Typescript. / Bibliography: leaves 239-263. / Microfiche. / xiii, 263 leaves, bound ill. 29 cm

The consumption of seafood in the United States has increased rapidly in recent years due to high quality protein and health benefits of seafood. Seafood can be a carrier for bacteria normally distributed in the marine environment and, in some cases, can be contaminated by human pathogens. Therefore, there is a potential health risk if seafood is consumed raw or undercooked. However, information regarding prevalence of foodborne pathogens in retail seafood products and the ability of pathogens to survive in the products during refrigerated and frozen storage is limited. The objective of this study was to generate such information for a better understanding of distribution of foodborne pathogens in seafood products and provide data which might be used for risk assessment of foodborne infection associated with seafood consumption. A total of 45 seafood products were collected from local retail stores and analyzed for aerobic plate counts (APC) and psychrotrophic bacterial counts (PBC) as well as presence of foodborne pathogens, including Escherichia coli O157:H7, Salmonella, Listeria monocytogenes, Staphylococcus aureus, Vibrio parahaemolyticus, and Vibrio vulnificus according to procedures described in the U.S. Food and Drug and Administration Bacteriological Analytical Manual (BAM). Presumptive isolates for each foodborne pathogen were further characterized by biochemical reactions using commercial identification kits and confirmed with polymerase chain reaction (PCR) assay. The samples had bacterial populations ranging from 1.90 to 6.11 CFU/g for APC and from 2.00 to 6.78 CFU/g for PBC. According to the microbiological criteria of International Commission on Microbiological Specifications for Foods (ICMSF), all 45 samples were considered acceptable quality (APC < 10⁷ CFU/g, E. coli < 3 MPN/g) with most samples (93.3%) being good quality (APC < 5 × 10⁵ CFU/g, E. coli < 3 MPN/g). No E. coli O157:H7, Salmonella, S. aureus, V. parahaemolyticus, and V. vulnificus was detected in any samples. Two previously frozen shrimp products (4.4%) were confirmed to carry L. monocytogenes. Studies of growth and survival of L. monocytogenes (3 strains), S. aureus (2 strains), and Salmonella (2 serovars) in raw yellowfin tuna meat stored at 5 - 7 °C for 14 days revealed that L. monocytogenes had the ability to multiply in the tuna meat during refrigerated storage while populations of S. aureus and Salmonella were reduced by 1 to 2 log CFU/g after 14 days at 5 - 7 °C. Studies of holding raw yellowfin tuna meat contaminated with L. monocytogenes, S. aureus, and Salmonella at -18 ± 2 °C for 12 weeks observed that all three pathogens, except Salmonella Newport, in tuna samples survived the frozen storage with less than 2- log of reductions in the populations over 12 weeks of storage. No viable cell of Salmonella Newport was detected in samples after 42 days storage at -18 °C. Raw seafood can be a carrier of foodborne pathogens, particularly L. monocytogenes, and many foodborne pathogens can survive in frozen products for several months. Consumption of raw or undercooked seafood products may lead to human infection if the products are contaminated with pathogens. Therefore, sanitation standard operating procedure (SSOP), good manufacturing practice (GMP) and hazards analysis and critical control points (HACCPs) programs shall all be implemented in the seafood industry to prevent seafood products from being contaminated with foodborne pathogens during handling and processing. Moreover, proper storage of raw seafood products and avoiding cross-contamination during handling at the retail levels also helps to minimize risk of human infection associated with ready-to-eat products. / Graduation date: 2013

Abstract In Taiwan, long-line fishing has been the major technique in fishery. With the enhancement of fishing techniques, the fishing zone of Taiwan has spread all over three of World Oceans, and Taiwan has been regarded as one of five largest pelagic fishing countries. Pelagic long-line fishery plays a crucial role in economic development in Taiwan. In recent years, the fishery environments, whether in domestic or foreign fishing zone, have been dramatically changing. Since the United Nations Convention on the Law of the Sea has been resulted, all of coastal nations have subsequently set up the Exclusive Economic Zone (EEZ) or marine economic development zone, which is stretched out 200 nautical miles from a nation¡¦s coast. However, the establishment of marine economic development zone also brings about the high seas¡¦ largely shrinking. Since the past, the increasing extinction of fish species is mainly resulted from illegal fishing techniques, fishing in the fishing-prohibited zone or during the prohibited period, catching fingerlings and using illegitimate fishing gear. Under such a decreasing fishing circumstance, those Taiwanese long-line fishing vessels under 100 tonnes, mostly fishing in the South Pacific Ocean, are