Triploids are a popular product in commercial oyster aquaculture and make up most of the hatchery-produced Crassostrea virginica farmed in the Chesapeake Bay. Despite their importance to commercial aquaculture, the potential of genetically improving triploid C. virginica from selective breeding and breeding strategies for their improvement had not been evaluated. In this dissertation, the prospect of improving triploid C. virginica through selective breeding was assessed with a quantitative genetic analysis from a field test, and breeding strategies for genetically improving triploids were compared by computer simulation. Heritability and genetic correlations involving commercial traits in triploids, including mass mortality associated with late spring conditions, or “triploid mortality,” were estimated from twenty paternal half-sib triploid families and forty full-sib tetraploid families reared at three sites in the Chesapeake Bay. A triploid mortality event only occurred at a site on the bayside of the Eastern Shore of Virginia (Nandua Creek), with three triploid families having survival less than 0.70 between May 7 and July 9. The heritability of survival in triploid families during the triploid mortality event was high (1.06 ± 0.32), suggesting selective breeding can reduce the risk of these mortalities in the future. Genetic correlations between survival in triploids at Nandua Creek and the other two sites, York River and Choptank River, were low (0.46 ± 0.22, 0.46 ± 0.24), indicating a weak relationship between genes causing “triploid mortality” and genes causing mortality at York River and Choptank River. Heritability for total weight, meat weight, and shape traits in triploids was often high (> 0.30) and higher than that previously reported for diploid C. virginica. Genetic correlations between traits in triploids and tetraploids were always positive and ranged from 0.30 to 1. Although the positive genetic correlations indicate that selecting for genetic improvement of tetraploids will also lead to genetic improvement in triploids, the estimates had high standard errors, leaving the strength of the relationship unclear. Breeding strategies for genetically improving triploids were compared by simulation with a focus on the effect of genetic correlations between ploidies. The strategies were 1) separate diploid and tetraploid family breeding programs, without phenotyping triploids and 2) a single family breeding program phenotyping diploids, triploids, and tetraploids. The strategy of phenotyping all ploidies resulted in more genetic improvement of triploids when between-ploidy genetic correlations were low (0.33 – 0.66), and the two strategies had similar results at higher genetic correlations (0.75 – 0.90). The higher or similar improvement of triploids across moderate genetic correlations suggests the single breeding program is the better approach, especially if robust estimates of between-ploidy genetic correlations are unavailable. Potential exists to genetically improve triploid C. virginica in the Chesapeake Bay through selective breeding, including reducing the risk of “triploid mortality.” Phenotyping diploids, tetraploids, and triploids in a single breeding program is likely to yield the highest possible improvement in triploids if using family selection. Future studies should assess the benefit of applying genomic selection to polyploid oyster breeding. Genomic selection may be highly advantageous for improving triploids because it could enable identification of individual diploids and tetraploids that have the highest genetic value for triploid production.

In the United States, the Magnuson-Stevens Reauthorization Act mandates that all federally fished species must have catch limits, which can be challenging for data-limited species. One approach is to assess and manage a group of species with similar life history characteristics, vulnerability to the fishery, and overlapping geographic distributions in a single management unit, or a complex (i.e., stock or species complex). Using the Gulf of Alaska (GOA) Other Rockfish complex as a case study, the main goals of this dissertation are five-fold: 1) review species complexes in the United States; 2) compare multivariate techniques for assigning species to complexes; 3) group species based on spatial and temporal patterns using a new application of a species distribution model (i.e., Vector Autoregressive Spatio-Temporal model, VAST, model); 4) compare catch advice between existing assessment models used for species complexes with that from the new spatio-temporal modelling (i.e., VAST) application; 5) refine management advice on appropriate species groupings and associated catch limits for this complex. In Chapter 1 a review was undertaken of all managed and assessed complexes in the United States, thereby identifying regional differences in management strategies and assessment models used to set catch limits for established complexes. The remaining chapters focused on the GOA Other Rockfish, a group of 27 Sebastes species. In Chapter 2, a suite of multivariate methods (e.g., cluster analyses and ordination techniques) was developed and applied on an array of datasets (e.g., life history values, fishery-dependent catch, and fishery-independent surveys), to examine how species groupings can vary depending on the methods or data utilized. Results indicated that the species composition for the two main gear types, trawl and longline gear, were different. Chapter 3 addressed the complex membership using a spatio-temporal species distribution model, which was used to investigate the temporal and spatial relationships among species and compared with groupings based on harvest fractions and life history values. Main results for species groupings were consistent across methods from Chapter 2 and 3, suggesting that rockfish belonging to a sub-group of the GOA Other Rockfish (i.e., members of the Demersal Shelf Rockfish) should be removed and managed separately from the Other Rockfish complex throughout the GOA management area. Using the resultant complexes, Chapter 4 compared two assessment models for the GOA Other Rockfish: the currently used random effects model and a newly, developed spatio-temporal model (VAST). While the results of this research are specific to the GOA Other Rockfish, the lessons and recommendations are applicable to other complexes with similar data availability. Multiple data sources and a variety of methods should be used to identify or verify complex membership, where the best species groupings are those that are consistent across all analyses. Variation in groupings across analytical methods and data inputs can provide further insight into data needs or species that warrant careful monitoring. Additionally, new assessment models for species complexes should be explored and tested to ensure results adequately reflect the status of the complex and provide reasonable harvest limits.

