Thesis (M.S.)--University of North Carolina at Wilmington, 2005. / Includes bibliographical references (leaves: 29-34)

Statistical age-structured models are widely used in fisheries stock assessment. These models have been become increasingly complex over recent decades, allowing them to incorporate a larger variety of fisheries data. These typically include information regarding annual fishery yields, indices of abundance and catch composition data, which reflect the distribution of ages in the harvested population each year. In some fisheries, age composition can be determined annually through the examination of annuli on hard parts, such as otoliths or scales. These methods are, however, costly, time consuming and require a relatively high level of expertise on the part of data collectors. Alternatively, length frequency distributions within the annual catch are relatively simple and inexpensive to acquire, and can be employed to extrapolate age structure given that some information regarding age length relationships in the population is known. This type of data is therefore critical for many age-structured fisheries models. Length frequency data are compiled from length measurements of a sub-sample of the commercial catch. Even when they derive from a relatively large sample size, however, these data depend on a number of biological, economic and logistical factors. In some fisheries, for example, larger, more valuable fish may be separated from the overall catch and sold quickly, before port samplers have chance to gather sub-samples (Burns et al. 1983). This can reduce the relative frequency of large individuals in length frequency data. Alternatively, fish may become stratified in holding bins or storage containers according to size, due to their slippery texture and body shape (Hilborn and Walters 1992). With smaller, shorter individuals falling to the bottom where they are less likely to be picked up and measured, length frequency data may contain a disproportionately high frequency of large fish. This study used simulations to examine the impact of these two types of bias in length frequency data on a statistical age-structured model. The model, which was similar to those used in stock assessments for black sea bass (Centropristis striata) and gag (Mycteroperca microlepis) in the southeastern United States, produced erroneous population estimates when given biased data. Length frequency data that contained too many small fish caused stock status estimates to became overly pessimistic, indicating that populations were more heavily depleted than was actually the case. This type of bias supported overly conservative management measures, which posed an unnecessary cost to fishermen. Conversely, when the data included too many large fish, estimates of stock status were overly optimistic, and supported management actions that did not effectively protect the stock from overfishing. These results indicate that the quantity of length frequency data alone does not protect against bias when using complex age-structured models. The likelihood and magnitude of bias in these must also be examined in order to determine whether results are likely to be biased. For a given fishery, it is therefore critical that potential sources of bias in length frequency data be thoroughly inspected, and that the modeling approach used to assess the stock be appropriate based on the availability and accuracy of the data. / Master of Science

Red porgy <i>Pagrus pagrus</i> is a reef fish important to both recreational and commercial fisheries off the coast of the southeastern United States. Stock assessments performed on this species since 1985 have shown a population in decline. As a result, a number of management actions were put in place, including a harvest moratorium in 1999. Stock assessments for many marine species, including red porgy, rely on a combination of fishery-dependent and fishery-independent data. When a moratorium is in place, the flow of fishery-dependent data is interrupted, making assessments more reliant on fishery-independent information. To investigate how loss of fishery-dependent data, as during a moratorium, would affect stock assessment results for red porgy, I conducted model simulations to represent moratoria of various durations. The most recent red porgy stock assessment model developed during a 2002 workshop was used as a tool in these simulations. I found that biological reference points, such as biomass and fishing mortality, and population projections were more variable for longer simulated moratoria. When fishery-dependent data were removed, minor fluctuations in length and age frequencies resulted in larger fluctuations in estimates of biological reference points. The simulated moratoria also resulted in a slight bias toward over-estimating stock productivity. Similar simulations and analyses were conducted to determine the effects of reducing fishery-independent data from the Marine Resources Monitoring, Assessment, and Prediction (MARMAP) program. Length and age data of reduced MARMAP sample sizes were bootstrapped from original data, and used as input for the stock assessment model. Biological reference points and population projections were more variable for small MARMAP sample sizes, due to the incomplete representation of the length and age frequencies of the population. Reduced sample sizes also showed a slight bias toward predicting a more productive population. These types of simulations emphasize the benefits of investigating potential effects of data reduction on assessment results prior to implementing management strategies, such as a moratorium or sampling change, that cause data loss. Although decreasing red porgy data resulted in slight changes in assessment results, there are more data available for this species than other species in the snapper-grouper complex. For these lesser-studied species, reducing data could dramatically affect assessment capabilities. To investigate this, I compiled available data for these species and identified the stock assessment method used. I then predicted assessment capabilities for each species under a moratorium and if the MARMAP survey was eliminated. A moratorium could reduce assessment capabilities for 37 of the 73 species, and 63 species would require management based on key species. Removing MARMAP data would reduce assessment capabilities of eight species, many of which are economically important. There was an overwhelming need for a reliable catch-per-effort index, information that could improve assessment capabilities of 67 species. This index could be obtained by expanding the MARMAP survey, from a fishery observer program, or from commercial logbooks. By linking the red porgy stock assessment, an evaluation of sampling regimes and data loss during a moratorium, and the expansion of this stock assessment strategy to multiple species, managers will ultimately benefit from increased ability to manage stocks experiencing varying regulations and data availability. / Master of Science

