, or shift to shallower habitats. Cobia are tolerant of high temperatures (32°C) and low oxygen (1.7-2.4 mg/l) which should allow them to withstand the detrimental effects of climate change in Chesapeake Bay, at least through mid-century. Hypoxia and elevated temperatures reduce survival of cobia that are exercised to exhaustion. Although the physiology experiments and habitat models suggest cobia will withstand climate change through mid-century, declines in their suitable habitat in Chesapeake Bay are expected by end-of-century. I project arrival time to occur earlier and departure time to occur later when temperatures are warmer and that by mid- and end-of-century cobia may spend on average up to 30 and 65 more days, respectively, in Chesapeake Bay. As conditions worsen in more southern estuaries, cobia may shift spawning habitat in estuaries and bays further north, such as Delaware Bay, New York/New Jersey Bight, and Long Island Sound, where conditions are more thermally suitable. Over the next 60-80 years, suitable cobia habitat is projected to shift northward from spring to fall and to decrease over the U.S. continental shelf. As cobia shift into new areas, the development of regulations in more northern states will become necessary to promote a sustainable cobia fishery. As species shift their distributions as a result of climate change, it is imperative that we understand why and how these shifts are occurring so that both managers and fishers can ensure important resources continue to be fished sustainably.