Rozprawy doktorskie na temat „Pelagic Fisheries”

Most of the scientific knowledge on the pelagic fish (the clupeids Stolothrissa tanganicae and Limnothrissa miodon and the centropomid Lates stappersii) of Lake Tanganyika is from research carried out in localised areas. This makes it difficult to extend the results to the whole lake. Consequently, there is the need to study the pelagic fish resources on a lake-wide basis using the same data collection procedures. Within the framework of an international fishery research project, data from the commercial fisheries targeting the pelagic fish stocks were simultaneously collected at various sampling sites in the riparian countries. Fishery-independent data were also obtained from lake-wide research surveys. The life histories of the three fish species appear to be similar throughout the lake. However, fish distribution across the lake is very uneven. The clupeid S. tanganicae mostly occur in the northern half of the lake and is much reduced in southern areas. This appears to be a recent contraction of the distribution range of this species. Limnothrissa miodon is more evenly distributed than S. tanganicae. The two species have a different inshore-offshore, size-related distribution across the lake. Nursery grounds of the first are close to the shore while those of S. tanganicae are in open, pelagic waters. With increase in size, S. tanganicae tend to move inshore while large L. miodon display the opposite movement. Lates stappersii stock, although relatively common, tends to be at higher concentration in the deep, steep central and southern basins. The feeding ecology of L. stappersii varies depending on the area and prey availability, but is mainly based on S. tanganicae and pelagic shrimps. Local occurrence of S. tanganicae is associated with that of copepod prey. The fish stocks experience different exploitation rates across the lake. While the fishing pressure is not excessive in the most of the lake areas, in others local overfishing is taking place. The biological characteristics of the pelagic fish species are discussed for the management of the lake fisheries. Fisheries management options are formulated on the basis of the assessment of the current exploitation levels.

Climate change and fisheries have affected marine environments worldwide leading to impacts on ecosystem structure and functioning. However there is clear evidence of spatial variability in the response of these impacts both within and among marine ecosystems. Although several studies have tried to explain the effect of these impacts on marine food webs, it is unclear how they interact, and how they may affect marine ecosystems remains an important unanswered question. This suggests the urgent need for multiple-trophic level and ecosystem-based management approaches to account for both fisheries and climate change impacts at ocean basins across the globe. Marine apex predators, such as seabirds, are vulnerable to the effects of both climate and fishing impacts, and can be used as reliable and sensitive bio-indicators of the status of the marine ecosystem. The Celtic Sea ecosystem is a productive shelf region in the Northeast Atlantic. It is characterized by high fish and invertebrate biodiversity. In addition, internationally important numbers of seabirds, such as Northern gannet Morus bassanus (L.), Manx shearwater Puffinus puffinus (B.), Common guillemot Uria aalge (P.) and Black-legged kittiwake Rissa tridactyla (L.), breed along the Celtic Sea coasts. In recent years, fisheries from across Europe have intensively exploited the Celtic Sea, leading to changes in stock structure. Moreover, the increase in annual average Sea Surface Temperature by 0.67 oC over the past two decades has altered the composition of plankton communities. These impacts, independently and in tandem, are likely to have had dramatic effects upon the Celtic Sea food web emphasizing the need to enhance our understanding of this important marine ecosystem. In this thesis the effects of climate change and fisheries on the Celtic Sea pelagic food web are evaluated, in particular focussing on the response of seabird populations. This is in part because of recent declines in the breeding success of many seabird colonies in the northeast Atlantic, particularly around the North Sea. Long-term data across four trophic levels (phytoplankton, zooplankton, mid-trophic level fish and seabirds) and different modelling approaches are used to determine factors influencing seabird productivity at different geographical scales. First, I review the direct and indirect effects of climate change and fisheries upon marine ecosystems, as well as their impacts upon marine birds. Second, I use data collected during 1986-2007 from a single seabird colony, across four trophic levels, to investigate long-term direct and indirect climate effects. The results suggest only a weak climate signal in the Celtic Sea, and this is only evident between mid-trophic level fish and certain species of seabird. Third, a similar multi-trophic level approach across three nearby regions in the southwest UK (Irish Sea, Celtic Sea, and English Channel) reveal no evidence of a bottom-up signal during the period 1991-2007. These findings are in contrast with the nearby North Sea region, where a strong bottom-up effect was found to affect seabird populations, highlighting the importance of regional-based studies across multiple trophic levels. Finally, to provide a more complete picture of the Celtic Sea, and how it might respond to changes in fisheries management and climatic variation, I use the complex tropho-dynamic ecosystem model Ecopath with Ecosim. The main focus is on how seabird biomass changes in response to the application of different fisheries regimes likely to be implemented under forthcoming reforms to the Common Fisheries Policy (e.g. the application of quotas and discard bans), as well as future climate change scenarios, in order to provide guideline support for resource management and seabird conservation in the Celtic Sea. The results suggest that some seabird guilds (gulls and some other scavengers) may be negatively affected by a reduction in discards, while other species (offshore divers) will benefit from a decrease in the fishing of pelagic fish species. Climate change is likely to have a negative impact across all trophic levels with a strong negative impact upon seabird populations. Therefore seabirds are likely to show species-specific responses to both climate variation (bottom-up effect) and changes in fishing practices, in particular our findings suggest that for some species climate may outweigh the fisheries impacts even when fisheries pressure is reduced by 50%. In summary, this study suggests that despite the generally negative impact of climate described for some regions in the Northeast Atlantic, the Celtic Sea ecosystem seems to be more resilient. However, both climate and fisheries and the interactions between these factors should be taken into account in the formulation of future management plans for the Celtic Sea ecosystem. The use of multiple-trophic level and ecosystem-based approaches over multiple spatial and temporal scales has helped to elucidate possible trophic mechanisms that are the response to future fishing and climate impacts in the Celtic Sea. The results of this study could have implications for both management plans and conservation policy.