Made available in DSpace on 2014-12-17T14:05:21Z (GMT). No. of bitstreams: 1 EuricoADJ_TESE.pdf: 2589936 bytes, checksum: be1dedfbfc2d5720f10af387bc96dda3 (MD5) Previous issue date: 2012-06-01 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / Esp?cies da fam?lia Lutjanidae representam um importante recurso pesqueiro em todas as ?reas de sua ocorr?ncia. No Brasil a explora??o comercial se iniciou na d?cada de 60 e nos anos 80, j? demonstrava decl?nio nos volumes de captura. A diminui??o de capturas aponta que os lutjan?deos devem ser manejados conservativamente. Estudos sobre a estrutura gen?tica das popula??es e dados gen?ticos para monitoramento dos estoques ao longo da costa brasileira atrav?s de marcadores moleculares, s?o escassos. Nesta regi?o, as esp?cies Lutjanus analis e L. jocu desempenham papel social para a subsist?ncia das comunidades de pescadores artesanais. O presente trabalho avaliou a variabilidade gen?tica inter e intrapopulacional, assim como o n?vel de estrutura??o gen?tica populacional de L. analis ( cioba) e L. jocu ( dent?o) ao logo do litoral brasileiro, analisando a regi?o hipervari?vel 1 da regi?o controle D-loop do DNAmt. Ambas as esp?cies demonstram constituir um ?nico grande estoque que permite compreend?-los como popula??es panm?ticas. De fato, a elevada variabilidade gen?tica demonstrada pelos altos ?ndices de diversidade nucleot?dica e haplot?pica, n?o revelam sinais de deprecia??o gen?tica frente a explora??o pesqueira. Os padr?es demogr?ficos hist?ricos destas esp?cies demonstram concord?ncia com eventos ocorridos no Pleistoceno. Os dados gen?ticos n?o excluem riscos futuros para ambas as esp?cies decorrentes da cont?nua explora??o destes estoques

This study examined the effects of the January 2010 cold spell on mangrove utilizing coral reef fishes off the southeast coast of Florida, USA, in the vicinity of Biscayne National Park (BNP). An ongoing, fishery-independent mangrove visual survey documenting fish assemblages in BNP provided data from the years 1998 to 2014 for examination. Of particular interest were the presence, abundance, and size structure for five mangrove utilizing coral reef fishes: sergeant major (Abudefduf saxatilis), yellowfin mojarra (Gerres cinereus), schoolmaster snapper (Lutjanus apodus), gray snapper (Lutjanus griseus), and great barracuda (Sphyraena barracuda). These species were selected for analysis due to their economic and ecologic importance, their potential as environmental indicators, their connectedness to multiple habitats, and their abundance within the available data set. Data were collected using a modified visual ‘belt transect’ method, consisting of 60 m2 transects running parallel to the mangrove shorelines. Data for average length of fish were reconstructed to form standard normal distributions and the resulting lengths were assigned to various age-classes to create species-specific length-frequency distributions. Variations in presence and abundance were examined across three time periods (1998-2009; 2010-2011; 2012-2014), as well as comparisons of length-frequency distributions. Following the January 2010 cold spell, the presence and abundance values for the two years immediately following the event were significantly decreased compared to the years prior to the cold spell for most of the five species at either mainland (ML) or leeward key (LK) locations. Additionally, the presence and abundance estimates typically remained statistically decreased when compared against the remaining years in the available data set. The size structures for the majority of the five species at either location, however, were not consistently significantly different between the three time periods, as was hypothesized. Instead, the analyses showed mixed results, with the size structure typically shifting towards smaller individuals immediately following the event. These findings suggest that drops in water temperature resulting from cold spells are capable of directly impacting mangrove utilizing reef fish species, albeit to varying degrees depending on various factors, such as physiological tolerances, ecological life history strategies, and habitat requirements.