Coastal sharks represent a group of stocks for which observation, assessment, and management are particularly challenging. Large distributional ranges, complex migratory behavior, low economic value, and relatively few observations in fishery independent surveys hinder relative abundance estimation. Assessing stock status of coastal sharks is encumbered by limited data availability, data quality, and knowledge of life history strategy. Further, coastal sharks are challenging to manage due to their slow intrinsic population growth rates, competing stakeholder interests, history of overexploitation, and in some cases, subjection to international exploitation. This dissertation aimed to improve the capacity to observe relative abundance of coastal sharks. Because a comprehensive survey is unavailable across the full distribution of coastal shark species in the southeast United States, several spatially-limited surveys are conducted, each assumed to represent an independent measure of relative abundance. When compiled, these indices of abundance regularly conflict, obscuring the true trend in stock abundance and potentially biasing estimates of stock status from stock assessments. Using age-structured simulations for Atlantic sharpnose and sandbar sharks, we tested whether dynamic factor analysis (DFA) is an appropriate statistical approach to reconcile conflicting survey indices. The resulting DFA trends were then input into a stock assessment model and results were compared to those generated from inputting conflicting indices into a corresponding assessment model. DFA proved useful in clarifying underlying patterns in stock abundance when the stock abundance exhibited sufficient contrast, and DFA trends were shown to produce more consistent (precise) assessment results. This dissertation serves to improve the capacity to observe patterns in relative abundance over time and likewise expand the toolbox for coastal shark stock assessments. Fishery management procedures (MPs) are pre-agreed upon frameworks designed to manage a stock and typically include information on how the stock is monitored, assessed, how stock status will alter management regulations (‘harvest control rule;’ HCR), and how the management regulations will be applied to the stock. No MP has been developed for coastal sharks in the United States. Consequently, we examined the impact of various HCR parameterizations and stock assessment frequency for the large coastal sandbar shark using a simulation approach termed management strategy evaluation. Notably, sandbar sharks are subjected to unregulated, international removals by Mexico, and the level of future Mexican removals was found to have a significant impact on the ability of the sandbar shark to recover. Trade-offs in management objectives with respect to various parameterizations of the harvest control rule were presented. Further, the frequency of stock assessments had a relatively small impact on the management objectives of the sandbar shark fishery. Through management strategy evaluation, international removals were identified as a potential barrier to sandbar shark recovery. Further, the vast resources required to undergo more numerous stock assessments could be potentially alleviated by reduction of future large coastal shark assessment frequency without compromising management success.