This study analyses the willingness of consumers to pay an extra price for shark-free eco-label products of fresh small pelagics compared to the ordinary ones. The data collected for this study derives from a contingent valuation survey conducted among 200 consumers, in Ravenna and Pavullo nel Frignano, in a fish market and a supermarket each. There have been administrated further questionnaires to one wholesaler and to the sales manager of the two fishmongers and two supermarkets per town. Open-ended questions of the consumers’ questionnaires have been analysed through cross section linear regressions with ordinary least squares (OLS), using software Gretl, while qualitative analyses on the close-ended have been done using Excel. Freshness, origin and method of production are the aspects considered mostly by the consumers. Among all the interviewed, general knowledge of labels of is scarce. Maximum prices proposed by the consumers indicate that future shark-free eco-label of small pelagic could be sold with a price ranging from 7 to 10 €. The regression shows that the extent of the additional price that the consumer is willing to pay is related to the degree of information of the BIO label. Moreover, consumers could be interested in a shark-free eco-label. All vendors currently have no interest in promoting eco-labels, as joining the certification is considered a cost, as well as keeping the certified lines separate from the non-certified ones without mixing the products. None will assume the risk of joining the certification first, preferring to let others pave the way. An economic estimation of the amount of money that fishers gain from the by-catch has been calculated using pelagic trawling shark by-catch data provided by the Experimental Centre for Habitat Conservation (CESTHA) and fish prices from ISMEA and NISEA dataset. The economic loss due to the release of sharks is lower compared to how much the vessels could gain by joining the shark-free eco-label.

The heterogeneity provided by structured habitats is important in supporting diverse and dense fish communities. The biogenic reefs created by the native Eastern Oyster, Crassostrea virginica, were once the dominant structural habitat in Chesapeake Bay, and have since declined to less than 1% of historic estimates. Conflicting results on the effects of oyster reef restoration on pelagic fish assemblages make further investigation necessary. Incorporating multiple sampling strategies may help elucidate oyster reef habitat influence on fish assemblages. This study used multi-panel gillnets, hydroacoustic technology, and day-night sampling to describe pelagic fish assemblages on and off oyster reef habitat in the lower Piankatank River, VA. Data from oyster reef habitat, adjacent sandy-mud bottom habitat, and unstructured sandy habitat outside of a reef restoration area compared fish diversity, species composition, and density among habitat types. A multivariate analysis using day of the year, day or night, and habitat type as model terms found temporal factors explained variation in fish distribution more than habitat. Fish diversity varied significantly with day or night and habitat type. Diversity and density were significantly higher at night, demonstrating the necessity of nocturnal sampling in fish assemblage research. Results from this study conclude that fish assemblages were not significantly more diverse or denser on reef than non-reef habitat. We suggest that future work should concentrate on studying areas where oyster reef habitat comprises a larger proportion of the study area.

Only a miniscule fraction of the world’s largest volume of living space, the ocean’s mid-water biome, has ever been sampled. As part of the International Census of Marine Life field project Mid-Atlantic Ridge Ecosystems (MAR-ECO), a discrete-depth trawling survey was conducted in 2009 aboard the NOAA ship Henry B. Bigelow to examine the pelagic faunal assemblage structure and distribution over the Charlie-Gibbs Fracture Zone (CGFZ) of the northern Mid-Atlantic Ridge. This is the first MAR-ECO project aimed specifically at describing diel vertical migration as a distributional phenomenon. Discrete-depth sampling from 0-3000 m was conducted during both day and night in similar locations using a Norwegian “Krill” trawl with five codends that were opened and closed via a pre-programmed timer. Seventy-five species of fish were collected, with a maximum diversity and biomass observed between depths of 700-1900 m. An incremental gradient in sea surface temperature and underlying watermasses, from northwest of the CGFZ zone to the southeast, was mirrored by a similar gradient in ichthyofaunal diversity. Using multivariate analyses, eight deep-pelagic fish assemblages were identified, with depth as the overwhelming discriminatory variable. Strong diel vertical migration (DVM) of the mesopelagic fauna was a prevalent feature of the study area, though the numerically dominant fish, Cyclothone microdon (Gonostomatidae), exhibited a broad (0-3000 m) vertical distribution and did not appear to migrate on a diel basis. In all, 3 patterns of vertical distribution were observed in the study area: a) DVM of mesopelagic, and possibly bathypelagic, taxa; b) broad vertical distribution spanning meso- and bathypelagic depths; and c) discrete vertical distribution patterns. Overall species composition and rank order of abundance of fish species agreed with two previous expeditions to the CGFZ (1982-83 and 2004), suggesting some stability in the ichthyofaunal composition of the study area, at least in the summer. Frequent captures of putative bathypelagic fishes, shrimps, and squid in the epipelagic zone (0-200 m) were confirmed. The results of this expedition reveal distributional patterns unlike those previously reported for open ocean ecosystems, with the implication of increased transfer efficiency of surface production to great depths in the mid-North Atlantic.

The pelagic stingray, Pteroplatytrygon violacea, is a bycatch species in the global pelagic longline fishery. However, little research has been conducted on its basic biology, including prey composition, trophic positioning, and habitat utilization. Descriptions of the habitat utilization have largely been through indirect analyses of catch rates in commercial fisheries, which also provided no information on actual behaviors. The first chapter of this thesis will describe the habitat utilization and behavior of four individual pelagic stingrays using electronic tagging technology. Prior diet descriptions were hampered, in part, by low sample sizes and accordingly provided little information on the ecological interactions of these animals. Similarly, the second chapter of this thesis will therefore provide a new diet description for the pelagic stingray using a combined analysis of traditional stomach contents with stable isotope values, thereby addressing both ingestion and assimilation. A more robust study of the trophic dynamics of the pelagic stingray, in conjunction with the description of its habitat utilization, will provide a better understanding of its role within the pelagic ecosystem. Ultimately, the goal is to obtain knowledge of the less economic species with good science so when management approaches shift from species-specific to ecosystem based, the transition will already have known information to change efficiently.