struggling with many changes, such as international fishing limitation, the fishing vessels decreasing policy, the diminishing amount of fish caused by climate changes, the raising oil price and cost. Respecting the situation that most of long-line fishing vessels are managed by ship owners instead of fishery companies, and the fishing-related records are too scarce to provide for reference, this research will explore how the 100-tonne-under long-line fishing vessels owners can manage their business in South Pacific Ocean. All information in this study is acquired from Fisheries Agency in Taiwan and interviews with long-line fishing vessels owners. The questions asked in those interviews mainly target fishing benefit, cost, method of supplies, and the policy on captain and crew management. Based on the analysis of those cases mentioned above, we can figure out the practical operation and management of the 100-tonne-under long-line fishing vessels owners in Taiwan. Furthermore, this study also points out current difficulties in fishery management, providing for those vessels owners as the crucial reference of increasing competitive advantages. Keywords: Long-Line Fishing, South Pacific Ocean, Business Management, Yellowfin Tuna, Cost-Benefit Analysis

Yellowfin tuna Thunnus albacares is a commercially and economically important fisheries species, which comprises the second largest component of South Africa’s catch of tuna and tuna-like species. Catches of the species off South Africa are treated as two discrete stocks by the two tuna Regional Fisheries Management Organisations (tRFMOs) under whose jurisdictions they fall. Individuals caught off the Western Cape, west of the boundary between the tRFMOs at 20°E, are included in assessment and management of the Atlantic Ocean yellowfin tuna stock by the International Commission for the Conservation of Atlantic Tunas (ICCAT), and those caught east of this boundary are assessed and managed as part of the Indian Ocean stock by the Indian Ocean Tuna Commission (IOTC). The boundary between these stocks is based on the confluence of the two oceans in this region and does not incorporate the population structure of species. For sustainable exploitation of fisheries resources, it is important that the definition of management stocks reflects species’ biological population structure; the fine-scale stock structure of yellowfin tuna off South Africa is therefore a research priority which this study aimed to address by means of population genomics analyses. Yellowfin tuna exhibit shallow genetic differentiation over wide geographic areas, and as such traditional population genetic approaches have limited power in resolving fishery significant population structure in the species. Herein, a population genomic approach was employed, specifically, genome-wide analysis of single nucleotide polymorphisms (SNPs) discovered using a next-generation DNA sequencing approach, to confer (i) increased statistical power to detect neutral structuring reflecting population connectivity patterns and (ii) signatures of local adaptation. The mitochondrial Control Region (mtDNA CR) was also sequenced to compare the resolving power of different approaches and to permit coalescent based analyses of the species evolutionary history in the region. Neutral SNP loci revealed significant structure within the dataset (Fst=0.0043; P<0.0001); partitioning of this differentiation within the dataset indicated significant differentiation between yellowfin tuna from the Western Cape and the Gulf of Guinea in the eastern Atlantic Ocean, with no significant differentiation between individuals from the Western Cape and Western Indian Ocean regions. This indicates two population units wherein there is a separation of the Gulf of Guinea from the remaining samples (Indian Ocean including Western Cape) that are largely derived from a single genetic population. This pattern was also supported by assignment tests. Positive outlier SNPs, exhibiting signatures of diversifying selection, suggest that individuals from these regions may be locally adapted, as well as demographically isolated. The mtDNA CR did not reveal any significant genetic structure among samples (Fst=0.0030; P=0.309), demonstrating the increased resolving power provided by population genomics approaches, but revealed signatures of historical demographic fluctuations associated with glacial cycles. Based on the findings of this study, it is suggested that yellowfin tuna caught off the Western Cape of South Africa are migrants from the Indian Ocean population, exhibiting significant genetic differentiation from the Atlantic Ocean Gulf of Guinea individuals, and should thus be included in the assessment and management of the Indian Ocean stock. It is therefore recommended that the boundary between the Atlantic and Indian Ocean yellowfin tuna stocks, under the mandates of ICCAT and the IOTC respectively, should be shifted to approximately 13.35°E to include all individuals caught in South African waters in the Indian Ocean stock.