All estuarine crabs have two larval stages, the zoea and the megalopa. Zoeae are entirely planktonic, whereas megalopae begin as plankton before beginning to search for settlement substrates as late stage megalopae. At both stages, crab larvae are subject to environmental conditions of the estuary. With changing environmental conditions due to anthropogenic activities and climate change, an understanding of how these planktonic larvae respond to environmental conditions is necessary for understanding subsequent larval supply to benthic populations and implication for fisheries management and habitat restoration. For this dissertation, I: 1) analyzed long-term timeseries in the lower Chesapeake Bay for spatial and temporal change in zoeal abundance and to identify the environmental drivers of these changes; 2) examined effects of climate and environmental conditions on long-term change of dominant crab zoeae in the lower Chesapeake Bay; 3) investigated how warming temperatures in the Bay affect phenology of dominant crab zoeae; and 4) conducted a field experiment in the lower Bay to characterize settlement pattern of megalopae and determine environmental predictors of settlement. Zoeal assemblages of the lower Chesapeake Bay were characterized by distinct assemblages in the tributaries versus the mainstem Bay. Zoeae of the estuarine mud crab (Rithropanopeus harrisii) and fiddler crabs (Uca minax and Uca spp.) dominated in the tributaries, whereas a more diverse assemblage of crab zoeae, including larvae of the mud crab Hexapanopeus angustifrons, pea crab Pinnixa sayana, blue crab Callinectes sapidus, squatter pea crab Tumidotheres maculatus, and fiddler crabs Uca spp. were dominant taxa in the mainstem. Salinity was the single most important factor explaining patterns in the composition of zoeal assemblages in space and time. Variability in total zoeal abundance and richness in both regions was also significantly related to salinity. Abundance of four dominant species, Callinectes sapidus, Hexapanopeus angustifrons, Dyspanopeus sayi, and Pinnixa chaetopterana, in the mainstem significantly decreased from 1985-2002, while no significant trend was observed for dominant species in the tributaries. Variability in abundance of dominant zoeae was significantly related to the North Atlantic Oscillation (NAO) and Atlantic Multidecadal Oscillation (AMO), which likely influenced zoeal abundance via streamflow into the Bay. From 1968 to 2002, I found no significant effect of warming on phenology of the zoeae of dominant species, except Rhithropanopeus harrisii, which had an earlier start of season (date of 10% of highest peak of abundance) as water temperature increased. in a field experiment, settlement of C. sapidus megalopae was episodic, beginning in mid-July and extending into November. in contrast, the settlement periods of R. harrisii and D. sayi were shorter than C. sapidus, begining in early-July and ending in early October. Local conditions, especially salinity and water temperature, were as important as factors associated with transport processes (e.g., tidal range, wind direction, lunar phases) in determining settlement of crab megalopae. This dissertation illustrated that zoeal assemblages and successful settlement of megalopal stage of crabs in the lower Chesapeake Bay were sensitive to changes in environment conditions. These changes in zoeal abundance and settlement success have important implications for adult populations of estuarine crabs.

Juvenile dispersal is a life history strategy found across taxa and habitat types. In this dissertation, I examine juvenile dispersal in an evolutionary context and explore the conditions that support high dispersal, which necessitates subsequent ontogenetic habitat shifts. I use a sea turtle study system to evaluate the genetic and behavioral patterns associated with juvenile dispersal and ontogenetic shifts in marine environments. Specifically, I focus on four sea turtle species found in the northeastern Gulf of Mexico in the early life stage known as the 'lost years': green turtles (Chelonia mydas), Kemp's ridleys (Lepidochelys kempii), loggerheads (Caretta caretta), and hawksbills (Eretmochelys imbricata). I use mitochondrial DNA (mtDNA) haplotypes and ocean transport probabilities to estimate contributions from source rookeries to sampling sites in the Gulf of Mexico as well as assess gaps in the available genetic datasets. The mixed stock analyses indicate that the majority of 'lost years' green turtles I sampled originate from nesting beaches along the coast of Mexico, with smaller contributions from Costa Rica and Suriname. More broadly, I identify gaps in available genetic data across species, life stages, and ocean basins, particularly among early juveniles. I use telemetry data to characterize sea turtle 'lost years' movements with respect to the continental shelf and proximity to the coast, potential recruitment to coastal habitats, and passive versus active behavior by using oceanographic surface drifters as a control. The West Florida Shelf is a high-use area, particularly among green turtles and Kemp's ridleys. Finally, I analyze genome-wide single nucleotide polymorphisms to test whether mtDNA haplotype data accurately reflect overall population structure for defining management units. These data provide valuable insight into the elusive 'lost years' juvenile dispersal life stage in sea turtles and fill substantial data gaps impeding management for species conservation.