The feeding behavior of fishes is a topic that has piqued the interests of many researchers given the dynamic and ancestral nature of aquatic prey-capture. This study examines aquatic feeding in terms of the suction and ram components of feeding in smallmouth bass, Micropterus dolomieu, and how they modulate their kinematic behavior when attacking pelagic and benthic prey. Relative to other Micropterus genera, the reduced gape in smallmouth bass suggests they may create considerable suction pressure – stronger subambient pressure pulled through a smaller opening creates greater velocity. Suction feeding is useful when feeding on benthic prey, such as crayfish. Ram feeding is utilized when capturing pelagic prey, such as goldfish, because prey swimming in the water column can be overtaken with body speed. Prey-capture experiments using high-speed cinematography and pressure transducers were conducted to determine if smallmouth bass modulate their feeding performance between pelagic and benthic prey items. Results indicate that smallmouth bass modulate their behavior to include both aspects of ram and suction feeding when presented with differing prey, utilizing greater ram when feeding in the water column and stronger suction when feeding off the substrate (MANCOVA, p

Thesis: Ph. D., Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2018.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 138-154).
Highly migratory marine fishes support valuable commercial fisheries worldwide. Yet, many target species have proven difficult to study due to long-distance migrations and regular deep diving. Despite the dominance of oceanographic features, such as fronts and eddies, in the open ocean, the biophysical interactions occurring at the oceanic (sub)mesoscale (< 100 km) remain poorly understood. This leads to a paucity of knowledge on oceanographic associations of pelagic fishes and hinders management efforts. With ever-improving oceanographic datasets and modeling outputs, we can leverage these tools both to derive better estimates of animal movements and to quantify fish-environment interactions. In this thesis, I developed analytical tools to characterize the biophysical interactions influencing animal behavior and species' ecology in the open ocean. A novel, observation-based likelihood framework was combined with a Bayesian state-space model to improve geolocation estimates for archival-tagged fishes using oceanographic profile data. Using this approach, I constructed track estimates for a large basking shark tag dataset using a high-resolution oceanographic model and discovered a wide range of movement strategies. I also applied this modeling approach to track archival-tagged swordfish, which revealed affinity for thermal front and eddy habitats throughout the North Atlantic that was further corroborated by synthesizing these results with a fisheries-dependent conventional tag dataset. An additive modeling approach applied to longline catch-per-unit effort data further highlighted the biophysical interactions that characterize variability in swordfish catch. In the final chapter, I designed a synergistic analysis of high-resolution, 3D shark movements and satellite observations to quantify the influence of mesoscale oceanography on blue shark movements and behavior. This work demonstrated the importance of eddies in structuring the pelagic ocean by influencing the movements of an apex predator and governing the connectivity between deep scattering layer communities and deep-diving, epipelagic predators. Together, these studies demonstrate the breadth and depth of information that can be garnered through the integration of traditional animal tagging and oceanographic research with cutting-edge analytical approaches and high-resolution oceanographic model and remote sensing datasets, the product of which provides a transformative view of the biophysical interactions occurring in and governing the structure of the pelagic ocean.
by Camrin Donald Braun.
Ph. D.

A growing recognition of the need for effective marine environmental management as a result of the increasing exploitation of marine biological resources has highlighted the need for high speed ecological seabed mapping. The practice of mapping making extensive use of satellite remote sensing and airborne platforms is well established for terrestrial management. Marine biological resource mapping however is not readily available except in part from that derived for surface waters from satellite based ocean colour mapping. Perhaps the most fundamental reason is that of sampling difficulty, which involves broad areas of seabed coverage, irregularities of seabed surface and depth. Conventional grab sample techniques are widely accepted as a standard seabed mapping methodology that has been in use long before the advent of acoustic techniques and continue to be employed. However. they are both slow and labour intensive, factors which severely limit the spatial coverage available from practical grab sampling programs. While acoustic techniques have been used for some time in pelagic biomass assessment, only recently have acoustic techniques been applied to marine biological resource mapping of benthic communities. Two commercial bottom classifiers available in the market that use normal incidence echosounders are the RoxAnn and QTC View systems. Users and practitioners should be cautious however when using black box implementations of the two commercial systems without a proper quality control over raw acoustic data since some researchers in their studies have indicated problems with these two bottom classifiers such as, among others, a depth dependence. In this thesis, an alternative approach was adopted to the use of echosounder returns for bottom classification.The approach used in this study is similar to,~ used in the commercial RoxAnn system. In grouping bottom types however, Multivariate analysis (Principal Component Analysis and Cluster Analysis) was adopted instead of the allocation system normally used in the RoxAnn system, called RoxAnn squares. In addition, the adopted approach allowed for quality control over acoustic data before further analysis was undertaken. As a working hypothesis, it was assumed that on average 0 and aE2 = 0 where E1 and E2 are the roughness and hardness indices, respectively, and RO is the depth. For roughness index (E1), this was achieved by introducing a constant angular integration interval to the tail of the first OM returns whereas for hardness index (E2), this was achieved by introducing a constant depth integration interval. Since three different frequencies, i.e. 12, 38 and kHz, were operated, Principal Component Analysis was used here to reduce the dimensionality of roughness and hardness indices, formed from the three operated qu frequencies separately. The k-means technique was applied to the first principal component of roughness index and the first principal comp component of hardness index to produce separable seabed types. This produced four separable seabed types, namely soft-smooth, soft-rough, hard-smooth and hard-rough seabeds.Principal Component Analysis was also used to reduce the dimensionality of the area backscattering coefficient sA, a relative measure of biomass of benthic mobile biota. The bottom classification results reported here appear to be robust in that, where independent ground truthing was available, acoustic classification was generally congruent with ground truth results. When investigating the relationship between derived bottom type and acoustically assessed total biomass of benthic mobile biota, no trend linking the two parameters, however, appears. Nevertheless, using the hierarchical agglomerative technique applied to a set of variables containing average first principal component of the area backscattering coefficient sA, the average first principal component of roughness and hardness indices, the centroids of first principal component of roughness and hardness indices associated with the four seabed types and species composition of fish group of the common species in trawl stations available, two main groups of quasi acoustic population are observed in the North West Shelf (NWS) study area and three groups are observed in the South East Fisheries (SEF) study area. The two main groups of quasi acoustic population in the NWS study area and the three main groups of quasi acoustic population in the study area are associated with the derived seabed types and fish groups of the common species.

