Recent evidence suggests that overfishing of large predatory fishes has resulted in substantial population declines and pelagic longline (PLL) fishing is a major contributor. The primary objective of this dissertation is understanding factors that affect the interactions between marine fish PLL fishing. These factors are important to determine vulnerability of bycatch and target species, especially when PLL catch and effort data are used to estimate stock abundance. Chapter 1 reviews 107 publications/reports on this topic. Results indicate that accurate characterization of PLL gear performance requires empirical measurement of horizontal and vertical gear movement; and pop-up satellite tags (PSATs) are best suited for quantifying pelagic fish vertical habitat use if: (i) sampling resolution and data storage are not a function of tracking duration and (ii) substantial monitoring durations are employed. This review documents the current state of knowledge for these factors and guidance for future research. In Chapter 2, hook time-at-depth was monitored for commercial PLL sets targeting swordfish, Xiphias gladius. Temperature-depth recorders (TDRs) were deployed at the hook, systematically along the entire gear length. Results indicated that: (i) hook depth predictions based on catenary geometry drastically overestimated actual fishing depths and (ii) using catenary geometry fails to capture within- and among-set variability, potentially resulting in biased stock assessments. Chapter 3 used temperature-depth data from PSATs on swordfish and blue marlin (Makaira nigricans) and similar data from TDR monitored near-surface and deep PLL fishing to determine the diel probability of these species encountering PLL hooks. Results indicated that blue marlin and swordfish inhabit surface waters at night with similar probability of encountering PLL hooks but may have different vulnerabilities due to temporal separation in feeding with blue marlin preferring daytime and twilight and swordfish preferring nighttime. Therefore, reducing fishing during daylight hours may reduce blue marlin bycatch during PLL targeting swordfish. Chapter 4 alternated non-offset and 10° offset circle hooks during PLL fishing and compared the relative performance on catch rates, percent mortality, and deep hooking percentage. Results indicated that 10° offset circle hooks can reduce fishing efficiency and conservation benefits commonly associated with circle hooks.

My study investigated the evolution of oxidative metabolism in fishes. While intense selection for, or against, non-synonymous point mutations in coding sequence drives the evolution of mitochondrial OXPHOS genes, genome-specific mechanisms such as gene duplication events can play major roles in the evolution of nuclear OXPHOS genes. My thesis focused on the mitochondrial enzyme cytochrome c oxidase (COX), principally in fish because of their evolutionary origins and functional diversity in terms of energy metabolism. In the first part of my thesis, I examined a highly aerobic group of fishes (billfishes and tunas) to study the evolution of mitochondrial COX genes. Though the study began as a structure-function analysis of COX, my approach changed when my preliminary results called into question the accepted phylogenetic relationships of my species of interest. We generated a robust multigene phylogeny of this group to interpret data in a phylogenetically informative context. Phylogenetic analyses in this group provided us with a framework to study the evolution of mitochondrial OXPHOS genes, but unexpectedly revealed that: 1) billfishes are only distantly related to tunas, and share greater evolutionary affinities with flatfishes (Pleuronectiformes) and jacks (Carangidae), and 2) regional endothermy has evolved in a non-scombroid suborder in teleosts. These results collectively imply that regional endothermy has evolved independently at least twice within teleost fish. The second part of my thesis explored the evolution of the nuclear COX subunits, focusing on their origins in fish. Isoform transcription profiles coupled with phylogenetic analyses for each subunit show that vertebrate isoforms arose from a combination of early whole-genome duplications in basal vertebrates or specific lineages (e.g. teleosts), and more recent single gene duplication events. While there is evidence for retained function of some COX orthologues across fishes and mammals, others appear to have diverged in function since their earlier radiation, possibly contributing novel evolutionary functions. Together these two studies provide insight into the evolutionary forces facilitating adaptive change in mitochondrial and nuclear OXPHOS genes. / Thesis (Master, Biology) -- Queen's University, 2009-09-11 11:00:12.562

Orientador: Fabio Porto-Foresti / Resumo: The billfish are oceanic pelagic species often caught by the tuna fleet and with great interest of sport fishing. This group of fish has specific legislation prohibiting the marketing and export of two species, Kajuikia albida e Makaira nigricans, in Brazil. DNA barcode is a universal system of molecular identification based on a sequence of mitochondrial DNA cytochrome oxidase subunit I (COI) of about 650 base pairs, serving as an identifying genomic mark in each species. This system has been used successfully to identify mischaracterized samples illegally marketed, like sample materials from sharks and other endangered species of organisms. The Barcode DNA technique was used to identify billfish marketed in the second largest fishing warehouse in Latin America, the CEAGESP-SP and the international airport of São Paulo, Brazil. 302 samples of billfish were collected during three inspection actions carried out by IBAMA, the executing agency of the national environmental policy. After DNA sequencing procedures it was possible to identify 72 samples (91.14%) by CEAGESP at the level of species, being 21 (29.17%) identified as Xiphias gladius, 44 (61.1%) as Istiophorus platypterus and 7 (8.33%) as Kajikia albida, this latter species determined as a market prohibited in Brazil and considered vulnerable in the list of endangered species of the IUCN and in the official list of species of endangered Fauna - Fish and Aquatic Invertebrates. At the International Airport of Guarulhos it ... (Resumo completo, clicar acesso eletrônico abaixo) / Mestre

