Dissertations / Theses on the topic 'Bycatches (fisheries)'

The panga, Pterogymnus laniarius (Cuvier, 1830), is a South African endemic sparid fish species. On the Agulhas Bank, South Africa it is a commercially important species, caught as bycatch in the hake directed trawlfisheries and targeted by offshore hook-and-linefishers. Recently there has been considerable interest shown in directing further fishing effort on this species. The lack of a suitable management procedure for teleost bycatch in South Africa was the principal reason for undertaking this study. This thesis investigates aspects the panga's life history, particularly those aspects that have management implications. A full knowledge of this species' distribution and abundance was necessary as this could highlight the existence of any nursery areas, ontogenetic migratory patterns and areas of high spawner biomass. The derived parameter estimates were then included as inputs into stock assessment models to determine the status and productivity of the resource. Growth studies based on sectioned sagittal otoliths revealed that the panga was a relatively slow growing fish with ages of 16 years being recorded. Growth was best described by the von Bertalanffy growth model as Lt=379.4(1-e⁻°·¹³⁽t ⁺ ¹·⁷⁸⁾). Total, natural and fishing mortalities were estimated at 0.36 year⁻¹, 0.28 year⁻¹ and 0.08 year ⁻¹, respectively. Detailed histological examination of the gonads revealed that panga is a late gonochorist, males and females maturing after a non-functional intersexual stage. Females mature at approximately 200 mm fork length or 4 years of age. Reproduction occurs throughout the year although there is a slight peak in winter. Gametogenesis was found to be similar to that of other sparid fishes and marine teleosts in general. The panga feeds predominantly on crustaceans with a distinct ontogenetic shift in feeding habits. Juvenile fish feed predominantly in the water column on mysids after which they move to the benthos. Subadult fish feed principally on ophiuroids and amphipods. Adult fish remain on or near the benthos, feeding predominantly on crabs, and on polychaetes, ophiuroids and fishes to a lesser extent. Several aspects of the panga's biology contribute to its ability to sustain a higher fishing pressure than other sympatric sparid species. These include its late gonochoristic reproductive style, protracted spawning season, maturation before recruitment and preference for soft substratum prey that enables it to utilise large areas of the Agulhas Bank. The panga's longevity, slow growth and low natural mortality rate, however, mitigated against these factors and were considered in the stock assessments. A heterogeneous Geographical Information System (GIS) was developed to analyse the distribution and abundance patterns of the panga. The GIS developed in this thesis makes a significant contribution towards the development of a South African Fisheries Information System to analyse and manage fish resources in general and bycatch resources in particular. The GIS developed in this study combines statistical Generalized Additive Modelling and standard GIS methods. Analysis of fourteen biannual fishery independent biomass surveys, disaggregated by life history stage, revealed that a nursery area for immature fish (<23 cm TL or < 4 years of age) exists on the Central Agulhas Bank. After sexual maturation, approximately 40% of the biomass migrated eastwards, colonising large areas of the Eastern Agulhas Bank.ilie location of the nursery area appears to be a result of the pelagic eggs and larvae being advected towards the coast in an anti-cyclonic gyre, stemming off the Agulhas current and later deposited over the Central Agulhas Bank. The weak bottom currents on the Central Agulhas Bank prevented juvenile loss to the Benguela system. The eurytopy of adult fish to various physical variables such as temperature, dissolved oxygen and stronger currents enabled it to reduce conspecific competition and migrate eastwards with distribution primarily determined by depth. Relative biomass estimates revealed a gradual increase in biomass of 5.5% per annum between 1988 and 1995. Predictions from yield-per-recruit, biomass-per-recruit and spawner biomass-per-recruit analyses showed that there was scope for further exploitation. A FSB₅₀ fishing strategy was considered to be the most appropriate fishing strategy as it did not reduce the spawner biomass-per-recruit to less than 50% of unexploited levels. Effort control was considered the most effective management tool as the age-at-50%-selectivity occurred after age-at-sexual maturity and releasing undersized fish was undesirable due to heavy mortalities resulting from severe barotrauma. The panga resource was also assessed using an age-structured production model. The values for the free parameters of the model were estimated using biomass indices derived from fishery-independent trawl surveys. Although the data were fairly uninformative about the productivity of the resource, the results indicated robustly, that the population has recovered from low levels in the mid-1970's and could sustain higher levels of fishing intensity. Risk analysis calculations were used to assess the sustainability of different catch scenarios. The level of sustainable catch was found to be sensitive to the selectivity pattern of the gear utilised. Both stock assessment methods used in this study to investigate the status of the panga resource showed that the resource could theoretically sustain higher catches. It was found that although the stock could be harvested using available fishing methods, the sympatry of this species with other commercial species was of concern as the latter would form a significant bycatch in a panga directed fishery. The failure of current harvesting methods to address the bycatch problem highlights the management problem in South Africa and stresses the need for creativity by both scientists and fishers in designing new and improved methods for selectively harvesting bycatch fish resources. Considering that no suitable method is currently available to fish the panga stock in a directed fishery the fishery should be managed as status quo until some suitable and efficient gear is developed.

The silky shark Carcharhinus falciformis forms the primary elasmobranch bycatch in tuna purse seine fisheries using fish aggregating devices (FADs) in all of the world’s tropical oceans. Its life-history traits of slow growth, late maturation and low fecundity make it vulnerable to over exploitation, as is apparent from historical bycatch trends. Very little is known about the associative behaviour of this species with floating objects, information which is essential in formulating effective mitigation and management measures. This study aims to address this knowledge gap through the use of various electronic tagging techniques in conjunction with dietary analysis. Dietary data were collected from 323 silky sharks incidentally caught at FADs. Approximately 40 percent of the diet consisted of prey associated with FADs while the remaining 60 percent were non-associated species of crustaceans, cephalopods and fishes. These results suggest that the associative behaviour is not primarily driven by trophic enhancement, but is likely a combination of predator avoidance, social interactions and feeding. Fine-scale behavioural data from silky sharks associated with drifting FADs were collected through the use of acoustic telemetry techniques. Acoustic tags were implanted into 38 silky sharks (69- 116 cm TL) at eight FADs. FADs were equipped with satellite linked acoustic receivers and abandoned to drift freely. Presence/absence and swimming depth data were telemetered via the Iridium satellite system. A total of 300 d of behavioural data were collected from 20 tagged individuals. Individuals remain associated with the same FAD for extended periods (min = 2.84 d, max = 30.60 d, mean = 15.69 d). Strong diel patterns were observed in both association and swimming depth. Typically individuals moved away from FADs after sunset and return later during the night, then remain closely associated until the following evening. Vertical behaviour also changed around sunset with sharks using fairly constant depths, within the upper 25 m, during the day and switching to rapid vertical movements during the night, with dives in excess of 250 m recoded. Broader scale movement behaviour was investigated using pop-up archival satellite tags (PSATs). Tags were deployed on 46 silky sharks (86-224.5 cm TL) for a total of 1495 d. Light data were used to calculate geolocation estimates and reconstruct the sharks’ trajectories. Movement patterns differed between animals and according to deployment duration. Several extensive horizontal movements were observed, with an average track length of 3240 km during an average tag deployment of 44.02 d. Horizontal movement patterns were found to correlate very closely with drift patterns of FADs. Consequently, it appears that the movement behaviour of juvenile silky sharks is strongly influenced by the movement of drifting FADs in this region. Ghost fishing of silky sharks through entanglement in FADs was also investigated using data derived from PSATs as well as underwater visual censuses. Thirteen per cent of the tagged sharks became entangled in FADs and entangled sharks were observed in 35 percent of the 51 FADs surveyed. Using this information in conjunction with estimated time that sharks remained entangled in the FAD (from depth data from PSATs), and scaling up according to estimates of FAD numbers, it was found that between 480 000 and 960 000 silky sharks are killed annually in this manner in the Indian Ocean. Subsequent management measures in this region prevent the deployment of FADs with netting that could lead to entanglement. Overall, floating objects appear to play a significant role in the juvenile life stages of silky sharks in this region. While their association with floating objects is clearly advantageous in an evolutionary sense, under current tuna fishery trends, this behaviour is certainly detrimental for the population.