A growing recognition of the need for effective marine environmental management as a result of the increasing exploitation of marine biological resources has highlighted the need for high speed ecological seabed mapping. The practice of mapping making extensive use of satellite remote sensing and airborne platforms is well established for terrestrial management. Marine biological resource mapping however is not readily available except in part from that derived for surface waters from satellite based ocean colour mapping. Perhaps the most fundamental reason is that of sampling difficulty, which involves broad areas of seabed coverage, irregularities of seabed surface and depth. Conventional grab sample techniques are widely accepted as a standard seabed mapping methodology that has been in use long before the advent of acoustic techniques and continue to be employed. However. they are both slow and labour intensive, factors which severely limit the spatial coverage available from practical grab sampling programs. While acoustic techniques have been used for some time in pelagic biomass assessment, only recently have acoustic techniques been applied to marine biological resource mapping of benthic communities. Two commercial bottom classifiers available in the market that use normal incidence echosounders are the RoxAnn and QTC View systems. Users and practitioners should be cautious however when using black box implementations of the two commercial systems without a proper quality control over raw acoustic data since some researchers in their studies have indicated problems with these two bottom classifiers such as, among others, a depth dependence. In this thesis, an alternative approach was adopted to the use of echosounder returns for bottom classification.
The approach used in this study is similar to,~ used in the commercial RoxAnn system. In grouping bottom types however, Multivariate analysis (Principal Component Analysis and Cluster Analysis) was adopted instead of the allocation system normally used in the RoxAnn system, called RoxAnn squares. In addition, the adopted approach allowed for quality control over acoustic data before further analysis was undertaken. As a working hypothesis, it was assumed that on average 0 and aE2 = 0 where E1 and E2 are the roughness and hardness indices, respectively, and RO is the depth. For roughness index (E1), this was achieved by introducing a constant angular integration interval to the tail of the first OM returns whereas for hardness index (E2), this was achieved by introducing a constant depth integration interval. Since three different frequencies, i.e. 12, 38 and kHz, were operated, Principal Component Analysis was used here to reduce the dimensionality of roughness and hardness indices, formed from the three operated qu frequencies separately. The k-means technique was applied to the first principal component of roughness index and the first principal comp component of hardness index to produce separable seabed types. This produced four separable seabed types, namely soft-smooth, soft-rough, hard-smooth and hard-rough seabeds.
Principal Component Analysis was also used to reduce the dimensionality of the area backscattering coefficient sA, a relative measure of biomass of benthic mobile biota. The bottom classification results reported here appear to be robust in that, where independent ground truthing was available, acoustic classification was generally congruent with ground truth results. When investigating the relationship between derived bottom type and acoustically assessed total biomass of benthic mobile biota, no trend linking the two parameters, however, appears. Nevertheless, using the hierarchical agglomerative technique applied to a set of variables containing average first principal component of the area backscattering coefficient sA, the average first principal component of roughness and hardness indices, the centroids of first principal component of roughness and hardness indices associated with the four seabed types and species composition of fish group of the common species in trawl stations available, two main groups of quasi acoustic population are observed in the North West Shelf (NWS) study area and three groups are observed in the South East Fisheries (SEF) study area. The two main groups of quasi acoustic population in the NWS study area and the three main groups of quasi acoustic population in the study area are associated with the derived seabed types and fish groups of the common species.

Dans le cadre de l’Approche Ecosystémique des Pêches (AEP), il est nécessaire d’évaluer l’impact de la pêche thonière tropicale à la senne sur les espèces ciblées et sur les espèces accessoires. Parmi ces dernières, les espèces de la mégafaune, telles que des requins, raies, cétacés, tortues, oiseaux marins, sont souvent emblématiques et vulnérables. Les thoniers senneurs tropicaux recherchent activement à la surface de l’eau tout indice de la présence de bancs de thon (e.g. oiseaux, objets flottants, baleines, dauphins ou requins baleines). Dans l’est de l’océan Atlantique et l’ouest de l’océan Indien, les deux modes de pêches principaux sont les captures de thons en bancs libres et celles sur bancs associés à un objet flottant, naturel ou artificiel, rassemblés ici sur sous le terme de dispositif de concentration de poisson (DCP). Les calées associées aux requins baleines et aux cétacés sont toutefois peu étudiées. L’objectif de cette thèse est donc d’analyser les co-occurrences et/ou interactions spatio-temporelles entre requins baleines, cétacés et pêche thonière à la senne, dans une perspective de conservation de l’écosystème. Ce travail, basé sur des données de livres de bord et d’observateurs scientifiques embarqués, a montré que la co-occurrence pêche thonière/ mégafaune se localise dans des strates spatio-temporelles relativement précises: i) du Gabon à l’Angola (avril–septembre), ii) dans le Canal du Mozambique (juin–septembre) et iii) à l’est des Seychelles (avril–septembre). Les baleines et requins baleines étant planctivores, la co-occurrence avec la pêche à la senne est principalement liée à une forte productivité primaire (appréhendée à travers des proxys tels que la concentration en chlorophylle-a). De plus, les calées sur ces deux groupes étaient assez élevées avant 2000 (jusqu’à 20% des calées), et qu’elles sont moins fréquentes aujourd’hui (AC3 et 1,5% des calées associées à des baleines et des requins baleines, respectivement). L’impact de la pêche à la senne sur ces espèces semble relativement faible au regard du taux de mortalité apparente de 1,4% pour les requins baleines et 5,6% pour les cétacés. Des marquages satellites réalisés sur les requins baleines, confirment ces observations sur le plus long terme, mais la taille de l’échantillon limite la formulation de conclusions définitives. Concernant les dauphins, bien que présents sur les zones de pêche, ils interagissent très peu avec celle-ci, soulignant ainsi une différence majeure avec l’océan Pacifique est où ce mode de pêche est majoritaire. La diversité spécifique des espèces cible et accessoire associées aux calées sur mégafaune a également été étudiée. Les requins baleines sont associés aux listaos et à l’albacore (dans une large gamme de tailles), alors que les baleines le sont principalement à de gros albacores. De plus, la capture accessoire associée à ces deux groupes de mégafaune est relativement faible et dominée par le requin soyeux et la diversité spécifique est proche de celle trouvée sous les bancs libres de thons. Enfin les effets de mesures de conservation vis-à-vis de la mégafaune encerclée ou de mesures de gestion de l’effort de pêche, notamment les moratoires sur DCP réelles ou simulées (e.g. moratoires élargis), ont été analysés. Les premières ont eu un effet limité en terme de captures cibles et accessoires, alors que les moratoires impactent peu le nombre de calées associés à la mégafaune, ceci en raison du décalage spatio-temporel des co-occurrences. Cependant des moratoires élargis pourraient être bénéfiques pour les thons juvéniles et certaines espèces associées. Par l’analyse quantitative des interactions entre la pêche thonière à la senne et la mégafaune, cette thèse apporte des connaissances essentielles sur les espèces étudiées dans le cadre de la mise en place d’une AEP, applicable à la pêche thonière tropicale
In the frame of the Ecosystem Approach to Fishery (EAF) management, impact of the tropical tuna purse-seine fishery on targeted and incidentally captured species should be investigated. They may include megafauna species, such as sharks, rays, cetaceans, turtles or sea birds, which often are emblematic and vulnerable species. Tropical tuna purse-seiners actively search, at the surface of the sea, for clues indicating the presence of tuna schools (e.g. birds, floating objects, whales, dolphins or whale sharks). In the eastern Atlantic and western Indian Oceans, the main two fishing modes are sets on free swimming tuna schools and schools associated to natural or artificial floating objects, thereafter called Fish Aggregating Device (FAD). However dedicated studies on fishing sets associated to whale sharks and cetaceans are still lacking. The aim of this thesis is therefore, using logbook and scientific onboard observer data, to investigate the spatio-temporal co-occurrences and/or interactions between whale sharks, cetaceans and the tuna purse-seine fishery within an ecosystem conservation perspective. This work underlines that the megafauna/ fishery co-occurrence occurs in specific spatio-temporal strata: i) Gabon to Angola (April–September), ii) the Mozambique Channel (June–September), and iii) East of Seychelles (April–September). As baleen whales and whale sharks are filter feeders, the co-occurrence with the purse-seine fishery was mostly linked to highly productive environments (i.e. using proxys including chlorophyll-a concentration). In addition fishing sets involving megafauna were relatively high before 2000 (up to 20% of the sets), but are nowadays less frequent (AC3 and 1.5% of the sets associated to baleen whales and whale sharks). The purse-seine fishery appears to have a relatively low impact on megafauna species with mortality rates of 1.4% for whale sharks and 5.6% for cetaceans. Whale shark satellite tagging also confirms these results on the longer term, but the low sample size precludes any final conclusion. While dolphins are present in fishing areas, very few interactions with the fishery was detected, which highlights the striking difference with the eastern Pacific Ocean where half the sets are associated to dolphin herds. In addition, the diversity of targeted and bycatch species captured under whale shark and baleen whale sets was also investigated. Whale sharks are principally associated to skipjack and yellowfin (of various sizes) tunas and baleen whales mostly to large yellowfin tuna. In addition, bycatch species associated to these two megafauna groups was relatively low and dominated by the silky shark, and bycatch diversity was close to the one found for free swimming tuna schools. Finally, real and/or simulated encircled megafauna conservation measures or fishing effort management measures (especially FAD moratoria including larger ones) were investigated. The first ones were found to have limited consequences on tuna catch and bycatch. Conversely FAD moratoria had limited impacts on the number of megafauna associated fishing sets, due to the fact that the main spatio-temporal strata of megafauna and FAD sets differ. However larger and longer moratoria could be beneficial for juvenile tuna and some bycatch species. Overall, this thesis has lead to increase the knowledge on megafauna/ fishery interactions, essential in the general framework of setting up an EAF in the tropical tune purse-seine fishery

