Recent shifts towards ecosystem based fisheries management (EBFM) around the world have necessitated consideration of effects of fishing on a larger range of species than previously. Non-selective multispecies fisheries are particularly problematic for EBFM, as they can contribute to erosion of ecosystem structure. The trade-off between catch of productive commercial species and abundance of low-productivity species is unavoidable in most multispecies fisheries. A first step in evaluation of this trade-off is estimation of productivity of different species but this is often hampered by poor data. This thesis develops techniques for estimating productivity for data-limited species and aims to help clarify EBFM policy objectives for the fisheries of New South Wales (NSW), Australia. It begins with development of an age-structured model parameterised in terms of optimal harvest rate, UMSY. UMSY is a measure of productivity, comparable among species and easily communicated to managers. It also represents a valid threshold for prevention of overfishing. The model is used to derive UMSY for 54 Atlantic fish stocks for which recruitment parameters had previously been estimated. In most cases, UMSY was strongly limited by the age at which fish were first caught. However, for some species, UMSY was more strongly constrained by life history attributes. The model was then applied to twelve species of Australian deepwater dogshark (Order Squaliformes), known to have been severely depleted by fishing. Results showed that the range of possible values of UMSY for these species is very low indeed. These findings enabled a preliminary stock assessment for three dogsharks (Centrophorus spp.) currently being considered for threatened species listing. Preliminary results suggest they have been overfished and that overfishing continues. Finally, an Ecopath with Ecosim ecosystem model, representing the 1976 NSW continental slope, is used to illustrate trade-offs in implementation of fishing policies under alternative policy objectives. Results are compared with those of a biogeochemical ecosystem model (Atlantis) of the same system, built by scientists from CSIRO. While there were large differences in model predictions for individual species, they gave similar results when ranking alternative fishing policies, suggesting that ecosystem models may be useful for exploring broad-scale strategic management options.

The heterogeneous landscape of Florida Bay provides habitats for a variety of predators and prey. This dissertation examined the bottom-up transfer of affects from environmental variability through prey composition up to competition and predation affects on top predator distribution and foraging ecology in Florida Bay. Line transect surveys for bottlenose dolphins and seabirds were conducted in Florida Bay during the summer months of 2002 - 2005. Photo-identification techniques were implemented to identify individual dolphins. Synoptic with this survey effort, habitat characteristics (temperature, salinity, dissolved oxygen, turbidity, chlorophyll a, depth and bottom type) and prey composition (bottom trawl or gillnet) were sampled. Comparison of envelope maps from generalized additive models determined that predictive capacity of dolphin habitat did not improve by incorporating fish distribution data. However, models of dolphin distribution based solely on environmental proxies of fish distribution resulted in high predictive capacity. During the 2005 summer, shark distribution was sampled using a longline. The abundance of sharks was only correlated to fish catch from trawls on a regional scale. Larger sharks, of species that may threaten dolphins, were only caught in the Gulf zone of the Bay. Analysis of dolphin distribution revealed high individual site and foraging tactic fidelity. Dolphins were spatially coincident with habitat characteristics that encouraged the use of each individual's preferred foraging tactic. Depth was identified as the primary variable determining dolphin foraging tactic choice. Depth plays a significant role in the benthic composition of Florida Bay, which subsequently impacts prey communities and affects dolphin distribution, foraging and social ecology. Ordinations determined that fish distribution was also principally affected by depth and bottom type. Shallow environments frequently corresponded with mudbank habitat (depth < 1m) where the sighting rates of seabirds (cormorants, osprey, pelicans, terns) and foraging dolphins peaked. In conclusion, subtle relief in South Florida's bedrock topography dramatically affect benthic composition within Florida Bay, providing patchy habitats for prey and predators. The Florida Bay ecosystem will change with expected sea level rise, including spatial shifts of mudbank habitats. Top predator populations in Florida Bay will be forced to modify their distribution and foraging ecology accordingly. / Dissertation