Bycatch is one common aspect of fisheries worldwide and recognized as one of the significant impacts over protected and threatened species, chondrichthyans among them. This thesis aims to help mitigate and provide tools to aid the conservation of chondrichthyans. In the first data chapter I developed a model of risk assessment to quantify relative vulnerability of the group based on spatial overlap of natural distributions and fishing events and related to the species resilience. In this study I used commercial fisheries data provided by the Australian Fisheries Management Authority and applied the method to bycatch chondrichthyans and target species. Results were consistent with IUCN status of the species, including cases with regional differences from global status. In the second data chapter, spatial and seasonal distribution of chondrichthyan bycatch events in southern and eastern Australia were analysed. Results indicate differences in rates between gears and also the importance of oceanographic factors to bycatch ratio as well to catch per unit of effort whilst diversity is more influenced by gear type. The spatial analyses also indicated hotspots for bycatch in the Great Australian Bight and Bass Strait. In the third data chapter, I estimated the age, growth and reproductive parameters of the Eastern Fiddler Ray Trygonorrhina fasciata and the Sydney Skate Dipturus australis, two endemic species often caught as bycatch. Age estimates, based on vertebrae bands, were used to calculate growth parameters, which were similar to related species. Moreover, based upon the somatic and gonad indexes, reproductive biology information of these species is provided. In the fourth data chapter I describe the diet and estimated trophic levels of these batoids. Results indicated a diet consisting largely of crustaceans and place the species within the range of trophic level for closest relatives and support their status as mesopredators on the region.

Over the past decade there has been global concern about the bycatch of seabirds, turtles and sharks in fishing operations, in particular longline and trawl fisheries, which have been widely held responsible for their declining population s and threatened conservation status. This thesis addresses the issue of bycatch in a holistic manner, taking into account that species, whether they be target or non-target, do not exist in isolation from each other and their environment. South African fisheries incidentally catch approximately 21 000 seabirds, 165 turtles and 43 000 pelagic sharks per year, including 21 Endangered species. Decreasing CPUE and size-frequency data for Blue Prionace glauca and Short- finned Mako Sharks Isurus oxyrinchus caught in the large pelagic longline fishery suggests exploitation of these species is unsustainable. A decreasing trend in the biomass index was also observed for the Yellow-spotted Catshark Scyliorhinus capensis and the Biscuit Skate Raja. straeleni. An argument for the likelihood of fisheries mortality contributing to the slower than expected turtle population recovery rates is presented, which is supported by results from satellite tracking of Leatherback Turtles Dermochelys coriacea indicating a high degree of overlap with fishing effort. Satellite tracking of Black-browed Thalassarche melanophrys and White-capped T. steadi Albatrosses reveal striking differences in their foraging patterns and presents evidence that Black-browed Albatrosses, in particular, forage to a large extent on natural prey, despite the availability of discards from fishing vessels in the Benguela. Therefore, given the high albatross mortality in the trawl fishery, the benefit of a management decision to limit discarding as a mitigation measure is likely to outweigh the disadvantage of reduced food supply. Reducing bycatch is dependent on the development of effective and relatively inexpensive methods which do not impact on target catches and/or other vulnerable species. In the demersal longline fishery, two methods of optimising line sink rates to reduce seabird bycatch were investigated: increasing mass of weights and decreasing the spacing between weights. This study indicated that while the target species is unlikely to be affected by increased weighting, other vulnerable species of fish and sharks may be affected. Other mitigation experiments investigated line sinking rates and the use of circle hooks in pelagic longline fisheries. The implications of night setting on Swordfish Xiphias gladius catches, fishery closure during full moon and the appropriateness of the international standard 5% fin to trunk ratio for the South African fishery, were also investigated. Lastly, the spatial and temporal overlap of catches of seabirds, turtles and sharks were investigated through a conservation planning exercise using MARXAN and potential areas for closure identified.

Lake Erie supports one of the world's largest freshwater commercial fisheries. Bycatch has become a concern in current fisheries management. This study focused on four species in Lake Erie that include two major commercial and recreational species, walleye (Sander vitreus) and yellow perch (Perca flavescens); an invasive species, white perch (Morone americana); and an endangered species, lake sturgeon (Acipenser fulvescens). The analyses were based on two datasets, the Partnership Index Fishing Survey (PIS) data and the commercial gillnet logbook data. The bycatch of walleye, yellow perch and white perch was predicted by a delta model developed on the PIS data. Discards were estimated as the difference between predicted bycatch and landed bycatch. Results highlighted bycatch and discard hotspots for these three species that have great management implications. Three classification tree models, a conditional inference tree and two exhaustive search-based trees, were constructed using the PIS data to estimate the probability of obtaining lake sturgeon bycach under specific environmental and gillnet fishing conditions. Lake sturgeon bycatch was most likely to be observed in the west basin of Lake Erie. The AdaBoost algorithm was applied in conjunction with the generalized linear/additive models to analyze catch rates of walleye, yellow perch and white perch. Three- and five-fold cross-validations were conducted to evaluate the performance of each candidate model. Results indicated that the Delta-AdaBoost model yielded the smallest training error and test error on average. I recommend the Delta-AdaBoost model for catch and bycatch analyses when data contain a high percentage of zeros.<br>Master of Science

Marine vertebrate species face unprecedented and ever increasing pressures as a result of human activity, primarily fishing, in the global oceans. One area of growing concern has been for the impacts of small-scale fisheries on these species. Over the past decade it has become increasingly clear that these under-studied fisheries have sizeable levels of catch and bycatch of many threatened and endangered species of sea turtles, seabirds and small cetaceans. This thesis presents a collection of chapters that investigate aspects related to the interactions of small-scale fisheries with threatened marine vertebrates. We identify sizeable rates of bycatch of small cetaceans and seabirds for multiple small-scale longline and gillnet fisheries in both Peru and Ecuador. Catch rates of small cetaceans by the Peruvian small-scale driftnet fleet are estimated to exceed 10,000 dolphins and porpoises annually. A trial of acoustic alarms (pingers) in this same fishery showed a 37% reduction in small cetacean bycatch while not reducing target catch and represents a promising bycatch mitigation measure. Seabird bycatch was also found to be high in both longline and gillnet fisheries and included a wide range of seabird species including the critically endangered waved albatross (Phoebastria irrorata). Through post-capture satellite tracking of loggerhead turtles (Caretta caretta) we show that these turtles are present in pelagic waters off the coasts of Peru and Chile for extended periods during which they are at risk of repeat interactions with small-scale longline fisheries operating throughout their foraging habitat. Through scan and focal sampling of the endangered marine otter (Lontra felina) we also show that otters making den sites in human fishing communities face additional risks due to entanglement in fishing gear or interactions with feral animals but, if properly managed, these sites could serve as stepping stones for marine otters along the coast. The results presented here, gathered using a wide range of techniques, including onboard observer and shore-based monitoring, satellite tracking, bycatch quantification, and bycatch mitigation experiments, represent an attempt to better characterize and quantify the interactions of small-scale fisheries with threatened marine vertebrates toward identifying solutions that can lead to sustainable fisheries and populations of these protected marine species.

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.

Some of the key elements to assess the status of any wildlife population in a given geographical area are the levels of recruitment, survival and mortality. Whilst most of the information on marine turtles has been obtained from nesting sites, turtles spend most of their lives at sea. The conservation status of marine turtles in the southeast Pacific is poorly documented. This is particularly true for countries like Peru, where nesting events are very rare, although five species of turtles from populations from all over the Pacific basin, use these waters as foraging grounds. Little information exists on the threats to turtle populations in foraging areas or the magnitude of these impacts. Small-scale fisheries are a globally important economic activity serving as a source of food and employment for ca. 1 billion people; however we show that they also have serious impacts on marine turtle populations from all over the Pacific basin in the form of incidentally captured marine turtles. The five chapters that constitute this thesis are intended to increase our understanding of small-scale fisheries impacts on this taxon during their aquatic life stages. This work focuses on describing these fisheries, their impacts on marine turtles and proposes methodologies to monitor and assess the level of bycatch from small-scale fisheries. We also discuss alternative ways to prevent fisheries interactions and promote the involvement of artisanal fishermen in the southeast Pacific in implementing conservation solutions.

