The striped bass (Morone saxatilis) is an anadromous fish distributed along the eastern coast of North America that currently supports one of the most lucrative and important commercial and recreational fisheries in the region. Since the recovery of the Atlantic stock after a collapse in the late 1970s, studies have focused on understanding the connectivity of major spawning grounds and improving methods of abundance estimation. Studies support strong site fidelity of striped bass to major estuaries along the Atlantic coast, but there has been disagreement about connectivity within the largest spawning ground, the Chesapeake Bay. Additionally, no estimates exist for striped bass abundance within the Chesapeake Bay. The objectives of my thesis were to examine the fine scale genetic population structure of striped bass within the lower Chesapeake Bay, and to test the feasibility of a novel, fishery-independent molecular methodology, close-kinship mark-recapture analysis (CKMR), to estimate spawning adult abundance within the Rappahannock River. Sampling of 1,132 adult striped bass and 389 young-of-year (YOY) striped bass was done during the 2016 and 2017 spawning seasons on major spawning grounds of the James, Mattaponi, and Rappahannock rivers. Twenty microsatellite loci were used to examine both the spatial genetic heterogeneity among the river systems and the temporal heterogeneity between sampling years within a river. Significant population pairwise FST values were recovered from 18 of the 21 pairwise comparisons. However, mean FST values between temporal comparisons were higher than those among spatial comparisons, suggesting a lack of biologically meaningful population structure among rivers. Additional analyses and a 30-year tagging data set also support a rate of connectivity among the major rivers high enough to maintain similar allele frequencies. Combined, the data support one genetic stock of striped bass within the lower Chesapeake Bay. The same suite of markers was then used to test the feasibility of CKMR to estimate adult abundance of striped bass within the Rappahannock River system. Using existing sampling programs, 371 spawning adults and 389 YOY were collected on the spawning and nursey grounds of the Rappahannock River in 2016. These samples yielded 2 parent-offspring pairs, resulting in an abundance estimate of 145,081 adult spawning striped bass. Additional analyses indicated that a relatively precise estimate (recovery of 50 POPs) would be made if sample sizes totaled 850 adults and 850 YOY. CKMR can be a feasible option of abundance estimation for striped bass. Overall, my study has provided the first estimate of abundance for Chesapeake Bay striped bass, and has provided strong support of a single, spawning stock of striped bass within the Chesapeake Bay.

Unusual mortalities of cultured Crassostrea virginica in late spring have been reported from farms in the Chesapeake Bay from 2014 to 2017. None of the usual causes (e.g. disease, poor husbandry) were likely responsible, and mortalities occurred without clear signs of biological or physical stressors. Mortalities in the spring of 2014 were particularly high on over a dozen farms in Virginia, most of which were on the bayside of the Eastern Shore. Estimated losses were over 50%; however, mortalities only occurred within a four-week period between mid-May and early June. Farmers that had unusually high mortality in their crop were exclusively growing triploid oysters, which implicated triploidy as an important factor and even led to calling these events "triploid mortality." Many affected farmers were also growing a "northern cross," oysters made by crossing brood stock from New England to brood stock from Virginia, and relatively high fecundity was found in some triploid oysters sampled from these farms. It was hypothesized that the genetic contribution from the New England parent of the northern cross was causing aberrant gametogenesis in triploid oysters during the late spring, and that this caused triploid mortality. A controlled field test was conducted to evaluate this hypothesis and to further examine the role of genetics and gametogenesis in triploid mortality. to investigate the effect that ploidy and brood stock origin have on susceptibility to triploid mortality, four triploid and four diploid types of oysters, produced by crossing different combinations of brood stock of Virginia, Louisiana, and Maine origin, were deployed to three commercial oyster farms that experienced unusually high mortality in 2014, as well as to a control site lacking reports of unusual spring mortality. The survival and growth of oysters from each group were measured throughout the spring and summer of 2016. A mortality event (>20% mortality) was observed in late spring at one site. The mortality event was only associated with triploid groups, with cumulative mortality ranging from 12 to 24% among groups. Mortality in the "northern cross" was not especially high (23%). The effect that gametogenesis had on the mortalities was investigated by examining histological cross sections of triploid and diploid oysters from the site where triploid mortality occurred, as well as from the control site where there was no triploid mortality. Diploid oysters at the affected site became gravid and spawned earlier than diploid oysters at the control site. Gonad development in triploid oysters was abnormal and variable, so categories were developed for classifying gonad development in triploid oysters and making comparisons between sites. No obvious difference was observed in gonad development between triploid oysters at the two sites. Cross-sections from male triploids did not typically contain any spermatozoa, and cross sections from females usually contained only a few oocytes. Gonad development may not be strongly associated with triploid mortality, but the physiology associated with abnormal gametogenesis in triploid oysters could be a major contributing factor. More work is needed on the physiological consequences of gametogenesis in triploid oysters to explain triploid mortality.