Studies of widely diverse species of a protein are a powerful tool to gain information on the structure and function of the protein. We investigated the response of human, pig, shark and killifish cystic fibrosis trans-membrane conductance regulator (CFTR) to specific inhibitors of the channel: CFTRinh-172, GlyH-101, and glibenclamide. In several expression systems, including isolated perfusions of the rectal gland, primary cell cultures of rectal gland tubules and oocyte expression, we observed fundamental differences in the sensitivity to inhibition by these CFTR blockers. We used primarily two-electrode voltage clamping of cRNA microinjected Xenopus laevis oocytes. In oocyte studies, shark CFTR was insensitive to CFTRinh-172 (maximum inhibition 8 ± 1.4% at 20µM), pCFTR was insensitive to Glibenclamide (maximum inhibition 12.8 ± 4.2% at 200µM), and all species were sensitive to GlyH-101 (maximum inhibition with pCFTR of 80.2 ± 3.6% at 20µM). Shark CFTR was completely insensitive to inhibition by CFTRinh-172 in short circuit current experiments (2.5 ± 0.15 % inhibition of chloride secretion) compared to inhibition with GlyH-101 (56.5 ± 6.56 % inhibition of chloride secretion). Perfusion studies confirmed these results. These experiments demonstrate a profound difference in the sensitivity of different CFTR species to inhibition by CFTR blockers. However, the amino acid residues that have been proposed by site directed mutagenesis studies to be responsible for inhibitor binding are uniformly conserved in all four isoforms studied. Therefore, the differences cannot be explained by simply targeting one amino acid for site-directed mutagenesis. Rather, the potency of the inhibitory actions of CFTRinh-172, Gly-H101 and glibenclamide on the CFTR molecule is dictated by the local environment and the three dimensional structure of residues that form the vestibule and the chloride pore.

Recent shifts towards ecosystem based fisheries management (EBFM) around the world have necessitated consideration of effects of fishing on a larger range of species than previously. Non-selective multispecies fisheries are particularly problematic for EBFM, as they can contribute to erosion of ecosystem structure. The trade-off between catch of productive commercial species and abundance of low-productivity species is unavoidable in most multispecies fisheries. A first step in evaluation of this trade-off is estimation of productivity of different species but this is often hampered by poor data. This thesis develops techniques for estimating productivity for data-limited species and aims to help clarify EBFM policy objectives for the fisheries of New South Wales (NSW), Australia. It begins with development of an age-structured model parameterised in terms of optimal harvest rate, UMSY. UMSY is a measure of productivity, comparable among species and easily communicated to managers. It also represents a valid threshold for prevention of overfishing. The model is used to derive UMSY for 54 Atlantic fish stocks for which recruitment parameters had previously been estimated. In most cases, UMSY was strongly limited by the age at which fish were first caught. However, for some species, UMSY was more strongly constrained by life history attributes. The model was then applied to twelve species of Australian deepwater dogshark (Order Squaliformes), known to have been severely depleted by fishing. Results showed that the range of possible values of UMSY for these species is very low indeed. These findings enabled a preliminary stock assessment for three dogsharks (Centrophorus spp.) currently being considered for threatened species listing. Preliminary results suggest they have been overfished and that overfishing continues. Finally, an Ecopath with Ecosim ecosystem model, representing the 1976 NSW continental slope, is used to illustrate trade-offs in implementation of fishing policies under alternative policy objectives. Results are compared with those of a biogeochemical ecosystem model (Atlantis) of the same system, built by scientists from CSIRO. While there were large differences in model predictions for individual species, they gave similar results when ranking alternative fishing policies, suggesting that ecosystem models may be useful for exploring broad-scale strategic management options.

Variations in predator diets is important in ecology to help us understand their top-down effects on the ecosystem. In predator diets, their fatty acid signatures reflect the proportions of prey consumed. Since fatty acid signatures are compositional and often longer than the sample size, a standard MANOVA test is unsuitable. Here, non-parametric MANOVA techniques are developed to test for differences in fatty acid signatures among locations, years, and seasons which infer differences in diets. Simulations show that the test has good power and appropriate type I error rates. The tests developed were applied to data on Greenland Sharks to test for differences in diets between individuals from Cumberland Sound, Canada, versus those from Svalbard, Norway and whether there is a yearly and/or seasonal effect on the diets. Diet compositions were found to vary between the locations, seasons and years, possibly caused by differing prey species distributions, migrations, and climate change.