Conventional fisheries management approaches have been shown, in many instances, to have been ineffective in dealing with complex conservation concerns such as bycatch. Greater considerations for broader-scale and holistic approaches, as proposed by the 'Ecosystem Approach to Fisheries' (EAF) and the 'balanced harvesting approach', are beginning to challenge some of the negative misconceptions around bycatch, especially in small-scale fisheries. The need for a more holistic approach to fisheries management, particularly in small-scale fisheries, in South Africa is highlighted by its commitment to an EAF and the recent Small-Scale Fisheries Policy, for which the Marine living Resource Act of 1998 provides the legal framework to implement. The case study of the Olifants estuary small-scale traditional gillnet fishing community, located on the west coast of South Africa, provides a particularly relevant example of a complex fishery requiring a holistic approach. Current regulations prohibit the harvesting or retention of any bycatch species. Fisheries management worldwide and in South Africa, generally view gillnet fisheries as destructive, due to the occurrence of bycatch and the fact that many of these bycatch species are considered overexploited, which has led to numerous attempts over the years to phase out the Olifants gillnet fishery. The purpose of this study was to, firstly, use an EAF framework to contextualise the issue of bycatch in the Olifants gillnet fishery, and secondly, to identify the relative contributions of all fisheriy sectors to the four key selected linefish species caught as bycatch by the fishery. An extensive review and analysis of available secondary data, as well as primary data collected for this study, have estimated, with acknowledged limitations, the magnitude of the exploitation by all known fisheries of these species. Key information from small-scale fisher interviews and community-monitoring data highlight the capture rate of key linefish species by this fishery. This is echoed by recent landings for 2012 indicating the relative contribution of the national beache seine and gillnet fishery to the overall catch of (Elf [Pomatomus saltatrix] - 26.94%; Silver Kob [Argyrosomus inodorus] - 0.88%; White Stumpnose [Rhabdosargus globiceps] - 1.05% - excluding the recreational sector). A significant finding of this study is the substantial levels of cross-sectorial exploitation of Silver Kob and White Stumpnose, and to a somewhat lesser extent Elf and White Steenbras.

Mestrado em Biologia Marinha<br>Deep-sea resources have been increasingly exploited, and due to that, several ecosystems and species have been considerably affected. Deep-water sharks populations have been of the most disturbed by practices of unselected fisheries, bycatch and discard, mainly due to their low commercial value. Those practices make deep-water sharks very vulnerable to overfishing given their life-history traits, increasing their extinction risk. With the prohibition of the direct fishery, and implementation of quotas and TACs (Total Allowable Catches) regarding the deep-sea shark landings, the official landings have dramatically decreased after the 1990s. However, the IUU (Illegal, unreported and unregulated) catch has exponentially increased. With the analysis of catch per unit effort (CPUE), the depths, and the mean weight of the individuals over the years for each one of the nine most caught species in the Azores, we produced a descriptive analysis of the effect of fisheries in those species. The results show that some of these species have been suffering from a great fishing pressure, and their populations will be greatly affected in the near future if drastic measures are not taken when it comes to managing their long term sustainability.<br>Os recursos do mar profundo têm sido cada vez mais explorados, e devido a isso, vários ecossistemas e espécies têm sido gravemente afectados. As populações de tubarões de profundidade são das mais perturbadas, especialmente pelas práticas de pesca não seletivas, capturas acessórias e descarte, principalmente devido ao seu baixo valor comercial. Estas práticas tornam os tubarões de profundidade muito vulneráveis à sobrepesca dadas as suas características de história de vida, aumentando assim o seu risco de extinção . Com a proibição da pesca direta, e a implementação de quotas e TACs (Capturas Totais Admissíveis) na pesca de tubarões de profundidade, as capturas oficiais têm vindo a decrescer. No entanto, as capturas não reportadas têm vindo a aumentar exponencialmente. Com a análise da captura por unidade de esforço (CPUE), da profundidade, e do peso médio dos indivíduos ao longo dos anos de cada umas das 9 espécies de tubarões mais pescadas nos Açores, conseguimos fazer uma análise descritiva do efeito das pescas nestas espécies. Os resultados mostram que algumas destas espécies têm vindo a sofrer uma grande pressão por parte da pesca, e que as suas populações serão gravemente afetadas num futuro próximo se não forem tomadas medidas drásticas no que toca à gestão da sua sustentabilidade a longo prazo.

Firstly, I am very grateful to Birdlife International for the MSc scholarship. I am also very grateful to Professor Peter Ryan of the FitzPatrick Institute of African Ornithology, University of Cape Town, for agreeing to supervise this project and for his guidance, insights and comments on the write-up. I am grateful to Sarah Saldanha, for all the support during this MSc. Many thanks also to Dr Ross Wanless, Dr Rima Jabado and Ruben Rocha for all support, guidance and advice. I want to thank a lot Andy Angel for their accommodation and all support in South Africa. I am grateful to all the UCT staff and BirdLife Senegal Staff for all the support during this study. Many thanks to my family for all the encouragement and support. I want to thank to all the Cabo Verde fishers for their willingness to share their knowledge and experience. Finally, many thanks to the Conservation Biology class of 2019, for all their support.

Thousands of floating objects, known as drifting fish aggregating devices (dFADs), are released every year by commercial tropical tuna purse seine vessels in the three equatorial oceans to aggregate tuna and increase catch. The escalation in the number of dFADs deployed over the last three decades has caused changes in fishing effort that are poorly reflected in traditional indices of purse seine effort and catch per unit of effort (CPUE). In addition, concerns have been raised regarding the impacts of such high numbers of dFADs being deployed on both catch and bycatch species. I studied two aspects of dFAD deployments in order to clarify how dFADs are used by purse seiners and how they affect the magnitude of bycatch. My specific goals were to determine how often purse seine vessels fish on the dFADs they deploy and how regional dFAD density affects the magnitude of bycatch and catch. I analyzed commercial data, independent observer data, satellite buoy trajectories, and estimated floating object densities from the French tropical tuna purse seine fisheries in the Atlantic and Indian Oceans to examine these relationships. My results indicate that only 2.7-20.6% of dFAD fishing sets were on the dFADs that French purse seiners deployed over the period 2007-2013. Although this percentage increased over time, such a low percentage suggests that French vessels do not primarily increase CPUE by using the dFADs they deploy for directed fishing. If French purse seiners are not mainly using their own dFADs in this manner, then using a metric of nominal effort based on individual vessel activity is unlikely to produce reliable CPUE estimates for the fishery. While information about how often purse seiners fish on their own dFADs could be incorporated into indices of fishing effort, it may be just as important, if not more so, to quantify the collective component of dFAD releases for overall fishing effort. The results for the second objective showed that average dFAD density had a relatively weak relationship with total bycatch biomass. There was no statistically significant effect on mean total bycatch biomass, but dFAD density was related to heteroscedasticity in bycatch biomass. In particular, there was a significant negative relationship between dFAD density and the upper quantiles of the bycatch biomass distribution, suggesting that dFAD density determines the upper bound for bycatch biomass caught per set. These relationships were not constant across species, however, as the five most prevalent bycatch species (i.e., those caught in the greatest number of sets) showed a mix of positive, negative, or no relationships to dFAD density. The total biomass of catch increased significantly as average dFAD density increased both at the mean and throughout the majority of the distribution, although this effect only explained a small fraction of the total variance in catch biomass. at this time, the low amount of variance explained and the inconsistent impact of average dFAD density on bycatch and target species indicate that it would be ineffective to mitigate bycatch levels in these fisheries by attempting to control regional dFAD densities.

Horseshoe crabs (Limulus polyphemus) have been harvested along the east coast of the United States since the 1800s, however a Fishery Management Plan (FMP) was only recently created for this species. To date, there have not been any studies that have attempted to identify or quantify bycatch in the horseshoe crab trawl fishery. A horseshoe crab trawl survey was started in 2001 to collect data on the relative abundance, distribution, and population demographics of horseshoe crabs along the Atlantic coast of the United States. In the present study, species composition data were collected at sites sampled by the horseshoe crab trawl survey in 2005 and 2006. Seventy-six different taxa were identified as potential bycatch in the horseshoe crab trawl fishery. Non-metric multidimensional scaling (NMS) was used to cluster sites and identify the spatial distribution of taxa. Sites strongly clustered into distinct groups, suggesting that species composition changes spatially and seasonally. Species composition shifted between northern and southern sites. Location and bottom water temperature explain most of the variation in species composition. These results provide a list of species that are susceptible to this specific trawl gear and describe their distribution during fall months throughout the study area. Identifying these species and describing their distribution is a first step to understanding the ecosystem-level effects of the horseshoe crab trawl fishery.<br>Master of Science

In the southeastern United States, skimmer trawls, pusher-head trawls, wing nets, and small try nets (headrope length less than 12-ft (3.66-m)) are exempt from using a turtle excluder device (TED) and instead must adhere to tow time restrictions as a mode to mitigate sea turtle bycatch. However, observer and stranding data indicate that these tow times may often be exceeded and result in mortality of sea turtles. The National Marine Fisheries Service (NMFS) published a notice of proposed rulemaking in December 2016 to extend TED requirements to other trawl types, however there has been limited development of specialized TEDs for these smaller trawls. In anticipation of a regulatory change, we developed and identified multiple versions of a top-opening TED with a minimum width of 28-in (71-cm) and height of 24-in (61-cm) as the best option for small trawl gears. Prototypes were initially equipped within small try nets and tested for gear performance and sea turtle exclusion in Panama City, Florida. The final designs were then tested for target shrimp retention, bycatch reduction, and general usability of TEDs in the commercial fisheries. A paired comparison test was conducted in 8-ft (2.44-m) and 10-ft (3.05-m) try nets aboard the NMFS R/V Caretta, three commercial skimmer trawls in vesselsFarfantepenaeus duorarum) fishery. There was a general reduction of shrimp and bycatch averaging from a minimum loss of 3.31% in the Miami wing net fishery (FV FL-01) to 22.07% in the skimmer trawl fishery (FV LA-01). This dissertation research indicates that TEDs can function properly in small trawl types, however additional studies are recommended to minimize the shrimp loss and improve the overall TED effectiveness specific to each fishery and trawl type evaluated.

