Stable isotope techniques were applied to summer flounder, Paralichthys dentatus, in Chesapeake Bay to elucidate the relative importance of different prey groups on the growth and productivity of this species. Prior to field application, a laboratory diet-shift study was conducted to evaluate methodological assumptions and obtain necessary isotopic parameters. Specifically, the goals of the laboratory study were to 1) determine isotopic turnover rates and fractionations of δ13C and δ15N in liver, whole blood, and white muscle and 2) estimate the relative importance of growth and metabolic processes on isotopic turnover. Groups of captive juvenile summer flounder (130-255mm total length) were monitored for up to 180 days after switching their food to a new diet with different stable isotope values. Although differences existed between carbon (C) and nitrogen (N), the rate of isotopic change was consistently ranked liver>blood>muscle for the three tissues due to increased metabolic activities of liver and blood. Half lives ranged from 9-21, 20-44, 49-73 days for liver, blood, and muscle respectively. Fractionation estimates for δ15N in muscle (range: 2.4-4.2‰) corresponded with previous research, but estimates for δ13C (range: 0.1-4.8‰) tended to be greater than the traditionally assumed values of 0-1‰. Liver and blood fractionation estimates were similar to those of muscle, differing by usually <1‰. A generalized model for predicting the time scale of isotopic turnover from growth-based turnover parameters was also developed to help evaluate assumptions of isotopic equilibrium in the field. Information obtained from the laboratory study facilitated the use of stable isotopes as dietary tracers for wild summer flounder (138-624mm total length) in Chesapeake Bay. Summer flounder tissues (liver, blood, and muscle) and commonly consumed prey species were sampled seasonally during late spring / early summer (May-July) and fall (November) in 2006 and 2007. To account for similarity in isotopic measurements and to apply mixing models, prey species were aggregated into two trophic guilds: crustaceans (mysid shrimp, sand shrimp, mantis shrimp) and fishes (bay anchovy, juvenile sciaenids, spotted hake). Lack of δ13C differentiation among trophic guilds and summer flounder prevented the use of δ13C as a useful dietary indicator. Analysis of δ15N revealed that crustaceans comprised the majority of summer flounder diet, accounting for ~85-100% of flounder diets on average, except in spring of 2006 when fishes and crustaceans were equally represented in the diet. Summer flounder tended to occupy the same trophic level as the other fishes, suggesting more of a competitive relationship than a predatory one. However, a positive trend in δ15N with length in all tissues indicated that larger summer flounder fed at ~1 trophic level above smaller flounder. Differences in isotopic values between slow and fast turnover tissues did not reveal this ontogenetic dietary pattern at the level of the individual, because the changes in feeding were of small isotopic magnitude and occurred too gradually for reliable detection. Based on stable isotopic analysis, growth and production of summer flounder in Chesapeake Bay are highly dependent on assimilation of mysid, sand, and mantis shrimps, more so than previously expected based on stomach content research.