Gadiformes include some of the most important commercially harvested fishes in the world (e.g. cods, hakes, and grenadiers). Currently, different authors recognize anywhere between 11 and 14 families, approximately 84 genera, and over 600 species. The monophyly of the order has been supported by both morphological and molecular data, yet the relationships among families and subfamilies remain poorly understood and interpreting phylogenetic patterns to date has been difficult. My dissertation research on multi-scale phylogenetics of Gadiformes with emphasis on hakes (Merluccius, Merlucciidae) has three primary objectives: (1) to improve the understanding of the phylogenetic relationships among families of Gadiformes (Teleostei); (2) to analyze the phylogenetic relationships within the family Merlucciidae (Merluccius) and (3) to explore the evolution of the caudal skeleton using molecular, morphological and ecological data. in chapter two, a gene capture approach was used, targeting coding DNA sequences (CDS) from single-copy protein-coding genes to study the higher-level relationships (i.e., above the genus level) of Gadiformes. Matrices of 14,208 loci (~2.8 M bp) were generated from a total of 57 species representing all recognized Gadiformes families and subfamilies. Species tree and concatenated maximum likelihood analyses resolved a highly congruent and well-supported phylogeny at both shallow and deep levels that contributes towards stabilizing higher-level Gadiformes classification. in accordance with these results a revised classification of the group is provided in chapter two. in Chapter three the systematics, evolution, and taxonomy of a particularly problematic family, the hakes (Merluccius, Merlucciidae), using genomic data from 13,771 loci and 74 taxa were reassessed. This study resolved the controversy surrounding the taxonomic extent of Merlucciidae and the phylogenetic placement of the genera historically included within the family, based on complete taxonomic sampling at the family and subfamily levels among gadiforms. Additionally, the phylogenetic analysis confirmed an early separation of two lineages of Merluccius, the Old World and the New World clades. The Old World clade includes five well defined species and the New World clade includes three species and two complexes of species suggesting the presence of only one species in the eastern Pacific, as well as, one species in the Southern Ocean (Patagonia – New Zealand). Chapter four provided for the first time a description of the caudal skeleton for all the families among Gadiformes and explores the character evolution of 11 characters (morphological and ecological) mapped on a taxonomically robust phylogenetic hypothesis proposed in chapter two. The ancestral state reconstruction analyses suggest that the ancestral condition among gadiforms had a caudal fin and a pelagic origin. Its loss arose at least two times within Gadiformes resulting in two main phenotypes - the tailed and the tailless fishes, neither of which form a monophyletic grouping. This study is the most comprehensive phylogenomic study of Gadiformes to date. This dissertation used a novel molecular technique coupled with morphological and ecological data that resulted in a better understanding of the evolution of commercially and ecological valuable fishes, which is necessary for effective fisheries management and the preservation of reproductive and genetic diversity. Further steps, including morphological data of extant and extinct taxa, is essential to fully understand macroevolutionary patterns and processes in phenotypic evolution and lineage diversification of gadiforms.

This dissertation is from the Joint Program Degree from the College of William & Mary and University of Virginia and awarded by the University of Virginia.

Blue marlin Makaira nigricans and white marlin Kajikia albida (formerly Tetrapturus albidus) are overfished in the Atlantic Ocean, with the vast majority of fishing mortality resulting from the pelagic longline fishery that targets tunas (Thunnus spp.) and swordfish Xiphias gladius. Time series of catch-per-unit-effort (CPUE) data have been fundamental to assessments of blue marlin and white marlin stocks, but these time series have been affected by a shift over time in pelagic longline fishing practices from shallow to deeper sets. One method for adjusting CPUE data for changes in fishing practices is a habitat-based standardization that modifies fishing effort in proportion to the vertical distribution of the species of interest and the fishing gear. For these models to be successfully applied to population assessments, the vertical habitat utilized by blue marlin and white marlin must be known. Pop-up satellite archival tags (PSATs) provide a means of collecting high resolution vertical movement and distribution data for billfishes. In my study, 62 blue marlin and 40 white marlin were caught in recreational fisheries off the U.S. mid-Atlantic, Yucatan Peninsula, northern Caribbean, Venezuela, and Brazil, tagged with Microwave Telemetry, Inc. PTT-100 HR PSATs, and released. Data were recovered from PSATs attached to 57 surviving blue marlin and 36 surviving white marlin. PSATs successfully transmitted 18-100% of the data they recorded (mean 72%). The minimum 10-day displacements of both species averaged 242 km (range 9 to 942 km) and varied significantly between tagging locations, but not between species. Blue marlin spent a significantly higher (62%) amount of time in the upper 10 m of water than white marlin (56%). Both species spent greater than 95% of the time in water that was within 8o C of the sea surface temperature. Only 3.1% of white marlin demonstrated diel differences in the maximum depth of dives, while 29% of blue marlin dove into deeper waters during the day. Variables identified as explaining the most variation in dives were total dive duration, bottom time, ascent time, number of wiggles, wiggle depth, interdive interval, skew of ascent and descent, % time ascending, and % time descending. Using these variables, two dive types were identified through cluster analysis: simple dives representing traditional "U" and "V" shapes, and complex dives with multiple descents, plateaus, and wiggles. There were significant differences in dive variables among locations, individuals, diel periods, and dive types. There was significant overlap in range, habitat use, and vertical movement patterns, and therefore no strong evidence of niche partitioning between blue marlin and white marlin. My analyses can be used to further define the physical and physiological factors limiting marlins' vertical movements and therefore improve stock assessments based on longline CPUE data by correcting for changes in fishing practices.