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Agradecemos a compreensão. on 2017-09-28T14:11:18Z (GMT) / Submitted by CARLOS EGBERTO RODRIGUES JÚNIOR null (egberto_ibama@hotmail.com) on 2017-11-01T11:03:15Z No. of bitstreams: 1 Dissertação Carlos Egberto Rodrigues Junior repositorio.pdf: 4606348 bytes, checksum: c20c3df76e489701ead450f3ca92dcad (MD5) / Approved for entry into archive by LUIZA DE MENEZES ROMANETTO (luizamenezes@reitoria.unesp.br) on 2017-11-13T15:03:34Z (GMT) No. of bitstreams: 1 rodriguesjunior_cer_me_bot.pdf: 4606348 bytes, checksum: c20c3df76e489701ead450f3ca92dcad (MD5) / Made available in DSpace on 2017-11-13T15:03:34Z (GMT). No. of bitstreams: 1 rodriguesjunior_cer_me_bot.pdf: 4606348 bytes, checksum: c20c3df76e489701ead450f3ca92dcad (MD5) Previous issue date: 2016-12-15 / The billfish are oceanic pelagic species often caught by the tuna fleet and with great interest of sport fishing. This group of fish has specific legislation prohibiting the marketing and export of two species, Kajuikia albida e Makaira nigricans, in Brazil. DNA barcode is a universal system of molecular identification based on a sequence of mitochondrial DNA cytochrome oxidase subunit I (COI) of about 650 base pairs, serving as an identifying genomic mark in each species. This system has been used successfully to identify mischaracterized samples illegally marketed, like sample materials from sharks and other endangered species of organisms. The Barcode DNA technique was used to identify billfish marketed in the second largest fishing warehouse in Latin America, the CEAGESP-SP and the international airport of São Paulo, Brazil. 302 samples of billfish were collected during three inspection actions carried out by IBAMA, the executing agency of the national environmental policy. After DNA sequencing procedures it was possible to identify 72 samples (91.14%) by CEAGESP at the level of species, being 21 (29.17%) identified as Xiphias gladius, 44 (61.1%) as Istiophorus platypterus and 7 (8.33%) as Kajikia albida, this latter species determined as a market prohibited in Brazil and considered vulnerable in the list of endangered species of the IUCN and in the official list of species of endangered Fauna - Fish and Aquatic Invertebrates. At the International Airport of Guarulhos it was possible to identify 223 samples (100%), all identified as Xiphias gladius as declared by the exporter and indicated by its NCM (Mercosur Common Nomenclature). Molecular analysis has proven to be an excellent tool to identify billfish in Brazil in different centers such as Guarulhos International Airport and CEAGESP, SP. The identification of the white marlin being illegally traded in CEAGESP demonstrates the ineffectiveness of the current monitoring techniques used and emphasize the need for adopting better public policies for the conservation of the species. / Os peixes de bico são espécies pelágicas oceânicas frequentemente capturadas pela frota atuneira e com grande interesse da pesca esportiva. Este grupo de peixes possui legislação específica que proíbe a comercialização e exportação de duas espécies, Kajikia albida e Makaira nigricans desse grupo no Brasil. O DNA Barcode é um sistema universal de identificação molecular baseado em uma sequência de DNA mitocondrial Citocromo Oxidase subunidade I (COI) de aproximadamente 650 pares de base, servindo como código de barras de DNA de cada espécie. Este sistema tem sido utilizado com êxito para identificar amostras que são comercializadas descaracterizadas e de forma ilegal, como tubarões e outras espécies ameaçadas de extinção. A técnica de DNA Barcode foi utilizada para a identificação de peixes de bico comercializados no segundo maior entreposto pesqueiro da América Latina, CEAGESP, SP e no Aeroporto Internacional de Guarulhos, atualmente o maior volume brasileiro de exportações de peixes de bico no País. Foram coletadas 302 amostras de peixes de bico durante vistorias realizadas pelo IBAMA, 223 no aeroporto e 79 no CEAGESP, órgão executor da política nacional do meio ambiente. Após sequenciamento do DNA foi possível à identificação das espécies de 70 amostras (88,60%) coletadas no CEAGESP, sendo 21 (30%) identificadas como Xiphias gladius, 43 (61,42%) como Istiophorus platypterus e seis (8,57%) como Kajikia albida, esta última de comércio proibido no Brasil, e considerada vulnerável pela lista de espécies em perigo da IUCN e pela Lista Nacional Oficial de Espécies da Fauna Ameaçadas de Extinção - Peixes e Invertebrados Aquáticos. No Aeroporto Internacional de Guarulhos foi possível à identificação de 223 amostras (100%), sendo todas identificadas como Xiphias gladius conforme declarado pelo exportador e indicado pelo seu NCM (Nomenclatura Comum do Mercosul). A análise molecular demonstrou ser uma importante ferramenta na identificação de peixes de bico comercializados no Brasil em diferentes centros como o Aeroporto Internacional de Guarulhos e CEAGESP, SP. A identificação de agulhões branco sendo ilegalmente comercializados na CEAGESP demonstra a ineficácia das técnicas de fiscalização utilizadas e enfatizam a necessidade melhores políticas públicas para a conservação da espécie.