The population genetic structure of Atlantic yellowfin tuna (Thunnus albacares) has received little attention despite the substantial fishing mortality of juveniles caused by purse seining around fish aggregating devices in the Gulf of Guinea targeting multi-species schools that also include similarly sized skipjack tuna (Katsuwonus pelamis) and bigeye tuna (T. obesus). We used sequence data from 355 bp of the mitochondrial control region I as well as six microsatellite loci to examine: (1) population structure, and (2) to look for evidence of reproductive variance. We analyzed two samples of adults from the Gulf of Mexico (GOM) and one sample of early juveniles (20-50 mm) from the Gulf of Guinea (GOG). We found no evidence of geographic or temporal differentiation among the samples. Accordingly, the null hypothesis of panmixia for yellowfin tuna in the Atlantic Ocean could not be rejected. A sudden expansion analysis based on mtDNA control region I sequence data of yellowfin tuna was highly significant. Time estimates for expansion were between 40,000 and 80,000 years before present. The associated high levels of homoplasy could be masking any existing population structure. Additional sampling from additional locations and across several years will be needed to test the hypothesis of panmixia. We also provide preliminary evidence of the Allendorf-Phelps effect, which may contribute to reproductive variance. This is the first evidence of this effect in any other tuna or pelagic species. Data indicates that early juveniles sharing the same mtDNA control region I haplotype were caught in the same tow and had a significant probability of halfsibship status as calculated from their haplotype and genotype at one microsatellite locus through kinship analysis. Sampling throughout the spawning season and across several years, as well as analysis with additional microsatellite loci that have a more even distribution of alleles, will be needed to more fully identify the sibling status of larvae and early juveniles caught in the same tow as well as the extent of this reproductive variance.

The population genetic structure of Atlantic yellowfin tuna (Thunnus albacares) has received little attention despite the substantial fishing mortality of juveniles caused by purse seining around fish aggregating devices in the Gulf of Guinea targeting multi-species schools that also include similarly sized skipjack tuna (Katsuwonus pelamis) and bigeye tuna (T. obesus). We used sequence data from 355 bp of the mitochondrial control region I as well as six microsatellite loci to examine: (1) population structure, and (2) to look for evidence of reproductive variance. We analyzed two samples of adults from the Gulf of Mexico (GOM) and one sample of early juveniles (20-50 mm) from the Gulf of Guinea (GOG). We found no evidence of geographic or temporal differentiation among the samples. Accordingly, the null hypothesis of panmixia for yellowfin tuna in the Atlantic Ocean could not be rejected. A sudden expansion analysis based on mtDNA control region I sequence data of yellowfin tuna was highly significant. Time estimates for expansion were between 40,000 and 80,000 years before present. The associated high levels of homoplasy could be masking any existing population structure. Additional sampling from additional locations and across several years will be needed to test the hypothesis of panmixia. We also provide preliminary evidence of the Allendorf-Phelps effect, which may contribute to reproductive variance. This is the first evidence of this effect in any other tuna or pelagic species. Data indicates that early juveniles sharing the same mtDNA control region I haplotype were caught in the same tow and had a significant probability of halfsibship status as calculated from their haplotype and genotype at one microsatellite locus through kinship analysis. Sampling throughout the spawning season and across several years, as well as analysis with additional microsatellite loci that have a more even distribution of alleles, will be needed to more fully identify the sibling status of larvae and early juveniles caught in the same tow as well as the extent of this reproductive variance.