La mortalitat per captura accidental en les pesqueres de palangre representa una de les principals amenaces per a nombroses espècies d’ocells marins a nivell mundial. En el Mediterrani, aquesta mortalitat esta afectant seriosament a la viabilitat d’algunes poblacions d’ocells, en particular de les baldrigues endèmiques d’aquesta conca. No obstant això, la informació disponible sobre la intensitat i extensió del seu impacte és escassa i fragmentada. Així mateix, encara no s’ha implementat cap tipus de mesura per evitar aquesta mortalitat. La present tesis pretén avaluar i contribuir al coneixement sobre la problemàtica de les captures accidentals d’ocells marins en la pesca de palangre de l’oest del Mediterrani, així com identificar l’estratègia de mitigació més adient per a la flota estudiada. En particular, l’estudi s’ha focalitzat en els palangrers de fons ja que fan servir arts més perillosos per als ocells i, a més, existeix una menor informació disponible. En primer lloc, aquest estudi demostra una elevada mortalitat d’ocells marins als palangres, en particular de les 3 espècies endèmiques de baldrigues: cendrosa (Calonectris diomedea), balear (Puffinus mauretanicus) i mediterrània (P. yelkouan), la qual cosa posa de manifest la necessitat urgent de desenvolupar accions efectives per reduir les captures accidentals d’aquestes espècies. A més, s’ha pogut identificar diversos factors temporals, operacionals, espacials i meteorològics que influeixen en el risc de captura accidental, encara que destaca particularment l’estació de l’any i el moment del dia que es realitza la calada. Altres factors influents són el tipus d’esquer, les condicions de vent, la configuració del palangre, el nombre d’hams calats i la distància a les colònies de cria. En segon lloc, s’ha observat que la falta de disponibilitat dels descarts proveïts per la pesca d’arrossegament incita a que les baldrigues cendroses acudeixin amb major intensitat als palangrers, incrementant així el risc de captura accidental. Consegüentment, la imminent normativa adoptada per la Unió Europea, la qual pretén prohibir els descarts, podria agreujar el problema de les captures accidentals. En tercer lloc, l’examen de les baldrigues capturades accidentalment als palangres demostra l’existència d’una mortalitat desigual a nivell poblacional. Els adults són la classe d’edat més afectada. Així mateix, existeix un biaix cap a un dels sexes que varia entre períodes de cria i espècies. També s’ha trobat que la mortalitat als palangres en l’àrea d’estudi està afectant fonamentalment a les poblacions locals (Illes Balears), encara que també són capturades baldrigues provinents d’altres colònies, especialment durant l’època de migració. Per últim, l’assaig de diversos mètodes de mitigació adaptats als palangrers demersals, demostra que, fins al moment, la calada nocturna seria el mètode més eficaç per reduir les captures accidentals sense afectar les captures objectiu o altres espècies no comercials quan la pesca va dirigida al lluç europeu. Tanmateix, seria necessari confirmar els seus efectes sobre altres espècies objectiu de la flota. A més, una restricció temporal de l’activitat durant els mesos més conflictius podria reduir considerablement aquesta problemàtica, encara que s’hauria d’avaluar els seus efectes sobre el rendiment pesquer. Altres mètodes serien l’increment de la taxa d’enfonsament del palangre o evitar l’ús d’esquers atractius per als ocells. Malgrat tot, la alta diversitat d’estratègies i arts de pesca dificulta la identificació dels mètodes que puguin ser aplicables al conjunt de la flota. Consegüentment, es recomana constituir un joc de diferents mesures de mitigació que puguin ser adaptades a la major part dels mètodes de pesca.<br>Bycatch mortality in longline fisheries is considered the main threat for numerous seabirds worldwide. In the Mediterranean, this mortality is seriously affecting the viability of some populations. However, the information available on the level and extent of its impact is scarce. Likewise, no mitigation strategy has yet been implemented in the fleet. The present thesis aims to asses and contribute to the knowledge about the seabird bycatch in longline fisheries of western Mediterranean, as well as to identify the most appropriate mitigation strategy for the fleet. The study has focused on demersal longliners, since they use the most dangerous gear for seabirds and also because there is little information available. This study shows a high seabird mortality on longlines, in particular of the three endemic shearwaters: Scopoli’s (Calonectris diomedea), Balearic (Puffinus mauretanicus) and Mediterranean (P. yelkouan), calling for urgent actions to reduce their bycatch rates. There are several factors influencing on bycatch risk, but the most important are the season and the setting time. Other influential factors are the bait type, wind conditions, longline configuration, proximity to the colonies and the number of hooks set. Moreover, in Scopoli’s shearwater, the reduction of discards by trawlers led to increased interaction between these seabirds and longliners, thus increasing the bycatch risk. Consequently, the incoming legislation that intends to ban discards will likely aggravate this problem. This study also shows adult- and sex-biased mortality in longline fisheries. In addition, this mortality is more pronounced but not limited to the local colonies. It appears that night setting would be the most effective method to reduce bycatch without compromising target or non-commercial species. However, this should be confirmed in longliners targeting species other than European hake. A temporal closure of the fishery is also a promising strategy, although its effects on fishing activity should be carefully evaluated. Others methods include increasing the longline sink rate and avoiding baits attractive to seabirds. The high diversity of strategies and gears hampers the identification of solutions applicable to the whole fleet. Consequently, it would be necessary to establish a set of different measures that can be adapted to the majority of fishing methods.

A pesca de fauna acompanhante, o âbycatchâ, pode ser considerada uma das maiores ameaÃas à vida nos oceanos. A influÃncia das capturas de fauna acompanhante nos ecossistemas marinhos faz com que esta seja uma das questÃes de conservaÃÃo da natureza mais importantes atualmente. Por vÃrias dÃcadas existiu na costa de Fortaleza uma intensa atividade da pesca de arrasto de camarÃo, que acidentalmente capturava raias, com o uso de embarcaÃÃes motorizadas. Tal atividade foi proibida a partir de 2003, pela Portaria no 35 do MinistÃrio do Meio Ambiente (Instituto do Meio Ambiente e dos Recursos Naturais RenovÃveis). O objetivo do presente estudo foi avaliar se a proibiÃÃo da pesca de arrasto de camarÃo utilizando-se embarcaÃÃes motorizadas em Ãreas costeiras (1) afeta a abundÃncia de raias demersais; (2) que parcela das populaÃÃes dessas raias està sujeita ao efeito da proibiÃÃo da referida atividade pesqueira; (3) se espÃcies consideradas pela LegislaÃÃo Brasileira atual como sob algum grau de ameaÃa tambÃm sÃo afetadas por esta proibiÃÃo. No presente estudo, foram realizadas 14 amostragens cientÃficas na enseada do Mucuripe, Fortaleza/CE, entre setembro de 2004 e novembro de 2010, cada uma com 10 arrastos de fundo a cerca de 14 m de profundidade, utilizando rede de arrasto-de-portas. Foram ainda, compilados dados nÃo publicados de abundÃncia de raias capturadas como fauna acompanhante da pesca de arrasto de camarÃo, utilizando-se embarcaÃÃo motorizada, na enseada do Mucuripe, entre 1997 e 1998. A proibiÃÃo da pesca de arrasto de camarÃo utilizando-se embarcaÃÃes motorizadas, em Ãreas costeiras, afeta positivamente a abundÃncia de raias demersais previamente impactadas por essa atividade. AlÃm disso, Ãrea costeira investigada abriga todas as classes de tamanho das raias Dasyatis guttata e Gymnura micrura e portanto pode ser considerada uma Ãrea importante para a reproduÃÃo destas espÃcies. Por fim, essa mesma Ãrea abriga, ainda, diversas espÃcies consideradas pela LegislaÃÃo Brasileira atual como ameaÃadas (n=4) ou sobreexplotadas ou ameaÃadas de sobreexplotaÃÃo (n=7).<br>Bycatch fisheries may be considered one of the greatest threats to marine life. The influence of these captures in marine ecosystems makes it one of the most pressing issues on nature conservation today. For decades, there was in Fortaleza, CE, a shrimp otter trawl fisheries activity conducted by motorized boats that accidently captured batoids. This activity has been prohibited by the Brazilian Ministry of Environment since 2003. The goal of the present study was to evaluate if the prohibition of shrimp otter trawl fisheries activity conducted by motorized boats on coastal areas (1) affects the abundance of demersal batoids; (2) which portion of these batoidsâ populations is under the effect of the prohibition of this fishery activity; and (3) if species considered by the current Brazilian legislation as under any level of threat also are effected by this prohibition. In the present study, fourteen scientific sampling were carried out on Mucuripe Bay, Fortaleza, CE, between September 2004 and November 2010. During each survey, 10 stations were sampled with otter trawl net, circa 14 m depth. In addition, unpublished data on the abundance of batoids captured as bycatch by shrimp fisheries in this same bay, between 1997 and 1998, were compiled. The prohibition of the shrimp fisheries using motorized boats, in coastal areas, affects positively the abundance of demersal batoids previously impacted by this activity. Furthermore, the coastal area studied is used by all size classes of the batoids Dasyatis guttata and Gymnura micrura and, therefore, it may be considered important for reproduction of these species. Lastly, this same Bay is also home for several species that currently are considered by the Brazilian legislation as endangered (n=4) or overexploited or threatened of overexploitation (n=7).