This thesis presents a preliminary study on geochemical conditions within the Snapper Creek well field in Miami-Dade County, Florida. The study investigates the background groundwater chemistry within the Biscayne aquifer in order to provide information on the geochemical processes and water-rock interactions within the study site. In conjunction with hydraulic gradient information, major ion chemistry and deuterium and oxygen-18 data were used as environmental tracers to help describe the groundwater-surface water interactions between the well field and the Snapper Creek canal. Hydrologic data show there is potential for natural groundwater recharge from the canal within the shallow flow zone of the Biscayne aquifer and chemical data show evidence of canal-groundwater mixing within this zone. The limitations for the v environmental tracers employed within the study are addressed, as well as recommendations for further research involving natural geochemical tracers and groundwater-surface water interactions near municipal well fields. This study was part of a larger effort being conducted by the U.S. Geological Survey in order to assess municipal well field pumping effects on the Snapper Creek (C-2) canal. / by Dominick J. Antolino. / Thesis (M.S.)--Florida Atlantic University, 2011. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2011. Mode of access: World Wide Web.

Seafood substitution is a worldwide problem due to factors such as limited monitoring coupled with complex supply chains. Red snapper (Lutjanus campechanus) is a highly valued and overfished species that is commonly substituted with other fish, such as tilapia, rockfish, and other snapper species. DNA barcoding is typically used by regulatory agencies to detect seafood substitution; however, it is expensive and time-consuming. A rapid, real-time PCR assay targeting red snapper was developed previously for use in fisheries management; however, it has not been tested for its ability to detect red snapper species substitution. The objective of this study was to assess the ability of the real-time PCR assay to identify red snapper fillets and differentiate red snapper from common substitute fish species in combination with DNA barcoding. A total of 21 fresh/frozen fillets labeled as “red snapper” were tested with real-time PCR, along with 57 fresh/frozen fillets representing 15 of the most common categories of fish mislabeled as red snapper. All samples were tested with DNA barcoding to confirm the identity of fish species. Real-time PCR parameters were optimized to reduce background signals associated with cross-reactivity. Overall, real-time PCR identified 4 samples as red snapper: 3 were authenticated as red snapper with DNA barcoding and 1 was identified as mahi-mahi. Overall, 40% of all samples and 91% of “red snapper” samples were considered mislabeled according to DNA barcoding. Red snapper was substituted with other snapper species (e.g., Lutjanus malabaricus, Lutjanus peru, Ocyurus chrysurus, and Rhomboplites aurorubens), rockfish (Sebastes flavidus and Sebastes brevispinis), sea bream (Pagrus major/Pagrus auratus), and mahi-mahi (Coryphaena hippurus). The real-time PCR assay tested in this study can serve as a rapid screening test for the detection of mislabeled species, which can then be confirmed with sequencing techniques. This species identification technique has the potential to be used by regulatory agencies to rapidly determine the authenticity of red snapper on-site.

Cytokines are pleiotropic and redundant signaling molecules that govern the inflammatory response and immunity, a critical ecological parameter for organism success and population growth. Produced at the site of injury or pathogen intrusion by a variety of cell types, cytokines mediate cell-signaling in either an autocrine or paracrine manner. The type and magnitude of the cytokine milieu produced subsequently dictates the strength and form of immune response. As the most diverse vertebrate group, with a high sensitivity to contaminants, fish represent an important foci for the evaluation of immune system evolution, function, and alteration upon toxicant exposure. While many cytokines have been identified in teleosts, primary study has been limited to model species (e.g. zebrafish and fugu). However, evidence exists for several variations of cytokine genes within taxa, underscoring the need for species-specific evaluation. In this study, two pro-inflammatory cytokines (IL-1β and TNFα ), one chemokine (IL-8), and one anti-inflammatory cytokine (IL-10) were cloned, sequenced, and characterized for the first time in two commercially relevant Perciformes in the Gulf of Mexico, golden tilefish (Lopholatilus chamaeleonticeps) and red snapper (Lutjanus campechanus). The complete amino acid sequence was obtained and confirmed for IL-β and IL-8 from golden tilefish and for IL-8, IL-10, and TNFα from red snapper, with partial sequences obtained for the remaining proteins. The results indicate high homology among Perciformes for all cytokines studied, but divergence with other teleost orders, and low conservation when compared to birds, amphibians, and mammals. The sequences will be used to create a multi-plexed antibody-based assay for the routine detection of cytokines in teleost serum. This would allow the biochemical response to fish health challenges, such as oil spills and other contamination events, to be monitored at the protein level, building upon the current regime of genetic biomarkers. Thus, this work will aid in the understanding of how oil spills and other contamination events may alter the immune response in fishes.