Tuna are the major marine fishery in Sri Lanka, and yellowfin tuna (YFT) (Thunnus albacares) and skipjack tuna (SJT) (Katsuwonus pelamis) represent 94% of all tuna caught. The tuna catch in Sri Lanka has increased rapidly over recent years and this is true generally for the Indian Ocean. Tuna are a major animal protein source for 20 million people in Sri Lanka, while marine fisheries provide the main income source for most Sri Lankan coastal communities. While the importance of the fishery will require effective stock management practices to be employed, to date no genetic studies have been undertaken to assess wild stock structure in Sri Lankan waters as a basis for developing effective stock management practices for tuna in the future. This thesis undertook such a genetic analysis of Sri Lankan T. albacares and K. pelamis stocks. Samples of both YFT and SJT were collected over four years (2001 - 2004) from seven fishing grounds around Sri Lanka, and also from the Laccadive and Maldive Islands in the western Indian Ocean. Partial mitochondrial DNA (mtDNA) ATPase 6 and 8 genes and nuclear DNA (nDNA) microsatellite variation were examined for relatively large samples of each species to document genetic diversity within and among sampled sites and hence to infer stock structure and dispersal behaviour. Data for YFT showed significant genetic differentiation for mtDNA only among specific sites and hence provided some evidence for spatial genetic structure. Spatial Analysis of Molecular Variance (SAMOVA) analysis suggests that three geographically meaningful YFT groups are present. Specifically, one group comprising a single site on the Sri Lankan west coast, a second group comprising a single site on the east coast and a third group of remaining sites around Sri Lanka and the Maldive Islands. Patterns of variation at nDNA loci in contrast, indicate extensive contemporary gene flow among all sites and reflect very large population sizes. For SJT, both mtDNA and nDNA data showed high levels of genetic differentiation among all sampling sites and hence evidence for extensive spatial genetic heterogeneity. MtDNA data also indicated temporal variation within sites, among years. As for YFT, three distinct SJT groups were identified with SAMOVA; The Maldive Islands in the western Indian Ocean comprising one site, a second group comprising a single site on the east coast and a third group of remaining sites around Sri Lanka and the Laccadive Islands. The mtDNA data analyses indicated two divergent (M^ = 1.85% ) SJT clades were present among the samples at all sample sites. SJT nDNA results support the inference that multiple 'sub populations' co-exist at all sample sites, albeit in different frequencies. It appears that variation in the relative frequencies of each clade per site accounts for much of the observed genetic differentiation among sites while effective populations remain extremely large. Based on combined data sets for management purposes therefore, there is no strong evidence in these data to indicate that more than a single YFT stock is present in Sri Lankan waters. For SJT however, evidence exists for two divergent clades that are admixed but not apparently interbreeding around Sri Lanka. The identity of spawning grounds of these two clades is currently unknown but is likely to be geographically distant from Sri Lanka. Spawning grounds of the two distinct SJT clades should be identified and conserved.