Le plan de restauration des tortues marines aux Antilles françaises a été validé par le Conseil National pour la Conservation de la Nature en 2006. Les captures accidentelles dans les filets de fond, i.e. les trémail, folle et filet droit, sur le plateau continental constituent la principale menace. Des filets faisant varier la hauteur, le maillage et l’inclinaison ont été comparés à des filets professionnels au cours de 226 pêches expérimentales. Le trémail est peu sélectif. Des filets à profil bas permettent d’obtenir des rendements comparables et réduiraient les captures de tortues. Les captures accidentelles sont plus abondantes dans les trémails et les folles. Les pêches à longs temps de calée provoquent plus de 90% de taux de mortalité de tortues et augmentent les quantités de rejets. Près de deux milliers de tortues seraient capturées chaque année aux Antilles françaises, avec une mortalité avoisinant les 60%. Les tortues adultes pêchées l’ont été en période de nidification et les tortues dites résidentes sont dans la grande majorité des juvéniles ou sub-adultes, cause de la surexploitation locale passée et signe de populations non stables. La menace « pêche » est d’autant plus importante qu’elle touche les femelles nidifiantes, meilleurs espoirs de rétablissement des stocks. En étroite collaboration participative avec les professionnels de la mer, la protection des tortues et des ressources marines passerait par une réduction de la hauteur des filets et de leurs temps de calée et l’interdiction totale ou partielle de ceux à mailles larges<br>The national marine turtles recovery plan in FWI was adopted in 2006 by the National council for the nature conservancy. The bottom nets bycatch, i.e. the trammel, folle and gill nets, on the continental shelf are the main threat. Experimental nets with different heights, meshing and incline was compared to professional ones during 226 experimental trials. Trammel net is non selective. Low profile nets maintain a similar productivity and reduce the turtle bycatch. Trammel and folle nets cause more bycatch. The long soak times lead to more than 90 % of turtles mortality and more discards. Each year, about two thousands of turtles would be captured in FWI, with a mortality rate closed to 60 %. The mature turtles were captured during the nesting season and the resident ones are mostly juveniles or sub-adults, because of the local past overexploitation and indicator of non stable populations. The “fishery” threat is particularly important it affect nesting females, best stocks recovery hope. Closely to the marine professionals, the marine turtle and resources protection would be effective thanks to the reduction of the height and soak times nets and the total or partial ban of large meshing size nets

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2016-09-01T13:19:15Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) MTTolotti_EcologyConservationOceanicWhitetipShark_VF_FichaCatalografica.compressed aprovada.pdf: 5871232 bytes, checksum: 4af848c7c53529f3e28ffa5d085443f1 (MD5)<br>Made available in DSpace on 2016-09-01T13:19:16Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) MTTolotti_EcologyConservationOceanicWhitetipShark_VF_FichaCatalografica.compressed aprovada.pdf: 5871232 bytes, checksum: 4af848c7c53529f3e28ffa5d085443f1 (MD5) Previous issue date: 2016-02-19<br>CAPEs<br>O objetivo principal da presente tese consistiu em agregar informações ao conhecimento sobre o tubarão galha-branca oceânico (Carcharhinus longimanus), principalmente no que se refere à sua distribuição, índices de abundância e preferências de habitat. Apesar de ser uma espécie muito capturada na pesca oceânica de atuns afins, informações acerca destes aspectos ecológicos são escassas e até mesmo ausentes na literatura relacionada à espécie. A tese é apresentada como um conjunto de capítulos autônomos, representando artigos científicos individuais. No primeiro capítulo-artigo foram discutidos os possíveis efeitos de medidas de manejo restritivas, implementadas recentemente por Organizações Regionais da Pesca Atuneira e que incluem algumas espécies de tubarões oceânicos. Medidas restritivas isoladas terão pouco impacto na redução da mortalidade de tubarões oceânicos. Um conjunto de medidas mitigadoras integradas será mais eficaz na conservação e recuperação das populações dessas espécies. No segundo capítulo-artigo foram analisados dados de captura e esforço de 14.835 lançamentos de espinhel pelágico realizados por embarcações arrendadas da frota atuneira brasileira, nos anos de 2004 a 2010. A CPUE nominal exibiu uma tendência de aumento gradual ao longo dos anos, variando de 0,04 em 2004 para 0,15 em 2010. A CPUE foi padronizada através de uma abordagem delta-GLM, entretanto, o índice de abundância padronizado não diferiu significativamente da CPUE nominal. Os modelos indicaram que as capturas de tubarões galha-branca são maiores para a estratégia de pesca espanhola, que se caracteriza pela utilização de anzóis em profundidades mais rasas. No terceiro capítulo-artigo, a interação entre tubarões galha-branca e a pesca de rede de cerco nos Oceanos Atlântico e Índico foi analisada, com o objetivo de investigar o potencial da utilização do banco de dados dessa pescaria para derivar índices de abundância e determinar tendências populacionais para a espécie. Dados de observadores de bordo da frota francesa combinados com dados históricos da União Soviética foram utilizados na análise. A série temporal combinada incluiu os anos entre 1986 e 2014. No Oceano Atlântico não foi possível determinar uma tendência populacional, uma vez que o índice de ocorrência foi muito baixo e não variou significativamente com o tempo. No Oceano Índico foi observada uma mudança bem-marcada no índice de ocorrência, oscilando em torno de 20% entre meados dos anos 80 e 90 e caindo para menos de 10% a partir de 2005. No quarto capítulo-artigo, a vulnerabilidade do tubarão galha-branca à pesca de espinhel pelágico foi avaliada utilizando dados dependentes e independentes da pesca. Os dados dependentes incluíram informações de diários de bordo (1999- 2011) e observadores embarcados (2004 a 2010), num total de 65.277 lançamentos de espinhel. Os dados independentes foram obtidos a partir de 8 tubarões marcados com marcas do tipo “pop-up satellite archival tag” na área onde a frota de espinhel operou. Locais de marcação e desprendimento das marcas foram relativamente próximos uns dos outros. Entretanto, os indivíduos marcados tenderam a viajar longas distâncias antes de retornar para a área de marcação. Foi observado um certo grau de filopatria à área. “Hotspots” de alta utilização dos tubarões marcados correspondeu à área sob forte pressão pesqueira. Todos os tubarões exibiram uma forte preferência por águas quentes e rasas da camada de mistura, gastando, em média, mais de 70% do tempo acima da termoclina e 95% acima de 120 m. Esse resultado justifica a maior capturabilidade da espécie em espinheis mais rasos. No quinto e último capítuloartigo, os movimentos verticais dos tubarões marcados foram analisados em detalhe. Apesar da distribuição vertical restrita, os dados indicaram que o tubarão galha-branca apresenta padrões de movimento complexos, incluindo padrões de migrações circadianas distintos e mergulhos profundos. O padrão circadiano mais frequentemente observado é caracterizado de um deslocamento à superfície durante o nascer do sol e uma tendência a permanecer em profundidades mais baixas durante o dia. Os movimentos verticais também foram influenciados pela temperatura da superfície do mar, o que pode indicar a ocorrência de termoregulação para espécie. A integração dos resultados de cada capítuloartigo proporcionou boas perspectivas para o desenvolvimento de medidas de mitigação. A evidência em relação à preferência do tubarão galha-branca por águas quentes e rasas é sólida, indicando que a remoção dos anzóis rasos do espinhel pode ser proposta para reduzir a captura incidental da espécie. O fato de variações na CPUE já terem sido observadas, sugere que esta pode ser uma medida eficaz. O comportamento filopátrico observado para o OCS também indica que a espécie pode se beneficiar com a criação de áreas marinhas protegidas.<br>The ultimate goal of this thesis was to generate knowledge regarding the ecology of the oceanic whitetip shark (Carcharhinus longimanus) and contribute for an ecosystem-based fishery management. The work focuses on the interactions between tuna fisheries and the species and its habitat preferences. Despite being frequently caught on high-sea fisheries, there are wide knowledge gaps regarding the ecology of the oceanic whitetip shark. The thesis is presented as a set of selfcontained standalone chapters, constructed as individual research articles. The first article-chapter provides a discussion concerning pelagic sharks and the recent species-specific banning measures implemented by Regional Fishery Management Organizations (RFMOs) in charge of tuna fisheries. It is unlikely that banning measures alone can reduce the high level of fishing mortality and recover pelagic shark’s depleted populations. Managers should be fully aware that the development and implementation of mitigation measures are critical for a more effective conservation strategy. In the second article-chapter, catch and effort data from 14,835 longline sets conducted by foreign tuna longline vessels chartered by Brazil, from 2004 to 2010, were analyzed. The nominal catch per unit of effort (CPUE) exhibited a gradual increase, varying from 0.04 sharks/1000 hooks in 2004 to 0.15 in 2010. A CPUE standardization was performed using a delta-GLM approach, but the standardized index of abundance did not differ significantly from the nominal CPUE. The models indicated that the catches of oceanic whitetip sharks are higher for the Spanish fishing strategy, which is characterized by the deployment of hooks at shallower depths. In the third article-chapter, the interaction between oceanic whitetip sharks and the purse seine fishery in the eastern Atlantic and western Indian oceans was analyzed, in order to investigate the potential of using this fishery’s database to derive abundance indexes and determine population trends for the species. Observer data from the French purse seine fleet combined with a historic database from the Soviet Union were used in the analyses. The combined time series spanned from 1986 to 2014. The occurrence index was very low for Atlantic Ocean and no marked temporal trend was observed. For the Indian Ocean a well-marked change on the occurrence index was observed, fluctuating around 20% from mid 80’s to mid 90’s and dropping to less than 10% as from 2005. In the fourth article-chapter, a combination of fisheries dependent and independent data was used to assess the vulnerability of the oceanic whitetip shark to pelagic longline fisheries. Fisheries dependent data included information from logbooks (from 1999 to 2011) and onboard observers (2004 to 2010), totaling 65,277 pelagic longline sets. Fisheries independent data were obtained from 8 oceanic whitetip sharks tagged with popup satellite archival tags in the area where longline fleet operated. Tagging and pop-up sites were relatively close to each other, although individuals tended to travel long distances before returning to the tagging area. Some degree of philopatry was observed. High utilization hotspots of tagged sharks fell inside the area under strongest fishing pressure. All sharks exhibited a strong preference for the warm and shallow waters of the mixed layer, spending on average more than 70% of the time above the thermocline and 95% above 120 m. This result explains the higher catchability of the species on shallow longline gear. In the fifth and last article-chapter, the vertical movements of tagged oceanic whitetip sharks were analyzed in detail. Despite its restricted vertical distribution, the analyses reveled that oceanic whitetips perform complex movement patterns, including distinct diel patterns and deep diving behavior. A correlation between vertical movements and sea surface temperature was also observed, suggesting the occurrence of thermoregulation for the species. The combined results of each article-chapter have provided good insights towards the development of mitigation measures. The evidence regarding oceanic whitetip shark’s preference for warm and shallow waters is solid and this information suggests that the removal of the shallow hooks from the longline gear could be proposed as a technique to reduce OCS bycatch. The fact that CPUE variations were already observed suggests that this might be an effective measure. The philopatric behavior observed for the OCS also indicates that the species could benefit from time-area closure measures.