Atlantic billfish include sailfish (Istiophorus platypterus), blue marlin (Makaira nigricans), white marlin (Kajikia albida, formerly Tetrapturus albidus) and the spearfishes (Tetrapturus); these fishes are found in tropical and subtropical waters. The spearfishes include the longbill spearfish (T. pfluegeri), the Mediterranean spearfish (T. belone) and the roundscale spearfish (T. georgii). The International Commission for the Conservation of Atlantic Tunas (ICCAT) is the regional fishery management organization that conducts research to determine the condition of tuna and billfish resources and supports international cooperative management. ICCAT has determined that blue marlin and white marlin are overfished; the status of sailfish and spearfish are unknown, but overfishing is thought to be occurring. Management of these resources is complicated by uncertainty in the biological models, but uncertainty about the fishers who target these resources. This dissertation studied artisanal fishing fleets that target Atlantic billfish in Venezuela and Ghana, as well as studied recreational charter boat fishing fleets in South Florida and Senegal. The information from these fleets was used to develop performance indicators that evaluate the socioeconomic performance of these fleets. An allocation model was developed to determine the optimal allocation of billfish resources among recreational and artisanal fishers in Ghana, West Africa. Finally, the issues and challenges of managing Atlantic billfish were identified as well as a possible future framework. Results indicate that performance indicators can be used to contrast fleets with different operational objectives. Fishers do produce positive fishing profits in both artisanal and recreational fleets; however, Senegalese recreational anglers are particularly sensitive to fuel costs. Results of the allocation model suggest that the artisanal sector should be allocated 95% of the quota in Ghana. There is the possibility to over-allocate quota to the recreational sector due to methodological differences in determining benefit f and the practice of catch-and-release. ICCAT's limited purview over socioeconomics was identified as the major impediment to effective billfish management. Therefore, it is recommended that the institutional structure for billfish management be modified to include socioeconomic issues, most especially strengthening the link to local institutions in fishing communities.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2017-02-16T13:34:08Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) OsmanCrespo_Dissertação_PPGO.pdf: 2113471 bytes, checksum: adc84d0652f9664545cb0bdac4dae2cf (MD5) / Made available in DSpace on 2017-02-16T13:34:08Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) OsmanCrespo_Dissertação_PPGO.pdf: 2113471 bytes, checksum: adc84d0652f9664545cb0bdac4dae2cf (MD5) Previous issue date: 2016-06-27 / CAPES / O agulhão negro (Makaira nigricans) é uma espécie dentre os grandes peixes pelágicos que compõe o topo da teia trófica marinha, sendo sua preservação importante para a manutenção da dinâmica populacional desses ecossistemas. Esta espécie é uma das mais procuradas pela pesca esportiva no mundo, sendo, porém, alvo de sobrepesca devido sua captura frequente como fauna acompanhante na pesca de espinhel pelágico no oceano Atlântico. O objetivo do presente trabalho de pesquisa foi compreender os movimentos migratórios, a influência de fatores ambientais em padrões de movimento e utilização de habitat pelos agulhões-negro no oceano Atlântico Sul e como essa espécie interage com o aparelho de pesca. Para o levantamento de dados sobre a utilização de habitat foram utilizadas marcas PSATs (pop-up satellite archival tags) para monitorar o comportamento do animal registrando um fluxo quase contínuo de parâmetros ambientais especificados (temperatura, pressão [profundidade] e luminosidade), onde os dados são arquivados e transmitem a informação via satélite após se desconectarem do animal. Além disso, foram também analisadas as profundidades de atuação dos anzóis do espinhel na pesca comercial de atuns e afins no Atlântico Sul, para melhor compreender quanto o esforço de pesca atualmente empregado