Il mare Adriatico è uno dei bacini più produttivi dell’intero Mediterraneo, caratterizzato da un’ampia piattaforma continentale, da un notevole apporto fluviale e da un complesso pattern idrodinamico. In questo particolare ecosistema i piccoli pelagici ricoprono un ruolo fondamentale, sia da un punto di vista ecologico che socio-economico. E’ quindi importante avere una migliore comprensione di come la forzante ambientale influisce sulle dinamiche di questa specie in modo da pianificare un efficiente management dello stock seguendo i principi dell’Ecosystem Based Management (EBM). In questo lavoro sono state analizzate le dinamiche spazio-temporali dell’acciuga europea (Engraulis encrasicolus) utilizzando un approccio integrato. L’obiettivo principale è stato quello di individuare i possibili fattori che influenzano la selezione dell’habitat dell’acciuga ponendo principalmente l’attenzione sugli stadi giovanili, in modo da comprendere maggiormente i pattern di reclutamento di questa specie. La stima dell’abbondanza e della distribuzione spaziale dell’acciuga è stata effettuata tramite l’utilizzo della metodologia acustica. Inoltre sono stati applicati modelli statistici per descrivere l’habitat potenziale dell’acciuga a diversi stadi vitali (adulti e giovanili). In particolare sono stati analizzati dati di presenza/assenza derivati dai risultati di survey acustici svolti in Adriatico dal 2006 al 2010 accoppiati con dati ambientali derivati da satellite utilizzando i Generalized Additive Models (GAMs). I modelli stimati sono stati utilizzati in maniera predittiva per la costruzione di mappe di “habitat suitability” e per individuare le possibili relazioni con le forzanti ambientali. I risultati che emergono da questo lavoro sottolineano la complessità delle dinamiche di questa specie, specialmente in un ecosistema come il mare Adriatico. Le stime acustiche di biomassa hanno evidenziato le forti fluttuazioni interannuali della popolazione, caratteristica che è largamente osservata in molti altri ecosistemi e altre specie di piccoli pelagici. La distribuzione spaziale dell’acciuga, nel periodo di studio considerato, seguiva un andamento a patch con le densità più alte localizzate nella parte nord del bacino in prossimità della foce del fiume Po. I modelli stimati hanno identificato un certo grado di separazione tra l’habitat degli adulti e quello dei giovanili. L’habitat degli adulti era caratterizzato da aree con un ampio intervallo di profondità, ma con una predominanza per aree mediamente distanti dalla costa; inoltre gli adulti risultavano favoriti dalla presenza di alti livelli di produttività. I giovanili erano associati ad aree più costiere con bassi livelli di produttività; per questi ultimi è stata inoltre osservata una possibile associazione con aree caratterizzate dalla presenza di strutture oceanografiche a mesoscala (fronti, eddies, ecc.). Infine, dallo studio della distribuzione spaziale dell’acciuga (giovanili e adulti) e dei suoi potenziali predatori e dall’analisi degli output dei modelli stimati è stato ipotizzato e discusso un meccanismo che prova a spiegare le dinamiche di reclutamento dell’acciuga in Adriatico.
The Adriatic Sea is one of the most productive basins of the Mediterranean Sea, characterized by a wide continental shelf, strong river inputs and complex circulation patterns. In this unique ecosystem, small pelagic species play a fundamental role for both economical and ecological reasons. A better understanding of how environment can affect the dynamics of these species is crucial for an effective management of the resource following the Ecosystem Based Management (EBM) principles. In this work the spatio-temporal patterns of European anchovy (Engraulis encrasicolus) are investigated with an integrated approach. The main aim is to explore the possible factors that can affect habitat selection of the European anchovy (Engraulis encrasicolus) in the Adriatic Sea putting special emphasis on the study of the juvenile life stages in order to understand better the recruitment dynamics of this species. Acoustic methodology was used to estimate the abundance and the spatial distribution of anchovy. Moreover modeling techniques were applied in order to describe the potential habitat of European anchovy addressing different life stages (adults and juveniles). In particular, Generalized Additive Models (GAM) were applied to presence-absence data derived from acoustic surveys carried out in the western side of the Adriatic Sea from 2006 to 2010, along with satellite environmental data and Regional Oceanic Modeling System (ROMS) outputs. Selected models were used to construct habitat suitability maps over the whole Adriatic Sea and to explore the possible relationships between anchovy distribution and environmental forcing. The results arisen in this work highlight the complexity of anchovy dynamics, especially in a unique ecosystem such as the Adriatic Sea. Anchovy showed strong inter-annual fluctuations as most of small pelagic species do in several other ecosystems in the world. The distribution was patchy over most of the survey areas with the highest densities located in the northern part of the basin in proximity of the Po River mouth. The estimated models identified a certain degree of habitat separation between adults and juveniles. Suitable adult habitats were identified in water with a wide range of depths with a predominance of high productivity areas moderately far from the coastline. Juveniles selected coastal waters with lowmoderate level of productivity and they also seem to be associated with areas potentially affected by an important mesoscale component. From the analysis of the spatial distribution of juveniles, adults and potential predators and the outputs of the estimated models, a mechanism aimed to explain recruitment dynamics of anchovy in the Adriatic Sea is also hypothesized and discussed.