[For the Abstract, please see the PDF files below, namely "front.pdf"] CONTENTS. Chapter 1 Introduction. Chapter 2 Gross and microscopic visceral anatomy of the male Cape fur seal with reference to organ size and growth. Chapter 3 Age determination and growth in the male Cape fur seal: part one, external body. Chapter 4 Age determination and growth in the male Cape fur seal: part two, skull. Chapter 5 Age determination and growth in the male Cape fur seal: part three, baculum. Chapter 6 Suture age as an indicator of physiological age in the male Cape fur seal. Chapter 7 Sexual dimorphism in the adult Cape fur seal: standard body length and skull morphology. Chapter 8 Reproduction in the male Cape fur seal: age at puberty and annual cycle of the testis. Chapter 9 Diet and foraging behaviour of the Cape fur seal. Chapter 10(a) The Impact of the fur seal industry on the distribution and abundance of Cape fur seals. Chapter 10(b) South African Airforce wildlife rescue: Cape fur seal pups washed from Black Rocks, Algoa Bay, during heavy seas, December 1976. Chapter 11(a) Operational interactions between Cape fur seals and fisheries: part one, trawl fishing. Chapter 11(b) Operational interactions between Cape fur seals and fisheries: part two, squid jigging and line fishing. Chapter 11(c) Operational interactions between Cape fur seals and fisheries: part three, entanglement in man-made debris. Chapter 12 Concentrations of heavy metals (Cd, Cu, Pb, Ni & Zn) and organochlorine contaminants (PCBs, DDT, DDE & DDD) in the blubber of Cape fur seals. Chapter 13 Endoparasites of the Cape fur seal. Chapter 14(a) Preliminary investigations of shark predation on Cape fur seals. Chapter 14(b) Aggressive behaviour of an adult male Cape fur seal towards a great white shark Carcharodon carcharias. Chapter 15 Conclusions and future directions.

The purpose of this research was to explore the impact of finfish bycatch on the ocean shrimp Pandalus jordani fishery using two methods. One method looked at the breakage of the shrimp by finfish bycatch in the nets. The other looked at the impact of bycatch on fishing decisions. At-sea research found that finfish bycatch contributes to the breakage of ocean shrimp. However, the impact is small relative to breakage caused by other handling procedures. Bycatch was measured from each net of a double-rigged shrimp vessel, where one side employed a Nordmore grate bycatch reduction device (BRD) and the other served as a control. Shrimp catch was controlled for BRD use and catch day, and sampled throughout processing to evaluate breakage. At greater than 50% bycatch there was a significantly higher percentage of broken shrimp in the control side than in the BRD side for samples taken at the first and third sampling point (p<0.05). After this point the differences became non-significant. The percent breakage increased from a mean 2.4% broken before placement in the hold to a mean 18.0% broken in the final product. The impact of bycatch on fishing decisions was evaluated by distributing an expanded logbook to volunteer Oregon shrimp vessels in 1998. Logbook questions addressed the reasons and time involved for running to initial fishing grounds, relocating overnight, relocating between tows, dumping tows, and modifying gear. Completed logbooks were collected from 20 vessels representing 263 trips, 1043 fishing days, and 4727 tows. A soft mesh BRD was used at some point by 25% of vessels on 8.7% of trips and 3.3% of tows. Bycatch did not figure prominently in reasons given for choice of initial fishing grounds, relocating between fishing days, or relocating between tows. Bycatch was the main reason cited for dumping tows. In total, 430 (9%) tows were dumped. The estimated weight of fish and shrimp dumped equaled 11.3% and 0.3%, respectively, of the landed shrimp catch. Pacific whiting Merluccius productus caused 81.4% of the tows dumped due to bycatch. Opportunity costs attributed to bycatch alone were equivalent to net revenue resulting from 12.3 tows or $3,203 per study vessel. At the fleet level, opportunity costs due to dumped tows totaled 1,227 effort hours, 32.4 trips, or $155,070. This equates to a 4.6% loss in gross ex-vessel revenue.<br>Graduation date: 2002