Microbial communities associated with a particular space or habitat, or microbiomes, play significant roles in host health and the regulation of biogeochemical cycles. In oysters these microbiomes may be important contributors in the removal of biologically available nitrogen (N) from the coastal and marine environment through the process of denitrification. Denitrification is the microbially mediated step-wise reduction of nitrate (NO3-) or nitrite (NO2-) to N2 gas. Excess nitrogen in the Chesapeake Bay has been implicated in the increase of eutrophication and other detrimental effects including harmful algal blooms, hypoxia, and loss of benthic communities. Oyster reefs have been shown to enhance the rates of denitrification in nearby sediments, but little is known about the oyster microbiomes or associated microbes responsible for denitrification (denitrifiers). Furthermore, the identification of the oyster core microbiome, or set of resident microbes continually present in the oyster, is relatively unknown. Assessing the stable underlying core is necessary to evaluate and predict the effect of varying environmental conditions on the oyster microbiome and oyster denitrification. A combined 16S targeted metagenomic and metabolic inference approach was used in this study to investigate the gill, gut and shell microbiomes of the eastern oyster (Crassostrea virginica) and their associated denitrifiers in response to spatial and temporal changes. Denitrification activity was linked to community structure using methods such as quantitative PCR of nitrous oxide reductase genes (nosZ) and 15N isotope pairing technique with experimental flow-through design. The oyster gill, gut, and shell microbiomes all showed distinct and unique core microbiomes, suggesting an importance of the core to oyster function or health. Denitrifier abundance and activities were most consistent in the shell microbiomes indicating a stable, pool of potential denitrifiers for oyster denitrification. In comparison, oyster gill and gut denitrifier abundances and activities were highly variable and likely related to transient denitrifiers ingested with food particles. Additionally, denitrifiers demonstrated niche differentiation between the different oyster microbiomes, indicating different groups of denitrifiers are responsible for performing denitrification in the oyster. Assessing the stability and variability of the oyster microbiome and associated denitrifiers provides a greater understanding of the oyster’s role in denitrification and the mitigation of excess N in marine and coastal environments.

Batrachoidiformes, the toadfishes, are benthic fishes that inhabit nearshore subtidal and intertidal habitats, characterized by their dorsoventrally flattened bodies and large pectoral fins. These fishes lack dispersive larvae, and larval development is retained in nests guarded by their parents. To date, 82 species and 23 genera are accepted as valid. Previous studies recognized a single family, Batrachoididae, with four subfamilies: Batrachoidinae, Porichthyinae, Thalassophryninae, and Halophryninae. Interrelationships among subfamilies, however, are unresolved and interrelationships among species are problematic. Despite being a conspicuous member of the coastal fauna, the internal morphology of most species of Batrachoidiformes is unknown, being intraspecific and ontogenetic variations not reported for most species. Several characters used in previous analyses were found to have problematic construction or be intraspecifically variable. This new study reassessed the morphology of 66 species of 22 genera, representing most of the diversity of subfamilies of Batrachoidiformes. This investigation also endeavored in accounting for intraspecific and ontogenetic variations, in order to recognize the potential phylogenetic characters. The first chapter investigated the caudal skeleton of Batrachoidiformes, the posteriormost region of the axial skeleton. Results found high intraspecific variation in this region, especially in the shape of the epurals and the parhypural flange. Despite the high intraspecific variability, potentially informative characters were identified, such as the presence of a hypurapophysis-like process in seven genera of Halophryninae. The second chapter investigated the series of intermuscular bones and tendons within Batrachoidiformes. Variation in this series of sesamoid bones is not only poorly known in toadfishes, but teleost fishes in general. Results show that variation in intermuscular bones is high and potentially phylogenetically informative. For example, Batrachoidinae, Thalassophryninae, and Halophryninae have the origin of the first epineural articulating with the neural spine of the first vertebra. In Porichthyinae and other representatives of Percomorphacea the origin of the first epineural articulates with the neural arch of the first vertebra. The third chapter described the early ontogenetic changes of the skeleton of Porichthys notatus (Porichthyinae). These completely novel descriptions include tables of sequence of ossification and appearance of cartilages. The fourth chapter is the phylogenetic analysis. Previous characters were modified and new characters were proposed, resulting in a dataset of 191 morphological characters. One of the main results of this analysis is that Halophryninae is not monophyletic, with Allenbatrachus, Batrachomoeus, and Halophryne being more closely related to Porichthyinae, Thalassophryninae, and Batrachoidinae. This new phylogenetic arrangement and its supporting synapomorphies are discussed, including potential implications in the classification within this order.