The growth rate of a fish is a fundamental function used in stock assessments to estimate the population size and the fishery pressure affecting the species. There has been recent debate within the stock assessment community regarding which type of growth model best represents the true growth rate of yellowfin tuna (Thunnus albacares), in the Atlantic Ocean; specifically, should assessments use a traditional von Bertalanffy growth curve or a so-called “two-stanza” growth curve, which combines one growth rate for smaller individual tuna and another for larger sizes. Using a simulated population created with the software R, both growth models were compared under different scenarios. The first part of this thesis examines the effect of different fisheries and their associated gear selectivity. Purse seine, baitboat and pelagic longline fisheries, which target yellowfin tuna in the Atlantic Ocean, were incorporated into the analysis. The second part looks at different sources of variability that occur either in nature (observation error) or in the process of analysis (process error). These include different growth variation, looking only at the fast growing young fish and using a set birth date versus a spawning period. These scenarios were used to determine if the sample, derived from a fishery-dependent sample, reflects the true population. Three populations of yellowfin tuna were created: an un-fished population, a fished population from stock assessment data, and a fished population from simulation software called ‘Population Simulator’. These populations were all analyzed for the different scenarios as well as the different fisheries. The final part of this thesis looks at three similar tuna species; skipjack (Katsuwonus pelamis), bigeye (Thunnus obesus ) and albacore (Thunnus alalunga). The same scenarios and gear selectivities were applied to these tuna species. The results of this study showed that the two-stanza growth curve was not a better fit for yellowfin tuna population in the Atlantic Ocean than the traditional von Bertalanffy growth curve. There were several scenarios that favored the two-stanza growth curve, but either it was a sample population not representative of the Atlantic Ocean population, or the two-stanza had no initial growth rate, making it the same as a traditional growth curve. Based on these results, it was evident that the traditional von Bertalanffy growth curve was the more accurate growth curve to use for yellowfin tuna in the Atlantic Ocean and it is recommended that this growth curve be used in the stock assessments going forward.

La modélisation de la dynamique des populations de thons et grands pélagiques pour l'évaluation des stocks est confrontée à deux enjeux majeurs. (1) L'hypothèse forte de proportionnalité entre Captures Par Unité d'Effort de pêche (CPUE) et l'abondance des stocks. Les CPUE des pêcheries commerciales sont en effet les seules mesures relatives de biomasse utilisées pour l'évaluations des stocks de thons et grands pélagiques, malgré leur manque de représentativité de l'abondance de ces populations. (2) Le manque de données informatives pour modéliser la relation Stock-Recrutement (SR) ce qui conduit à utiliser des contraintes sur la "steepness" de cette fonction. Nous examinons comment l'introduction d'informations indépendantes des pêcheries commerciales dans les modèles pour l'évaluation des stocks thoniers permet de lever l'hypothèse de capturabilité constante et de mieux justifier le choix de la steepness de la relation SR. Le cadre statistique bayésien autorise la prise en compte d'informations supplémentaires via des distributions a priori informatives (priors). Cette thèse examine donc les possibilités d'élicitation de priors informatifs pour des paramètres démographiques et des paramètres liés à la capturabilité des engins de pêche, ainsi que l'utilisation de ces priors dans un modèle global. Les cas d'études sont les stocks de thon rouge (Thunnus thynnus) et d'albacore (Thunnus albacares) de l'Atlantique. La grande variabilité naturelle des taux de mortalités pré-recrutement pose des limites à l'utilisation des seuls traits d'histoire de vie pour l'élicitation de priors pour des paramètres démographiques. Par ailleurs, la relation SR pour les thonidés est remise en question par une valeur de steepness proche de 1. Il apparait que des priors informatifs sur la capturabilité dans un modèle hiérarchique global permettent de réduire les incertitudes dans le diagnostic sur l'état d'un stock thonier. Nous montrons ainsi que le diagnostic sur le stock Atlantique d'albacore est plus pessimiste qu'attendu la tendance à la hausse des capturabilités des principaux engins de pêche est prise en compte. L'élicitation de priors présente donc un fort intérêt pour utiliser des informations supplémentaires et extérieures aux CPUE et améliorer la perception de l'état des stock thoniers. / Modelisation of the