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.

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.

Indian National Centre for Ocean Information Services (INCOIS), Hyderabad, India provides fishery forecast services all along the Indian coast free of cost, referred to as ‘Potential Fishery Zone (PFZ) Advisories’. These services include georeferenced maps showing marked regions where probability of finding sizeable schools of fishes is high. These advisories are provided to help the fisher folks to improve their income from fishing by saving engine fuel for searching and locating fish stocks. Based on 124 controlled fishing experiments carried out in the PFZ and Non-PFZ zones along the Kerala coast during 2008-2012 periods, the present study evidenced that commercially important fishes were abundant in the PFZ, forming richer fisheries compared to the non-PFZ areas. The profit from controlled experiments showed consistently higher values in the PFZ than that in the non-PFZ. The highest profit during the entire controlled fishing experiments was obtained when the catch was dominated by relatively high-priced fishes such as tunas, carangids, seer fishes and mackerel. Indian oil sardine was the major single species obtained during the Northeast Monsoon (November-February), whereas, Indian mackerel dominated during the Southwest Monsoon (June-October) and Spring Intermonsoon (March – May) periods. Anchovies were found to dominate only in two fishing experiments in the entire study period. The analyses of catch data of the small pelagic fishes of interest (Indian oil sardine, Indian mackerel and Commerson’s anchovy) showed that the PFZ advisories better predicted the catches of Indian oil sardine during the Northeast Monsoon (November- February) and Indian mackerel during the rest of the period. Conversely, the catch data of controlled experiments showed that PFZ advisory has less efficiency to support the exploitation of anchovies. Attempts have been made to outline the recurrent PFZ along the Kerala coast based on the advisories generated for the study period (2008-2012). Altogether 432 PFZ advisories were digitised and month-wise repeat PFZs have been demarcated. In general, most of the very prominent recurrent PFZs were found within the 50m depth contour. The highest number of recurrent PFZs was in December, January and February. On the other hand, the lowest number of recurrent PFZs was found in April, May and June. Plankton components in the diet of Indian oil sardine, Indian mackerel and Commerson’s anchovy based on fortnightly fish samples analysed during a year period are presented. Coscinodiscus, Nitzschia, Pleurosigma and Thalassiosira were found in the gut of Indian oil sardine almost throughout the year, whereas microzooplankton was mostly dominant only during the October – December period. Coscinodiscus and Tintinids were predominant in the gut of Indian mackerel throughout the year. Furthermore, Thalassiosira, Ceratium, Dinophysis, Protoperidinium, Pyrophacus and copepods were also found in the gut of Indian mackerel almost throughout the year. The dominant value index showed the dominance of phytoplankton, microzooplankton and copepods in the diet of Indian mackerel throughout the year, indicating their almost equal preference for both phytoplankton and zooplankton. The food items in the gut content of Commerson’s anchovy showed characteristic difference from both Indian oil sardine and Indian mackerel and found to be a zooplankton feeder predominantly feeding on copepods, fish eggs, ostracods, lucifers and tintinids. The environmental observations based on monthly field sampling carried out in two locations (10m and 20m depth contours) situated off Kochi are presented. During seven out of nine observations, PFZ bands were observed around 10m location. High values of chlorophyll (> 3mg m-3) were found in August, September and October, which could be attributed to the combined effect of Cochin backwater influx and upwelling. The seasonal evolution of hydrographical parameters showed significantly higher concentration of nutrients and chlorophyll during the Southwest Monsoon period compared to the rest of the sampling. The chlorophyll concentration was found to be significantly higher in 10m location (PFZ) compared to the 20m location (non-PFZ). The status of the Length-Weight Relationship (LWR) and condition factor of Indian oil sardine, Indian mackerel and Commerson’s anchovy along the Kerala coast is presented. The LWR of Commerson’s anchovy is the very first detailed report from this region. LWR and condition factor of Indian mackerel and Oil sardine were not significantly different from the values reported in the historical studies, indicating that these parameters are not affected significantly by the expected long-term environmental changes. The results of the growth and maturity studies of the small pelagic fishes of interest have been discussed. The analyses were based on a fortnightly sampling carried out in two major landing centres during 2010 – 2011 periods. The maximum life span of Indian oil sardine was estimated to be 2.63 years. Two peaks of recruitment of juveniles to the fishery were observed; a large peak during July - August and a small peak in February - March. The length at first maturity was calculated as 15.7 cm while the length at first capture was 15 cm, suggesting that the peak exploitation of the species occurs before they attain sexual maturity. Comparison of the length at first maturity of oil sardine reported in historical studies with the present study shows that only minor variation exists between the two. The life span of Indian mackerel is estimated to be 2 years. The recruitment pattern showed the presence of mature mackerel all year round. However, two recruitment peaks of Indian mackerel were evident; June to August and February to March with the highest recruitment in July (28%). Probability of capture of mackerel showed higher values (22.43 cm) than the length at first maturity (17.7 cm) indicating that their peak exploitation occurs after attaining sexual maturity. Long-term changes in length at first maturity of Indian mackerel indicated a prominent decrease in length in the recent decade, probably indicating a response to the long-term environmental changes. The present study on the growth and maturity parameters of Commerson’s anchovy forms the first such study from Indian waters and the life span of the species was found to be 3.06 years. Two recruitment peaks of Commerson’s anchovy were observed; first during February – March and a second during June - July. The probability of capture of Commerson’s anchovy showed that they get exposed to maximum exploitation after they attain maturity. Lack of past data on length at first maturity of Commerson’s anchovy from the Indian coast hindered a possible comparison with the present data.