Traceable seafood can be linked back to its origin and method of catch. Improving the traceability of marine organisms involves establishing a transparent Chain of Custody (CoC) by collecting data at checkpoints throughout the supply chain, from ship to shore to store. This report explores the feasibility of integrating Radio Frequency Identification (RFID) technology into the United States Atlantic sea scallop (Placopecten magellanicus) fishery in order to improve traceability. This report serves as a forward-looking evaluation of RFID technology that is intended to inform interested stakeholders of its functionality and capabilities. It is not intended to serve as a management proposal.

No description available.

Gene flow is an integral biological process that can mediate speciation. While many consider the ocean to be an open environment, there are many barriers that limit gene flow, particularly in the western Atlantic. I analyzed data from two widespread, coral reef fishes, the bridled goby (Coryphopterus glaucofraenum) and sand-canyon goby (C. venezuelae), throughout their range in the western Atlantic. Using two genetic datasets, mitochondrial DNA (mtDNA) and genomic SNPs, I investigated the evolutionary history of these species and inferred the location and strength of putative barriers. My results suggest that several unique lineages have genetically diverged from one another in the presence of two major barriers. First, the Amazon River has isolated Brazil from the Caribbean and second, a unique lineage was found at an isolated oceanic island, Atol das Rocas, off the northeast coast of Brazil. Furthermore, minor barriers have caused slight genetic differentiation in each of the Caribbean species off the coast of Venezuela, while on the Brazilian coast, there are up to two barriers that separate three genetically unique areas. The stronger of the two barriers is located at Cabo Frio near an upwelling system and the weaker barrier coincides with the outflow of the São Francisco River. Overall, this research highlights how barriers impact speciation and genetic structure within these gobies in the western Atlantic and more broadly, deepens our understanding about the role of oceanographic features in the speciation process.

North American amphibians have recently been impacted by two major emerging pathogens, the fungus Batrachochytrium dendrobatidis (Bd) and iridoviruses in the genus Ranavirus (Rv). Environmental, seasonal and host factors may play important roles in disease dynamics, but few studies incorporate these components into their analyses. Here, we investigated the role of environmental, seasonal, genetic and location effects on driving Bd and Rv infection prevalence and severity in a biodiversity hot spot, the southeastern United States. We used quantitative PCR to characterize Bd and Rv dynamics in natural populations of three amphibian species: Notophthalmus perstriatus, Hyla squirella and Pseudacris ornata and more broadly in multi-species amphibian communities across Florida. We combined pathogen data, genetic and host metrics, and seasonal and environmental variables into statistical models to evaluate how these factors impact infectious disease dynamics. Occurrence, prevalence and intensity of Bd and Rv varied across species, populations, and sites. Pseudacris ornata was found to have high levels of Bd across sites. In Florida, both pathogens were found ubiquitously across sites and seasons and at high levels within three different host families. We conclude that Bd and Rv are more abundant in the southeastern United States than previously thought and that host, seasonal and environmental factors are all important for predicting amphibian pathogen dynamics. Incorporating seasonal, host and environmental information into conservation plans for amphibians is necessary for the development of more effective management strategies to mitigate the impact of emerging infectious diseases.

This thesis used geographic information systems and remote sensing to measure expansion of aquaculture Northwest Mississippi. A feature extraction technique was used to identify aquaculture from satellite imagery. Variations in well water depth were examined in relation to the changes in aquaculture to explore its affects on the Mississippi River Valley Alluvial Aquifer (MRVA) aquifer. A soil moisture index was used to investigate preferential expansion of aquaculture onto soil moisture types. This study found that aquaculture expanded from 66,000 acres in 1984 to 142,000 acres in 2001. Total acreage of individual counties from the Feature Extraction is higher than estimates provided by the Mississippi Agriculture Statistics Service. It was found that aquaculture expansion covered more acres of wet soil classes than dry soil classes and the volumes of expansion onto moist soils depth time series were highly variable across the study area and showed no conclusive relationship to aquaculture expansion.