population dynamics of tunas and tuna like species for stock assessment is facing two issues. (1) The hypothesis of proportionality between Catch Per Unit Effort (CPUE) and abundance (constant catchability). CPUEs from commercial fisheries appear to be the only relative measure of abundance in spite of their lack of representativity of the abundances of the populations. (2) The lack of informative data for the modelisation of the Stock-Recruit (SR) relationship, which leads to constraint this function on its steepness. The introduction of fisheries-independent sources of information is investigated in order to relax the assumption of constant catchability and to provide better justification of steepness choice for the SR relationship. The Bayesian statistical framework allows the consideration of additional information a priori via informative distributions (priors). This work investigate the elicitation of informative priors for demographic parameters and parameters related to the catchability of fishing gear, as well as the use of these priors into a surplus production model. The cases of the Atlantic bluefin tuna (Thunnus thynnus) and of the yellowfin tuna (Thunnus albacares}) were taken as examples. The large natural variability of pre-recruits mortality rates limits the use of life history traits for eliciting priors for demographic parameters. In addition, the SR relationship for tuna is challenged by a steepness value close to 1. It appears that informative priors on catchability parameters, in a hierarchical surplus production model, reduce uncertainties in the diagnosis on the status of tuna stocks. We show that the status of the Atlantic yellowfin tuna stock is more critical taking into account upward trends in the main fishing gears catchabilities. We conclude that prior elicitation is a reliable tool to take into account additionnal information and to improve tunas stock assessment.

Le thon obèse (Thunnus obesus), le thon alabore (Thunnus albacares) et le listao (Katsuwonus pelamis) comptent parmi les espèces de thons les plus utilisées en conserve. Lors de la fabrication de conserves de thon, la substitution d'espèce et/ou le mélange de différentes espèces de thon sont interdits par la réglementation européenne. L'authentification des espèces de thon reste complexe à cause du degré de similitude élevé entre les espèces de thon, ou encore, lorsque les caractéristiques morphologiques externes sont éliminées au cours du filetage et lors de la mise en conserve. Par conséquent, des substitutions involontaires ou frauduleuses peuvent se produire. Dans cette étude, le marqueur mitochondrial du gène de la sous-unité 2 de la NADH déshydrogénase a été utilisé pour identifier le thon obèse et le gène de la sous-unité II de la cytochrome c oxydase a été utilisé pour identifier le thon albacore et le listao en utilisant la PCR en temps réel basée sur la technologie TaqMan. Deux méthodes différentes basées sur la qPCR ont été développées pour quantifier le pourcentage de chair de chaque espèce présente au sein d'une boîte de thon. La première a été basée sur la quantification absolue avec standard externe réalisée avec les deux marqueurs. La seconde a été basée sur la quantification relative avec standard externe avec le gène endogène de l'ARN 12S. Sur la base de ces résultats, nous pouvons conclure que notre méthode peut s'appliquer pour quantifier les deux espèces de thon albacore et obèse génétiquement très proches lorsqu'elles sont utilisées dans un mélange binaire en conserve. / Bigeye tuna (Thunnus obesus), yellowfin tuna (Thunnus albacares) and skipjack tuna (Katsuwonus pelanis) are among the most widely used tuna species for canning purposes. Not only substitution but also mixing of tuna species is prohibited by the European regulation for canned tuna products. However, it can be difficult to authenticate the tuna species, due to their high degree of similarity or even when the external morphological characteristics are removed due to filleting before canning. Consequently, involuntary or fraudulent substitutions may occur during the canning process. In this study, the mitochondrial marker from NADH dehydrogenase subunit 2 gene was used to identify bigeye tuna and the mitochondrial marker cytochrome c oxidase subunit II gene was used to identify yellowfin tuna and skipjack tuna, utilizing TaqMan qPCR methodology. Two different qPCR-based methods were developed to quantify the percentage of flesh of each species used for can processing. The first one was based on absolute quantification using standard curves realized with these two markers ; the second one was founded on relative quantification with the universal 12S rRNA gene as the endogenous gene. On the basis of our results, we conclude that our methodology could be applied to authenticate the two closely related tuna species (bigeye tuna and yellowfin tuna) when used in a binary mix in tuna cans.