Relative to many highly migratory fishes, Striped Marlin, Kajikia audax, exhibit considerable stock structure. At least four genetically distinct stocks of Striped Marlin have been delineated in the Pacific and Indian oceans, although stock composition in the central North Pacific (CNP) remains unclear and the presence of an additional stock in the North Pacific has been suggested in two recent studies. The goals of this research were to clarify the number of Striped Marlin stocks in the North Pacific and utilize temporal sampling to better understand the stock dynamics of Striped Marlin exploited by the Hawaii-based pelagic longline fishery (HBPLLF). Fishery observers collected 417 samples of Striped Marlin from the HBPLLF from 2019-2020. Of these, 85 samples underwent genotyping-by-sequencing using DArTSeqTM and the data were co-analyzed with an existing single nucleotide polymorphism (SNP) dataset for 256 individuals of Striped Marlin collected from throughout the species’ range and reported in a previous study. Three of 12 Striped Marlin previously reported to comprise a putative second stock in the North Pacific and all with high observed heterozygosities were also re-sequenced to test the hypothesis that sample contamination resulted in the identification of a spurious stock. After re-sequencing, the observed heterozygosity of each of the three individuals was reduced by approximately 50%, confirming contamination and the original sequences for the 12 individuals comprising the putative second stock were removed from the dataset. Clustering analyses of the resulting dataset strongly supported a single North Pacific stock; the three re-sequenced individuals clustered into previously described stocks. The 73 (post-quality filtering) Striped Marlin sampled from the HBPLLF clustered into either the North Pacific (NPO; Japan, Taiwan, Hawaii, and California sample locations) or Oceania (New Zealand, western Australia, and eastern Australia sample locations) stocks, indicating mixing of the two stocks in the CNP. A panel of 48 SNPs with the highest power to discriminate between the two stocks was developed and 32 of these loci were used to genotype and assign an additional 325 Striped Marlin collected from the HBPLLF to stock of origin. Overall, 305 of these fish were assigned to stock of origin with high (> 90%) confidence and combined with DarTSeq-based assignments of the original 73 fish. Both stocks were present throughout the sampling period (NPO: 41.3%; Oceania: 58.7%). Temporal changes in stock composition were identified, with NPO fish dominant during the winter and spring, and Oceania fish dominant during the summer and fall. Although the HBPLLF is known to exploit mostly sub-adult Striped Marlin, 13 (3.1%) samples were found to be in an active spawning condition at the time of capture based on visual inspection. Of these, 10 assigned to NPO and two assigned to Oceania (the 13th fish assigned into Oceania but scores were below 90%). Factors that may influence the stock composition of Striped Marlin in the HBPLLF, including stock-specific movements to different spawning grounds and alternate feeding areas, as well as seasonally displaced recruitment to the HBPLLF, are discussed.

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.

Climate change has resulted in both increased mean water temperature and higher frequencies of extreme water temperatures in coastal areas. These new thermal regimes exert strong selective pressure on the thermal physiology of coastal aquatic species. Phenotypic plasticity (the ability of one genotype to display multiple phenotypes) and local adaptation (increased fitness to local environment due to natural selection) dictate both short-term (from hours to days to weeks) and long-term (from years to decades) resilience of a species. To better predict how a species will respond to the negative impacts of climate change, one first needs to know the current levels of variation in plasticity and local adaptation. Marginal populations are especially critical for the persistence of a species, as those populations can harbor unique genetic variation and the interaction between plasticity and local adaptation determines the boundaries of future distributional ranges. This dissertation focuses on the northern marginal population of spotted seatrout (Cynoscion nebulosus), an estuarine-dependent fish, and compares them with those from the core region of the distribution to elucidate the physiological, transcriptomic and genetic mechanisms of plasticity and adaptation. I discovered significant differences between fish from different areas at all three levels of biological organization: Chapter 1 shows different whole-organism metabolic physiology of fish sampled from distinct populations and the northern population is consistent with cold-adaptation, given the pressure of natural selection from more severe and frequent winter kills in the region. Chapter 2 presents functional genetic evidence that the cold-adapted northern spotted seatrout are more vulnerable to heat stress than the warm-adapted southern spotted seatrout, suggesting that differential gene expression is contributing to observed differences in thermal tolerance. A liver transcriptome is de novo assembled and serves as a valuable resource for future genetic studies of spotted seatrout. Chapter 3 discovers signatures of selection based on over 15,000 genome-wide single nucleotide polymorphism (SNP) markers. The pattern of genetic variation is consistent with thermal adaptation along the US east coast. Genes involved in metabolic pathways and transcriptional regulation are the main targets of natural selection. In summary, spotted seatrout are relatively resilient to the thermal effects of climate change due to a wide range of metabolic plasticity and adaptive potential in climate-related genetic variation. Range expansion at the leading edge, however, is largely constrained by the species’ cold tolerance limit. The northern and southern population will likely respond to climate change differently and this should be taken into consideration in future conservation management of this species.