se sobrepõe ao habitat utilizado pelos agulhões. O deslocamento horizontal durante o período de marcação variou de 374 a 1.838 km. Os resultados mostraram que os indivíduos maiores (>195 cm), considerados adultos, apresentaram deslocamentos direcionais segundo a estatística circular aplicada, enquanto que indivíduos juvenis ou menores (<195 cm) apresentaram deslocamentos considerados loopings ou sem direcionamento definido. Os dados de tempo em profundidade nos mostraram que a os indivíduos passam a maior porcentagem do tempo em águas superficiais acima dos 20m durante os períodos noturno e diurno. Os agulhões negros permaneceram a maioria do tempo dentro de uma curta faixa de temperatura, com uma média de 57% do tempo em temperaturas entre 26º e 28ºC. Os resultados quanto a sobreposição de habitat à espinhéis pelágicos nos mostrou uma relação de 59% da área rastreada sobreposta às armadilhas de pesca. A média de profundidade dos anzóis registrada foi de 49 m, sendo 90% da distribuição de profundidade dos anzóis entre 3271m. Essa distribuição vertical quando sobreposta ao padrão de utilização vertical do habitat pelos agulhões, revelou uma sobreposição que varia entre 11% e 35% durante o período diurno e 21% e 34% durante a noite. Os resultados obtidos na presente pesquisa são relevantes para uma melhor compreensão da biologia e ecologia dos agulhões negros no oceano Atlântico Sul, compondo um importante conhecimento sobre o comportamento da espécie e auxiliando para tomada de decisões e medidas de manejo e conservação da espécie a nível internacional. / Blue marlin (Makaira nigricans) is a species among great pelagic fishes that occupy the top of marine food web, being its conservation important to the maintenance of ecosystem population dynamics. Atlantic blue marlin is one of the favorite species targeted by recreational fishing in the Atlantic Ocean, however being overexploited because of its frequent capture as bycatch by commercial pelagic longline fishery. The main goal of this study was to understand migratory movement and the influence of environmental factors in movement patterns and habitat utilization by blue marlins in the South Atlantic Ocean and how this species interacts with pelagic longline gear. Pop up archival tags (PSATs) were used to collect habitat utilization data monitoring animal behavior through continuous records of specified environmental parameters (temperature, pressure [depth] and luminosity), transmitting such reports via satellite after pop-off. Furthermore, was also analyzed longline gears hook depths from commercial fisheries in South Atlantic to better understand how this fishing effort overlap to marlins habitat utilization. PSATs were programmed to record depth, temperature, and light intensity for a period of 180 days until release. The horizontal net displacement for all blue marlins ranged from 374 to 1.838 km. Results presented that larger individuals (>196 cm), considered adults, achieved directional movements according to circular statistics applied, while shorter individuals (<195 cm) presented displacement as looping or nondirectional. Time-at-depth histograms of blue marlin habitat utilization show that most individuals across all areas spent the majority of their time in shallow waters, above 20m, both during the day and night periods. Blue marlins spent most of their time within a relatively narrow temperature range, staying an average of 57% of their time in temperatures between 26° and 28°C. Overall, blue marlins had approximately 59% of their tracked range overlapped by the longline fishing gear. The average hook depth across all areas was 49 m with 90% percentile depth distribution of the hooks depth between 32-71 m. When this distribution was overlapped with the species vertical habitat utilization, the overlap ranged between 11 and 35% during daytime and 21 and 34% during nighttime. The results achieved in this study are relevant to better understand the biology and ecology of Atlantic blue marlins, composing an important knowledge about species behavior, which reduces current uncertainties about its biology and help to making decisions and take international conservation and management measures to the species.