The diets of green turtles from five dissimilar aggregations of juvenile C. mydas on the East Coast of Florida were analyzed. C. mydas were captured by tangle net from four of the study sites and a dietary sample was collected by an esophageal flushing technique. The gut content of stranded individuals was collected for the fifth site. The vegetation in these study areas differs in varying degrees of abundance and diversity. Analysis of the samples revealed the alga types preferred by green turtles from each population and provided the basis for examination of similarities and differences in their diets. Large numbers of the juvenile C. mydas worldwide are infected with a disease called Fibropapillomatosis (FP). The herpes-type virus that appears to cause the disease manifests as tumors normally on the fleshy parts of the body. The placement and size of the tumors can eventually impede the green turtle’s ability to swim and forage. Severe conditions of the disease lead to death either by starvation or the inability to evade predators. While the herpesvirus initiates FP, there are other environmental cofactors that may play a role in promoting the disease. Some toxic microalgae (dinoflagellates) of the genus Prorocentrum produces a known tumor promoter called okadaic acid. The acid has been shown to promote cutaneous tumors in laboratory mice. These Prorocentrum species live primarily as epiphytes, forming a mucilaginous attachment to seagrasses and macroalgae. Chelonia mydas may be consuming the toxic microalgae when they forage on vegetation. Samples of available vegetation at each study area were collected and examined to determine if C. mydas were potentially consuming Prorocentrum. Prorocentrum were quantified for diet items by counting the number of cells per wet weight of macroalgae. In most cases, the diet analysis and microalgae quantification results showed an association between the consumption of substrates utilized by Prorocentrum spp and a high prevalence of FP in that population.

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.

Coarse outcomes of prescribed fires are well-understood, but fine scale impacts on many assemblages are still unknown. When fire approaches, animals escape to unburned areas, hide in place, or are killed by fire. Treefrogs are unique in their use of trees for most of their adult nonbreeding activities. This reliance on uplands and three-dimensional landscape composition makes them a great model to study prescribed fire impacts. We focused analyses on an upland flatwoods specialist comprising 99% of our captures, the pinewoods treefrog Dryophytes femoralis. We assessed this species' responses to prescribed fire using two separate before-after-control-impact replicated field experiments in a Central Florida pine flatwoods landscape. In Study I, we assessed fire impacts on population and movement in canopies over six months (N = 76 frogs, 198 recaptures). We used single rope technique and climbing equipment to set PVC pipes as treefrog refugia at 3 m, 6 m, 9 m, and 9+ m in twelve longleaf pines, Pinus palustris, across four plots, two of which had fires scheduled during the study. Study II evaluated frog population changes in uplands in response to prescribed fires (N = 1804 frogs, 1790 recaptures). We collected 27 months of mark-recapture data by checking 240 open PVC pipes at 2 m in longleaf pines across eight plots with fires prescribed during the study. Using mark-recapture and mixed generalized linear models with Bayesian framework, we modeled abundance, survival, recapture, and vertical movement parameters. We found the prevailing mechanism for resiliency to fire for pinewoods treefrogs was refugia up pines, then recolonization of lower layers when they regreen post-fire. This finding substantiates others' conclusions that structural integrity of the community is key to sustaining native biodiversity. Future work and management should increase consideration of the three-dimensional structure of the habitat when developing burn prescriptions and study designs.

No description available.

Nymphon is the largest genus of Pycnogonida reaching its greatest diversity in the Polar regions. A revision of the genus within the Eastern Arctic has proved necessary due to the numerous nomenclatural complexities which have accumulated in the literature since its last major revision by Sars in 1891. This has been achieved using multivariate analyses involving the measurement of over 1500 specimens. Fifteen species are now recognized from the area and each has been redrawn and redescribed. It has not proved necessary to propose any new species. Two distinct sub-groups are found within the genus in this area, differing in leg morphology and reproductive strategy. The first group, exemplified by Nymphon stromi, has a leg morphology suited to walking or striding. A large number of lightly yolked eggs are typically produced and the larvae spend only a short period of their development on the male ovigers before they disperse. The other group, exemplified by Nymphon hirtipes, has a leg morphology more suited to clinging. Fewer eggs are produced but these are richer in yolk and the male overwinters with the larvae which are lost only when metamorphosis is nearly complete. These interspecific differences have been discussed and it is thought that they may enable direct competition to be avoided by the exploitation of different facets of the same environment. In addition, differences in the musculature have been discussed for species within Nymphon and for the Pycnogonida generally. The male ovigers of all species examined show various adaptations which increase the surface area compared with that of the female. These modifications have been discussed and are shown to afford a greater area for attachrnent of the maturing egg masses. A histological examination of the internal structure of the femoral cement glands of Nymphon hirtipes has revealed that the adult males have a broad band of glandular tissue lying under the epidermis whereas specimens in the final larval stage have little or none. The life-cycle of Nymphon hirtipes is postulated, showing the species to take between two and a half and three years to attain maturity. It breeds only once, during its final summer. This is compared with existing knowledge of the life cycles of shallow and tropical water species.