The ecosystem approach to fisheries management (EAFM) is a new paradigm in fisheries management, that incorporates multi-species, habitat, environmental, and socio-economic elements. Within the scientific community and on the political agenda, EAFM has been recognised as a powerful approach to assist with the management of depleted stocks. However, a clear consensus on how this approach should be implemented in practice is still lacking. The primary aim of this thesis was to apply an EAFM to pelagic fisheries in the Portuguese Continental shelf ecosystem (PCSE). Portuguese pelagic fisheries were chosen as a case study because its main resource sardine has considerably declined in the last two decades. To achieve this aim, a set of methodological approaches to EAFM were used in the context of this fishery. These methodological approaches included spatial analysis, ecosystem modelling (Ecopath with Ecosim) and statistical/indicators approach. This research advances the application of the EAFM in the Portuguese pelagic fishery by, developing tools to support the management of the fishery and by deepening understanding of the PCSE and sardine dynamics. The key findings showed that trophic interactions followed by fishing were the main drivers of PCSE while a rise in sea surface temperature (SST) followed by fishing had the largest impact on sardine decline. This research highlighted that the management besides fishing restrictions should consider other factors that turn out to be important drivers of future sardine change. They are a rise in SST, trophic interactions, especially between sardine and predators of sardine eggs, and the possibility of regime shift occurrence. Moreover, results demonstrated that the pelagic fishery has conflicting objectives between conservation and fisheries and spatial analysis can support their addressing through the assessment of the trade-offs between them. Briefly, this research can support strategic management advice for the pelagic fishery in the PCSE in the context of the EAFM.

Deep-sea fishes are one of the very interesting groups of animals that live in the darkness that is below the epipelagic or photic zone of the ocean. The deep-sea ecosystem is the largest habitat on Earth, covering 300 x106 km 2 that comprise about 63% of the earth’s surface, and is the main reservoir of global biodiversity (Smith et al., 2008). However, the deep-sea is the least productive part of the oceans, although some high biomass concentrations of fishes are found on the topographic features like seamounts, mid-oceanic ridges and continental slopes (Norse et al., 2012). Deep-sea fishes can be placed into mesopelagic, bathypelagic and benthopelagic categories, depending upon their depth preferences. Mesopelagic and bathypelagic species are true pelagic fishes, generally of small size even at their adult stage and unlikely to be exploited on a commercial scale (Valinassab et al., 2007). Lantern fishes (Myctophidae) and cyclothonids (Gonostomatidae) are the common mesopelagic fishes that live below the photic zone extending to 1000 m depth and they, along with bathypelagic fishes that live below 1000 m, are highly adapted to live in an environment where food is scarce. The deep-sea fishes from mesopelagic and bathypelagic depths have many unique and interesting adaptations for living in the extreme deep-sea environment.

Today, when so much is being said and written about our interests in the ocean, it is particularly important to retain our perspective. Of course, the present pattern is likely to change, although how rapidly or dramatically we do not know. What is certain is that we shall use the ocean more intensively and in a greater variety of ways. Our greatest need is to use it wisely. The general goal of ecological research to which marine biology makes an important contribution, is to achieve an understanding and to tum to our advantage all the biological processes that give our planet its special character. Marine biology is focussed on the problems of biological production, which are closely related to problems of production in the economic sense as well. Our most compelling interest is often narrower. It lies in ocean life as a renewable resource, primarily of protein-rich foods and food supplements for our domestic animals and to us and of secondary materials and drugs. At this point, it is time to inquire about the future expectations from the ocean which is or three dimensional environments provides protein rich seafoods alternate to agricultural products from land. Other than this, nonliving resources such as minerals, oil, medicinal properties of the various marine organisms etc. are resources we collect from the sea. The present harvest of marine living resources from the world oceans is about 87 million tonnes in 1996 (Anon., 1998). More than 90% of this harvest is finfishes: the rest consists of whales, crustaceans, molluscs and other invertebrates. It is now a common knowledge that fish is one of the few major foodstuffs showing an increase in global production that continues to exceed the growth rate of the human population. This increase has been accompanied by changing patterns of use. Although some products of high unit values that includes luxury foods, such as shellfish, have maintained or even enhanced their relative economic importance and the trend is that moderate catch is used directly for human consumption and the bulk is reduced to fishmeal for animal feed and manure. There are also large aggregations of pelagic animals that live further down and are associated particularly with the "Deep Scattering Layer" (DSL). the sound-reflecting stratum observed in all oceans which has vast potential to provide exploitable resources. 2