The Australian continental shelf is one of the few remaining areas of the world where sea turtle populations have been subject to relatively small levels of direct harvest and where nesting- and feeding-ground habitats remain essentially intact. The area supports six of the world’s seven sea turtle species (i.e., Chelonia mydas, Caretta caretta, Eretmochelys imbricata, Natator depressus, Lepidochelys olivacea and Dermochelys coriacea), contains significant nesting populations of three species (i.e., Chelonia mydas, Caretta caretta, Eretmochelys imbricata), the world’s only nesting populations of N. depressus and is the main feeding-grounds area of Natator depressus. The incidental capture of sea turtles in the trawl fisheries of northern Australia was a significant threat to sea turtle populations of Australia. Trawl by-catch mortality of Caretta caretta is considered to have contributed to the 80% decline in numbers of nesting sea turtles in eastern Australia, but this speculation is based on limited or unpublished data relating to mortality associated with trawl fisheries. There is limited information on the potential impact of trawl fisheries on other sea turtle species that occur in Australian waters. Turtle Excluder Devices (TEDs) were legislated for use in trawl fisheries of northern Australia in 1999. TEDs allow sea turtles to escape from trawl nets whilst enabling the trawl fishery to continue to operate and catch prawns. TEDs can be an effective solution to sea turtle by-catch, but the adoption and use of TEDs in a fishery needs to be monitored to ensure that the devices are having the desired outcome i.e., sea turtle exclusion. The scale and geographic extent of Australian trawl fisheries have the potential to result in a poor capacity to monitor the effective use of TEDs by fishers. TED compliance strategies (i.e., monitoring and enforcement) should be focused in areas where the effective use of TEDs would have the greatest benefit to sea turtle conservation i.e., areas where sea turtle by-catch or mortality is greatest. The present study adopted a comprehensive approach to understanding the interaction between trawling and endangered sea turtle species in waters adjacent to the Queensland east coast, by collecting and utilising baseline data on the size and distribution of sea turtle by-catch. Aspects of compliance strategies for TEDs that would contribute to the sustainable management of sea turtle by-catch in trawl fisheries are also considered. In this context, the following objectives are addressed in this thesis: (i) To estimate the number and species composition of sea turtles caught and killed in a multiple sector trawl fishery using spatial stratification; (ii) To examine the behavioural responses of sea turtles to trawl capture in order to investigate the potential for post-trawl mortality; (iii) To investigate the factors that influence the distribution pattern of sea turtles, and from this analysis, predict the relative in-water densities of sea turtles at broad spatial scales; and (iv) To develop a spatially explicit strategy for TED compliance (i.e., monitoring and enforcement), based on an assessment of the interaction between sea turtles and fishing effort. The thesis concentrates on sea turtle by-catch in the Queensland East Coast Trawl Fishery, but has broader implications for the management of sea turtles in their feeding-grounds. Baseline information on sea turtle by-catch was collected from select commercial fishers who voluntarily reported information on sea turtles caught in the Queensland East Coast Trawl Fishery. About 1,500 sea turtles were reported caught during ~24,000 days of trawling by 105 fishers who participated in a voluntary program to monitor sea turtle by-catch between 1991 and 1996. Stratified, weighted analysis of the data resulted in an annual estimated sea turtle catch of about 5,900 for the Queensland East Coast Trawl Fishery, given a mean annual total fleet effort of about 85,000 days fished per year. The catch was comprised of Caretta caretta (~50%), Chelonia mydas (27%), Natator depressus (16%) and Lepidochelys olivacea (6)%. The fishery had minimal catches of Eretmochelys imbricata and Dermochelys coriacea. Sea turtle by-catch was dominated by immature individuals, with between 60 and 80% of individuals caught being immature, based on approximate size-at-maturity for each species. Estimates of total mortality were based on observed rates as well as published mortality rates from USA shrimp trawl fisheries. In general, mortality rates of sea turtles caught in the Queensland East Coast Trawl Fishery were lower than mortality rates reported for other trawl fisheries in northern Australia and the USA. Lower mortality rates were probably a function of the tow duration associated with various sectors of the Queensland East Coast Trawl Fishery. However, the combined by-catch of sea turtles in the three major trawl fisheries of northern Australia (i.e., the Queensland East Coast Trawl Fishery, the Northern Prawn Fishery and Torres Strait Prawn Fishery) was estimated to be of sufficient magnitude to have contributed to the observed declines in nesting numbers of east Australian Caretta caretta. Estimates of the mortality of sea turtles in the trawl fisheries of northern Australia raise concerns about the likely impacts of these fisheries on other species of sea turtle, particularly Australian sub-populations of Natator depressus and Lepidochelys olivacea. These species frequent feeding-ground habitats typical of trawl grounds and are poorly monitored through nesting-ground surveys. The scale of impact estimated in this thesis indicates that the use of TEDs in the trawl fisheries of northern Australia is warranted. Mortality rates of trawl-caught sea turtles could be higher than currently estimated if sea turtles die after release as a consequence of the delayed effects of capture or secondary mortality resulting from changes in diving behaviour. Six trawl-caught sea turtles were monitored post-release using ultrasonic transmitters and Temperature Depth Recorders in order to assess their diving patterns for signs of modified behaviour. Two rodeo-caught sea turtles were monitored post-release as controls to the trawl-caught individuals. All sea turtles swam rapidly away from the point of release and displayed a period of frequent surfacing behaviour that was speculated to represent swimming and hyperventilation. The sea turtles then settled into a steady pattern where dive intervals were long and regular. This was speculated to represent recovery behaviour. ‘Normal’ activity patterns, as documented in the literature, were not apparent in the dive profiles of the trawl-caught sea turtles within the post-release monitoring period (i.e., 66 hours). Rodeo-caught sea turtles displayed ‘normal’ activity patterns at about 85 and 111 hours post-release. There was no evidence of delayed post-release mortality in the limited number of individuals monitored. However, the trawl-caught sea turtles displayed modified diving patterns that potentially made them more susceptible to secondary mortality such as boat strike or predation. Recovering sea turtles did not appear to undertake normal feeding activities, suggesting that sea turtles exposed to non-lethal interactions with human activities on a frequent basis may have lower growth rates. The results suggest that sea turtles are affected by interactions with humans to a much greater extent than previously thought and that the recovery period of such interactions can take several days The relative spatial distribution of sea turtles is poorly known and is insufficient for developing management plans, such as monitoring and enforcement strategies for TEDs. Sea turtle catch per unit effort from trawl captures and sea turtle sightings from aerial surveys were used to estimate the relative density of sea turtles in the waters adjacent to the Queensland east coast. As expected, sea turtles were not evenly distributed, with several areas having exceptionally high relative densities. In trawled areas, the relative density of sea turtles was significantly correlated with the benthic species trawled (e.g., species of prawn) as well as water-depth. Natator depressus and Lepidochelys olivacea had high relative densities in inshore, tropical waters less than 40 m deep, where tiger prawns (Penaeus esculentus, P. semisulcatus) and endeavour prawns (Metapenaeus endeavouri, M. ensis) were caught most commonly. Caretta caretta had high relative densities in inshore, sub-tropical waters less than 30 m deep, where banana prawns (Fenneropenaeus merguiensis) or bay prawns (Metapenaeus bennettae i.e., Moreton Bay) were caught most commonly. The relative density of sea turtles was predicted for the majority of waters adjacent to the Queensland east coast based on the mean sea turtle CPUE and information on target species caught most commonly and mean-depth trawled. The relative distribution of sea turtle density developed in this thesis provides the first broad scale maps that quantitatively identify areas that appear to be important as sea turtle habitat. This information could be used to assist the conservation management of sea turtles populations of eastern Australia. Sea turtle by-catch in northern Australia has been addressed through the mandatory use of Turtle Excluder Devices (TEDs) in otter trawl fisheries. However, the use of TEDs in a fishery needs to be supported by monitoring or enforcement to ensure that TEDs are used effectively, but this is difficult in fishery that operates over a large geographic scale. A pragmatic solution would be to target the monitoring and enforcement of TEDs in critical areas where reductions in sea turtle by-catch will make the greatest contribution to recovery of impacted populations of sea turtles. The spatial distribution of effort for the Queensland East Coast Trawl Fishery in the year 2001 was integrated with the relative density of sea turtles to identify critical areas for sea turtle by-catch. Critical areas for sea turtle by-catch were similar despite the use of qualitative or quantitative methods. The results suggest that effective TED use is most critical in the inshore waters of the Queensland east coast. Monitoring and enforcing TEDs in these critical areas would enable fisheries managers to measure progress towards the stated target of the 95% reduction in sea turtle by-catch and contribute to the sustainable management of the fishery. The use of TEDs in non-critical areas should also be monitored, but because of the lower contribution of these areas to sea turtle by-catch, monitoring and enforcement could take place with less intensity. Critical areas for monitoring the effective use of TEDs may change if the intensity of fishing effort changes and may become unnecessary should it be demonstrated that most fishers comply fully with TED regulations.