Movement patterns and space use by mature fishes are critical in determining the effectiveness of marine reserves in conserving spawning stock biomass and/or providing biomass to adjacent fisheries through 'spillover'. Home range sizes, activity patterns, site fidelity and habitat preferences were determined for acoustically-tagged snappers and groupers using a rigorously-calibrated array of omnidirectional hydroacoustic receivers deployed in the diverse coral reef environments of a no-take marine reserve (NTMR) network in the Dry Tortugas, Florida. An individual-based localizing tendency model of reef fish movement was parameterized from fine-scale acoustic telemetry data and integrated into a Spatial Management Performance Assessment (SMPA) simulation model for reef fish populations developed to quantitatively evaluate performance of no-take marine reserves in the Dry Tortugas, Florida. Spatially-explicit SMPA models were parameterized for three overfished stocks in the lucrative snapper-grouper fishery: red grouper (Epinephelus morio), black grouper (Mycteroperca bonaci), and mutton snapper (Lutjanus analis). SMPA models were used to evaluate the impacts of a variety of life histories, movement strategies and speeds, and management regulations upon long-term stock sustainability, as measured by annual changes in spawning potential ratio (SPR), and long-term stock productivity, as measured by annual changes in fisheries yield-in-weight per recruit (Yw/R). Under assumptions of constant regional fishing pressure, constant recruitment, and 'realistic' fish movement, SMPA simulation runs from initial conditions in 2000 suggested that by 2014, the Tortugas NTMR network should function to restore red grouper populations to 30% SPR, a Federal management benchmark for sustainability. Mutton snapper were the most mobile of the species investigated; if mutton snapper movements are ignored, their population is predicted to attain 30% SPR by 2014, but given 'realistic' mobility, they may not attain this target by 2021 without additional protections. Black grouper are currently fished at over 9 times sustainable levels. SMPA simulations suggest coupling an increase in minimum size at capture of 20 - 25 cm with NTMR implementation would result in substantial short term losses in yield, but would restore both black grouper and mutton snapper populations to 30% SPR by 2021 and lead to increased long-term yields. Although marine reserve sites are often chosen opportunistically, these findings strongly suggest that reserve designs (e.g. proper sizes and configurations) must take into account the scales and patterns of movement exhibited by the exploited stocks they are intended to protect. These modeling efforts also suggested reserves are not a panacea; in order to promote sustainability for severely depleted stocks, they must be accompanied by an overall reduction in fishing capacity. Although important questions remain concerning the movements of reef fish in response to habitat and density dependent processes, our analyses of realistic reef fish behaviors suggest that the NTMRs of the Dry Tortugas promote substantial gains in SPR, promoting long-term stock sustainability and enhanced egg production. Increased rates of movement diminish these benefits, but may also mitigate short-term losses in yield associated with NTMR establishment.

Overfishing of stock and decreasing biodiversity are grave concerns for the U.S. and the rest of the world. Understanding and applying spatial and temporal information of marine species’ reproductive ecology and critical life habitat is vital to the development of effective strategies for marine resource management. In the Caribbean, one of the critical science gaps hindering effective management is the lack of information on how environmental factors may make fish spawning aggregation (FSA) sites optimal for spawning. Understanding the patterns of seafloor characteristics of spawning aggregation sites is of great interest to managers who need a means to efficiently design marine protected areas to help rebuild regional fish stocks. The specific goals of the study were: (1) to map the seafloor at historically known grouper and snapper spawning aggregation sites in three different countries, and (2) to characterize quantitatively the geomorphology of the sites including horizontal and vertical curvature profiles of the reefs, bottom depth at spawning sites, distance between spawning sites and shelf-edges/reef promontory tips, and the shortest distance between the spawning sites and 100 m water depth. These data were field-collected with a GPS and single-beam eco-sounder that provided latitude/longitude and depth. The point data were interpolated to surfaces in GIS to determine slope, aspect, curvature, and distance from spawning sites and three-dimensional reef structures. This study revealed that all 12 known Nassau grouper spawning aggregation sites in Belize and 5 known sites in the Cayman Islands were located at convex-shaped seaward extending reefs (reef promontories) jutting into deep water, within 1 km of reef promontory tips. However, spawning aggregations did not always occur at the tips of reef promontories, though all were found along the shelf edges within 1 km of promontory tips. Sixteen sites were multi-species spawning sites. These general characteristics were used to predict an undiscovered multi-species spawning aggregation in Belize. A successful prediction in Belize, together with the compiled data from multiple sites indicate: 1) reef promontories are vital locations for transient reef fish spawning aggregations, and 2) this study provides a potential tool for prediction of unknown spawning sites in the Caribbean.