Thesis (Ph. D.)--Simon Fraser University, 2001. / Includes bibliographical references.

Thesis (M.S.)--Florida State University, 2006. / Advisor: Timothy S. Moerland, Florida State University, College of Arts and Sciences, Dept. of Biological Science. Title and description from dissertation home page (viewed Sept. 15, 2006). Document formatted into pages; contains x, 33 pages. Includes bibliographical references.

Orientador: Fausto Foresti / Resumo: Populações de elasmobrânquios têm sofrido declínios severos nas últimas décadas devido à massiva pressão pesqueira. Com características de vida que tornam a espécie mais suscetível à pesca, o tubarão-raposa Alopias superciliosus está classificado atualmente como vulnerável na lista vermelha de espécies ameaçadas da IUCN. A espécie apresenta maturação sexual tardia e somente dois (raramente quatro) filhotes a cada gestação, que dura aproximadamente 12 meses. Estas características evidenciam a necessidade de sistemas de manejo pesqueiro adequados à estruturação populacional da espécie, que se apresenta como um instrumento fundamental para sua conservação. Com o advento de novas tecnologias atualmente é viável utilizar ferramentas moleculares para elucidar questões evolutivas e genético-populacionais em organismos não modelos, gerando informações que podem auxiliar na elaboração de planos de manejo. Tendo em vista à escassez de informações sobre a dinâmica populacional do tubarão-raposa, o presente estudo teve como objetivo o desenvolvimento e aplicação de marcadores moleculares em amostras de A. superciliosus provenientes de diferentes localidades dos oceanos Atlântico e Índico. Um total de 12 marcadores moleculares do tipo microssatélite, sendo 11 polimórficos e 1 monomórfico, foram identificados e, a partir desta identificação, primers espécie-específicos foram desenvolvidos e padronizados. Para acessar a diversidade genética e populacional de A. superciliosus foram genotipad... (Resumo completo, clicar acesso eletrônico abaixo) / Doutor

Orientador: Fausto Foresti / Banca: Fernando Fernandes Mendonça / Banca: Diogo Teruo Hashimoto / Resumo: A pesca predatória vem ocasionando um enorme declínio de estoques e populações de inúmeras espécies marinhas. Tendo em vista a vulnerabilidade à exploração pesqueira da maioria das espécies de tubarões, associada às dificuldades de identificação morfológica devido às similaridades entre diversas espécies, agravada ainda, pela prática da pesca com a retirada de partes dos animais ainda antes dos desembarques, a geração de mecanismos alternativos de identificação de espécies são extremamente valiosos para oferecer uma ferramenta de controle e fiscalização da indústria pesqueira. No presente estudo foram desenvolvidos métodos de identificação simultânea, utilizando PCR - Multiplex para a identificação de espécies de tubarões com um importante valor econômico, sendo que as espécies analisadas foram divididas em seis grupos para serem aplicadas as técnicas de identificação. Com base na composição nucleotídica do gene mitocondrial ribossomal 16S de quatorze espécies de tubarões do Brasil, foram identificados os sítios polimórficos e desenhados primers espécie-especificos, para a utilização na identificação de espécies de tubarões espécimes desembarcados pela indústria pesqueira. A aplicação da metodologia resultou na caracterização de primers específicos que permitem a identificação particular de cada uma das espécies de tubarões Alopias superciliosus, Alopias vulpinus, Carcharhinus falciformes, Carcharhinus leucas, Carcharhinus longimanus, Carcharhinus plumbeus, Carcharhinus porosus, Carcharhinusn signatus, Galeocerdo cuvier, Isurus oxyhinchus, Isurus paucus, Prionace glauca, Rhizoprionodon lalandii e Rhizoprionodon porosus. Considera-se que a correta identificação do material desembarcado, que representaria o resultado da pesca das espécies de ocorrência na região, possa permitir o estabelecimento de estatísticas confiáveis nesta área, bem como ... / Abstract: The overfishing has caused a huge decline in stocks and populations of many marine species. Given the vulnerability to overfishing of most shark species, associated with difficulties in morphological identification due to similarities between different species, aggravated by the practice of fishing with the removal of parts of animals even before the landings, the generation of alternative mechanisms for species identification are extremely valuable to offer a tool to control and monitor the fishing industry. In this study we developed methods of simultaneous identification using PCR - Multiplex for identifying shark species with an important economic value, and the species were divided into six groups for application of identification techniques. Based on the nucleotide composition of the mitochondrial 16S ribosomal gene of fourteen species of Brazilian sharks, was identified polymorphic sites and species-specific primers designed for use in identification of species of sharks landed by the fishing industry. The application of the methodology resulted in the characterization of specific primers that allow the unique identification of each shark species Alopias superciliosus, Alopias vulpinus, Carcharhinus sickle, Carcharhinus leucas, Carcharhinus longimanus, Carcharhinus plumbeus, Carcharhinus porosus, signatus Carcharhinus, Galeocerdo cuvier, Isurus oxyhinchus, Isurus paucus, Prionace glauca, and Rhizoprionodon lalandii Rhizoprionodon porosus. It is considered that the correct identification of the material landed, which represent the result of fishing of the species occurring in the region, may permit the establishment of reliable statistics in this area, and make allowances for effective control and strict fishing, assisting in the preparation of proper plans and management of the fishery resources / Mestre