Biological and life history characteristics for a previously unstudied population of sailfish, Istiophorus platypterus, in the Arabian Gulf were investigated. Notable findings include temporal-spatial migration patterns for a genetically isolated population that is threatened by overexploitation. Conventional tagging resulted in 2053 releases and 114 recaptures (5.55%) inside the Gulf. Linear displacement ranged from 2.5 to 697 km, while days at liberty ranged from 17 to 818 days. Dead recoveries in Iranian gillnets account for 88.6% of recaptures. Modeling analyses produced a best estimate of annual survival probability (S) at 0.375 (slope = -0.101, SE = 0.324). Fifteen pop-up satellite archival tags were deployed on sailfish during 2001 - 2002 to track temporal and spatial movements. Extensive data from four tags showed 83.7% of time-at-depth was spent above 10 m with no significant difference (P &lt 0.05) in diel preference. Depth ranged from 0.0 m to 61.0 m, while temperature ranged from 19.7 ??C to 30.1 ??C. Small-scale movements of eight sailfish were measured using ultrasonic tracking for periods ranging from 3:33 to 53:06 hours. Track distances ranged from 5.5 to 78.5 km, while linear displacement ranged from 4.6 to 37.0 km. Average speed ranged from 0.29 to 0.75 m s-1. Vertical distributions showed 84.3% of time was spent above 10 m depth, even though water temperature showed negligible variation with depth. Mitochondrial DNA comparison of 147 sailfish produced 39 composite haplotypes using eight restriction enzymes. Significant differences occurred in the frequency between population groups inside and outside the Gulf (amova 34.8%, P &lt 0.01; FST = 0.356), along with evidence of restricted migration between them (average number of migrants, Nm = 0.903). Nine year classes (0-8) were determined from aging analysis of fin spines. Females (n = 50) ranged from 0 to 8 years, while males (n = 34) ranged from 0 to 6 years. Von Bertalanffy growth function indicated rapid growth during the first two years, after which males stabilized and females continued growing to a greater maximum mean length and weight. A comparison of allometric growth between sexes indicated no significant difference between length and other morphometric characters (P ranged 0.135 ??? 0.980).

Biological and life history characteristics for a previously unstudied population of sailfish, Istiophorus platypterus, in the Arabian Gulf were investigated. Notable findings include temporal-spatial migration patterns for a genetically isolated population that is threatened by overexploitation. Conventional tagging resulted in 2053 releases and 114 recaptures (5.55%) inside the Gulf. Linear displacement ranged from 2.5 to 697 km, while days at liberty ranged from 17 to 818 days. Dead recoveries in Iranian gillnets account for 88.6% of recaptures. Modeling analyses produced a best estimate of annual survival probability (S) at 0.375 (slope = -0.101, SE = 0.324). Fifteen pop-up satellite archival tags were deployed on sailfish during 2001 - 2002 to track temporal and spatial movements. Extensive data from four tags showed 83.7% of time-at-depth was spent above 10 m with no significant difference (P &lt 0.05) in diel preference. Depth ranged from 0.0 m to 61.0 m, while temperature ranged from 19.7 ??C to 30.1 ??C. Small-scale movements of eight sailfish were measured using ultrasonic tracking for periods ranging from 3:33 to 53:06 hours. Track distances ranged from 5.5 to 78.5 km, while linear displacement ranged from 4.6 to 37.0 km. Average speed ranged from 0.29 to 0.75 m s-1. Vertical distributions showed 84.3% of time was spent above 10 m depth, even though water temperature showed negligible variation with depth. Mitochondrial DNA comparison of 147 sailfish produced 39 composite haplotypes using eight restriction enzymes. Significant differences occurred in the frequency between population groups inside and outside the Gulf (amova 34.8%, P &lt 0.01; FST = 0.356), along with evidence of restricted migration between them (average number of migrants, Nm = 0.903). Nine year classes (0-8) were determined from aging analysis of fin spines. Females (n = 50) ranged from 0 to 8 years, while males (n = 34) ranged from 0 to 6 years. Von Bertalanffy growth function indicated rapid growth during the first two years, after which males stabilized and females continued growing to a greater maximum mean length and weight. A comparison of allometric growth between sexes indicated no significant difference between length and other morphometric characters (P ranged 0.135 ??? 0.980).

Commercial pelagic longline fishers within the U.S. Atlantic, Gulf of Mexico, and Caribbean are required to report all fishing interactions per each gear deployment to NOAA’s Vessel Logbook Program of the Southeast Fisheries Science Center to quantify bycatch, increase conservation efforts, and avoid jeopardizing the existence of vulnerable species listed under the Endangered Species Act (ESA). To provide additional accuracy, the Pelagic Observer Program (POP) of the SEFSC deploys professionally trained observers on longline vessels to produce a statistically reliable subset of longline fisheries data. A comparison of self-reported (“unobserved”) datasets versus observer-collected (“observed”) datasets showed a general consistency for most target species but non-reporting or under-reporting for a number of bycatch species and “lesser-valued” target species. These discrepancies between catch compositions and abundancies regarding targeted species, species of bycatch concern, and species of minimum economic value can provide insight into increased fisheries regulations, stricter requirements, or additional observer coverage.