Anthropogenically-induced climate change has resulted in increases in water temperature and the frequency and severity of hypoxic events in coastal areas worldwide. Temperature and hypoxia affect fishes' energetics which can, in turn, be reflected in changes in reproductive success and shifts in spatial distributions. in an effort to quantify these changes in Atlantic croaker (Micropogonias undulatus) and spot (Leiostomus xanthurus) in Chesapeake Bay. I: (1) estimated standard and maximum metabolic rates and hypoxia tolerances at five temperatures (10, 15, 20, 25 and 30°C) using intermittent-flow respirometry, (2) examined the effects of hypoxia exposure on metrics of reproductive potential and, (3) developed an individual-based, dynamic-seascape model of Atlantic croaker and spot based on data from the respirometry trials, The first set of experiments showed that metabolic scope (i.e., the difference between standard and maximum metabolic rates, and within which all aerobic metabolic processes must operate) increased with increasing temperature in both species between 10 and 20°C, but plateaued above 25°C in Atlantic croaker and above 20°C in spot. Except at 10°C, the metabolic scope of Atlantic croaker was less than that of spot at all temperatures. in contrast to previous studies with Atlantic croaker from the Gulf of Mexico, the relative expression of hypoxia-inducible factors and metrics of reproduction (gonadosomatic index, most-advanced oocyte stage, and proportion of atretic oocytes) did not differ between Atlantic croaker captured under normoxic and hypoxic conditions in Chesapeake Bay. Simulations of the movements and distribution of Atlantic croaker and spot using individual-based models suggested that these species would occupy areas with warmer and better-oxygenated water than indicated by trawl survey observations from 1988-2014. Additionally, simulations indicated that a greater proportion of Atlantic croaker and spot in the Virginia waters of Chesapeake Bay would occupy the lower portion of Chesapeake Bay than indicated by capture rates from the trawl survey. My research suggests Atlantic croaker and spot are well-adapted to the environmental conditions of Chesapeake Bay during summer and are likely not affected by the frequent hypoxic episodes occurring in the subestuaries of the lower Chesapeake Bay. The apparent larger effect of elevated temperature on the metabolic scope of spot may provide them a greater capacity for movement, growth, and reproduction in warmer conditions and thus, a competitive advantage over Atlantic croaker as water temperatures continue to rise due to anthropogenically-induced climate change. My results indicate that intermittent exposure to hypoxic conditions is unlikely to negatively affect the reproductive potential of Atlantic croaker. Additional research, however, is necessary to better understand how this intermittent hypoxia exposure affects the endocrine pathways controlling reproduction. Finally, although climate-change science frequently focuses on the effects of rising coastal water temperature, and fisheries science and management on the effects on fish distributions, the results of my individual-based models suggest that predicting the effects of anthropogenically-induced climate change should not focus on temperature alone, as this may not be the most important driver of changes in fish distribution. More specifically, other factors such as time-area specific hypoxic events, prey availability, and predator avoidance likely contribute to the spatial distributions of these species in Chesapeake Bay.

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.