Existem muitos estudos sobre a ocorrência de poluentes orgânicos persistentes (POPs) no ambiente marinho utilizando bioindicadores como os tubarões. Entretanto, no Brasil, ainda há carência de dados de POPs nesses organismos. O objetivo desta pesquisa foi investigar a ocorrência e o comportamento dos PCBs, pesticidas organoclorados e PBDEs no ambiente marinho, a partir da utilização dos tubarões como indicadores. Musculatura e fígado de vinte tubarões-azul (Prionace glauca) foram coletados em agostosetembro de 2008. Os PCBs foram os poluentes predominantes, presentes em 80% das amostras, com concentrações variando de <n.d. a 427,28 ng.g-1 de peso úmido. Os diclorodifeniletanos apresentaram concentrações variando de 0,43 a 202,42 ng.g-1 de peso úmido, no qual o 4,4´-DDE foi o composto mais significativo, com 77,6% de contribuição para os DDTs totais. As concentrações no fígado foram 1-2 ordens de grandeza mais elevadas, em relação às de musculatura. Houve um padrão de distribuição dos poluentes com níveis equivalentes entre indivíduos imaturos. Os machos maduros apresentaram concentrações de POPs sensivelmente maiores que as fêmeas maduras, indicando a transferência dos POPs para os filhotes. Os resultados demonstraram a ampla distribuição desses poluentes no ambiente marinho. / There are many studies about the occurrence of persistent organic pollutants (POPs) in the marine environment using sharks as bioindicators. However, there is still a lack of data of POPs in those organisms in Brazil. The goal of this research was to investigate the occurrence and behavior of PCBs, organochlorine pesticides and PBDEs in the marine environment, using sharks as indicators. Muscle and liver of twenty blue-sharks (Prionace glauca) were collected in august-september 2008. The PCBs were the predominant pollutants and being present in 80% of samples, with concentrations ranging from <n.d. to 427.28 ng.g-1 wet weight. The dichlorodiphenylethanes present concentrations ranging from 0.43 to 202.42 ng.g-1 wet weight, where the 4,4´-DDE was the most significative compound, with contributions of 77,6% of the total DDTs. The concentrations in the liver were 1-2 orders of magnitude higher than in the muscle. There was a distribution pattern of the pollutants, with equivalent levels among the immature specimens. The concentration of POP was significantly higher in the mature males and relatively lower in the mature female, showing the maternal transference of POPs to the pups. The results have demonstrated a wide distribution of these pollutants in the marine environment.