The oil sardine Sardinella longiceps and the Indian mackerel Rastrelliger kanagurta are tropical coastal and small pelagic fish, forming massive fisheries in India. They are governed by the vagaries of ocean climatic conditions. Until the mid 1980s, the oil sardine formed fishery almost exclusively along southwest coast, and did not form fishery along southeast coast. However oil sardine emerged as a major fishery in the last 30 years, and the average annual catch along Tamil Nadu coast alone recorded more than 1 lakh tonnes in the last five years. The Indian mackerel also formed a major fishery along southwest coast and a minor fishery along southeast coast. Similar to the oil sardine, the mackerel also is contributing a major fishery in the last 30 years along the southeast coast. It is not clear whether stocks of Sardinella longiceps and Rastrelliger kanagurta in the two regions are the same, and how similar or dissimilar is their spawning and diet. To understand this, samples of the two species were collected from Kochi (representing the southwest coast) and Chennai (representing the southeast coast). The study has attempted a comparison between the fishery as well as biological parameters namely morphometrics, maturity patterns, diet composition of the two species along the Kochi and Chennai coasts during 2010- 2012. The study revealed that there has been considerable increase in the landings of both the species along Kochi and Chennai coasts especially from the mechanised sector when compared to previous years. The analysis of morphometric characters showed that Sardinella longiceps and Rastrelliger kanagurta occurring along Kochi and Chennai coasts belong to a single stock. S. longiceps of both the coasts spawns once in a year lasting from June to September. The peak spawning period of R. kanagurta along Kochi was during June-August and along Chennai, during April-June. The length at first maturity of mackerel showed much variation during the period and was lower than that reported during the period prior to the 90s. The absolute fecundity was within the range of 4,072-63,475 and 10,116-1, 84,350 eggs in the case of S. longiceps and R. kanagurta respectively along both the coasts. The diet of S. longiceps consisted of phytoplankton as the major share in both the coasts, and the major phytoplankton species in the diet were almost the same. The diet of R. kanagurta was much diverse with phytoplankton and zooplankton, and in this species too, the major species in the diet were almost the same in the two locations. From the results obtained in the present study, no significant differences could be observed in the spawning and diet composition within each of the two species between the two locations. The results further show that the two species have adapted to the conditions and have established their populations along the southeast coast of India.

Oceanic pelagic shark species are under threat worldwide as fishing effort increases and they are taken as both targeted and bycatch. It is widely recognized that the life history characteristics of sharks make them inherently susceptible to overexploitation and as a result many shark-directed fisheries have collapsed. It is therefore essential that good-quality data are collected and analyzed in order to provide fisheries managers with the right information to manage these species sustainably. South Africa has a pelagic longline fishery which includes tuna-, swordfish-, and shark-directed vessels. This study analyzed logbook (1998 – 2010) and observer data (2002 – 2010) provided by the Department of Agriculture, Forestry and Fisheries in order to assess the catch composition and standardized catch-per-unit-effort (CPUE) of sharks captured as both targeted catch and bycatch. The study area consisted of four zones moving east of the 20°E meridian: the Agulhas Bank (20°E – 24°E), South Coast (25°E – 29°E), East Coast 1 (30°E – 32.8°E), and East Coast 2 (32.9°E – 36.5°E). The majority of fishing effort targeted at tuna was focused on the Agulhas Bank and consisted of foreign vessels which operated over the winter months, whereas local vessels targeted swordfish with consistent year-round effort along the upper east coast. Sharks made up 13% of total catches according to logbook data and catch composition was dominated by blue shark (Prionace glauca) and shortfin mako shark (Isurus oxyrinchus). Observer data identified a larger number of shark species than shown by logbooks, and notably, the crocodile shark (Pseudocarcharias kamoharai) made up 22.5% of shark bycatch on swordfish-directed vessels operating along the upper east coast. In addition, the observer data showed that although blue and mako shark dominated catches in the Agulhas Bank and South coast zones, carcharhinid sharks were more prevalent further east. Generalized linear models explained 54% of the variation in CPUE of shark bycatch, with year and target species being the two most important explanatory variables. The standardized CPUE index based on logbook data suggested a slightly increasing shark abundance trend between 1998 and 2010, but conversely, the index based on observer data suggested a decline between 2002 and 2010. Assuming that the observer data best reflected the actual CPUE trend (i.e. a declining trend), the increasing trend shown by logbooks over the same period most likely stems from initial under-reporting of shark capture events by skippers, followed by improved reporting in later years, thus masking the declining trend. Catch by target species revealed that swordfish vessels caught significantly more sharks per 1000 hooks than tuna vessels. The shortfin mako shark was one of the most common bycatch species, and also the primary target species of the shark-directed fishery. Generalized linear models of shortfin mako shark CPUE using the delta method produced similar trends than models of total shark bycatch; i.e. trends based on logbook data appeared stable but observer data showed a declining trend over time. Shortfin mako sharks were more abundant in the Agulhas Bank and South coast zones than along the East coast. A total of 817 shortfin mako shark samples were collected onboard a South African shark-directed pelagic longline vessel operating out of Cape Town and by the KwaZulu-Natal Sharks Board bather protection nets, set close inshore. Sharks collected inshore (from nets) were significantly larger than those collected offshore. More males than females were collected from the nets (2.3 males : 1 female), whereas the ratio for offshore samples was 1.1 : 1. Age and growth parameters were estimated from 89 sectioned vertebral samples consisting of 43 females and 46 males ranging in size from 90 cm to 299.4 cm fork length (FL). Annual band-pair deposition was assumed and growth was analyzed by fitting 3-parameter von Bertalanffy and Gompertz growth models. Parameter estimates for the Gompertz model were: K = 0.152 year¯¹ for males and 0.127 yearˉ¹ for females; L0 = 85 cm; L∞ = 295 cm for males and 315 cm for females; and longevity was 17 and 21 years for males and females respectively. Estimates for the von Bertalanffy model were: K = 0.08 yearˉ¹ for both sexes; L0 = 85 cm; L∞ = 354 cm for males and 321 cm for females; and longevity was 34 and 31 years for males and females respectively. Using these data, age and length at 50% maturity were calculated at 7 years and 199.1 cm FL for males, and 14 years and 252.8 cm for females. Litter size was in agreement with previous studies (9 to 14 pups). The gestation period was not estimated but parturition may be in late winter to spring. The stomach contents of 817 sharks showed that shortfin mako sharks are opportunistic feeders; elasmobranchs dominated in stomachs collected from sharks caught in nets near the shore (%F = 63.54%) whereas shark stomachs collected from the offshore contained mainly teleosts (70%). Length-frequency analyses revealed that large and reproductively active shortfin mako sharks were more common along the upper east coast and in the inshore environment, whereas juveniles and subadults preferred the oceanic environment, particularly over the Agulhas Bank and South Coast zones. The findings from the present study are a significant step forward towards developing a management strategy for protecting shortfin mako sharks in the South West Indian Ocean region.
Thesis (M.Sc.)-University of KwaZulu-Natal, Westville, 2013.