The Australian continental shelf is one of the few remaining areas of the world where sea turtle populations have been subject to relatively small levels of direct harvest and where nesting- and feeding-ground habitats remain essentially intact. The area supports six of the world’s seven sea turtle species (i.e., Chelonia mydas, Caretta caretta, Eretmochelys imbricata, Natator depressus, Lepidochelys olivacea and Dermochelys coriacea), contains significant nesting populations of three species (i.e., Chelonia mydas, Caretta caretta, Eretmochelys imbricata), the world’s only nesting populations of N. depressus and is the main feeding-grounds area of Natator depressus. The incidental capture of sea turtles in the trawl fisheries of northern Australia was a significant threat to sea turtle populations of Australia. Trawl by-catch mortality of Caretta caretta is considered to have contributed to the 80% decline in numbers of nesting sea turtles in eastern Australia, but this speculation is based on limited or unpublished data relating to mortality associated with trawl fisheries. There is limited information on the potential impact of trawl fisheries on other sea turtle species that occur in Australian waters. Turtle Excluder Devices (TEDs) were legislated for use in trawl fisheries of northern Australia in 1999. TEDs allow sea turtles to escape from trawl nets whilst enabling the trawl fishery to continue to operate and catch prawns. TEDs can be an effective solution to sea turtle by-catch, but the adoption and use of TEDs in a fishery needs to be monitored to ensure that the devices are having the desired outcome i.e., sea turtle exclusion. The scale and geographic extent of Australian trawl fisheries have the potential to result in a poor capacity to monitor the effective use of TEDs by fishers. TED compliance strategies (i.e., monitoring and enforcement) should be focused in areas where the effective use of TEDs would have the greatest benefit to sea turtle conservation i.e., areas where sea turtle by-catch or mortality is greatest. The present study adopted a comprehensive approach to understanding the interaction between trawling and endangered sea turtle species in waters adjacent to the Queensland east coast, by collecting and utilising baseline data on the size and distribution of sea turtle by-catch. Aspects of compliance strategies for TEDs that would contribute to the sustainable management of sea turtle by-catch in trawl fisheries are also considered. In this context, the following objectives are addressed in this thesis: (i) To estimate the number and species composition of sea turtles caught and killed in a multiple sector trawl fishery using spatial stratification; (ii) To examine the behavioural responses of sea turtles to trawl capture in order to investigate the potential for post-trawl mortality; (iii) To investigate the factors that influence the distribution pattern of sea turtles, and from this analysis, predict the relative in-water densities of sea turtles at broad spatial scales; and (iv) To develop a spatially explicit strategy for TED compliance (i.e., monitoring and enforcement), based on an assessment of the interaction between sea turtles and fishing effort. The thesis concentrates on sea turtle by-catch in the Queensland East Coast Trawl Fishery, but has broader implications for the management of sea turtles in their feeding-grounds. Baseline information on sea turtle by-catch was collected from select commercial fishers who voluntarily reported information on sea turtles caught in the Queensland East Coast Trawl Fishery. About 1,500 sea turtles were reported caught during ~24,000 days of trawling by 105 fishers who participated in a voluntary program to monitor sea turtle by-catch between 1991 and 1996. Stratified, weighted analysis of the data resulted in an annual estimated sea turtle catch of about 5,900 for the Queensland East Coast Trawl Fishery, given a mean annual total fleet effort of about 85,000 days fished per year. The catch was comprised of Caretta caretta (~50%), Chelonia mydas (27%), Natator depressus (16%) and Lepidochelys olivacea (6)%. The fishery had minimal catches of Eretmochelys imbricata and Dermochelys coriacea. Sea turtle by-catch was dominated by immature individuals, with between 60 and 80% of individuals caught being immature, based on approximate size-at-maturity for each species. Estimates of total mortality were based on observed rates as well as published mortality rates from USA shrimp trawl fisheries. In general, mortality rates of sea turtles caught in the Queensland East Coast Trawl Fishery were lower than mortality rates reported for other trawl fisheries in northern Australia and the USA. Lower mortality rates were probably a function of the tow duration associated with various sectors of the Queensland East Coast Trawl Fishery. However, the combined by-catch of sea turtles in the three major trawl fisheries of northern Australia (i.e., the Queensland East Coast Trawl Fishery, the Northern Prawn Fishery and Torres Strait Prawn Fishery) was estimated to be of sufficient magnitude to have contributed to the observed declines in nesting numbers of east Australian Caretta caretta. Estimates of the mortality of sea turtles in the trawl fisheries of northern Australia raise concerns about the likely impacts of these fisheries on other species of sea turtle, particularly Australian sub-populations of Natator depressus and Lepidochelys olivacea. These species frequent feeding-ground habitats typical of trawl grounds and are poorly monitored through nesting-ground surveys. The scale of impact estimated in this thesis indicates that the use of TEDs in the trawl fisheries of northern Australia is warranted. Mortality rates of trawl-caught sea turtles could be higher than currently estimated if sea turtles die after release as a consequence of the delayed effects of capture or secondary mortality resulting from changes in diving behaviour. Six trawl-caught sea turtles were monitored post-release using ultrasonic transmitters and Temperature Depth Recorders in order to assess their diving patterns for signs of modified behaviour. Two rodeo-caught sea turtles were monitored post-release as controls to the trawl-caught individuals. All sea turtles swam rapidly away from the point of release and displayed a period of frequent surfacing behaviour that was speculated to represent swimming and hyperventilation. The sea turtles then settled into a steady pattern where dive intervals were long and regular. This was speculated to represent recovery behaviour. ‘Normal’ activity patterns, as documented in the literature, were not apparent in the dive profiles of the trawl-caught sea turtles within the post-release monitoring period (i.e., 66 hours). Rodeo-caught sea turtles displayed ‘normal’ activity patterns at about 85 and 111 hours post-release. There was no evidence of delayed post-release mortality in the limited number of individuals monitored. However, the trawl-caught sea turtles displayed modified diving patterns that potentially made them more susceptible to secondary mortality such as boat strike or predation. Recovering sea turtles did not appear to undertake normal feeding activities, suggesting that sea turtles exposed to non-lethal interactions with human activities on a frequent basis may have lower growth rates. The results suggest that sea turtles are affected by interactions with humans to a much greater extent than previously thought and that the recovery period of such interactions can take several days The relative spatial distribution of sea turtles is poorly known and is insufficient for developing management plans, such as monitoring and enforcement strategies for TEDs. Sea turtle catch per unit effort from trawl captures and sea turtle sightings from aerial surveys were used to estimate the relative density of sea turtles in the waters adjacent to the Queensland east coast. As expected, sea turtles were not evenly distributed, with several areas having exceptionally high relative densities. In trawled areas, the relative density of sea turtles was significantly correlated with the benthic species trawled (e.g., species of prawn) as well as water-depth. Natator depressus and Lepidochelys olivacea had high relative densities in inshore, tropical waters less than 40 m deep, where tiger prawns (Penaeus esculentus, P. semisulcatus) and endeavour prawns (Metapenaeus endeavouri, M. ensis) were caught most commonly. Caretta caretta had high relative densities in inshore, sub-tropical waters less than 30 m deep, where banana prawns (Fenneropenaeus merguiensis) or bay prawns (Metapenaeus bennettae i.e., Moreton Bay) were caught most commonly. The relative density of sea turtles was predicted for the majority of waters adjacent to the Queensland east coast based on the mean sea turtle CPUE and information on target species caught most commonly and mean-depth trawled. The relative distribution of sea turtle density developed in this thesis provides the first broad scale maps that quantitatively identify areas that appear to be important as sea turtle habitat. This information could be used to assist the conservation management of sea turtles populations of eastern Australia. Sea turtle by-catch in northern Australia has been addressed through the mandatory use of Turtle Excluder Devices (TEDs) in otter trawl fisheries. However, the use of TEDs in a fishery needs to be supported by monitoring or enforcement to ensure that TEDs are used effectively, but this is difficult in fishery that operates over a large geographic scale. A pragmatic solution would be to target the monitoring and enforcement of TEDs in critical areas where reductions in sea turtle by-catch will make the greatest contribution to recovery of impacted populations of sea turtles. The spatial distribution of effort for the Queensland East Coast Trawl Fishery in the year 2001 was integrated with the relative density of sea turtles to identify critical areas for sea turtle by-catch. Critical areas for sea turtle by-catch were similar despite the use of qualitative or quantitative methods. The results suggest that effective TED use is most critical in the inshore waters of the Queensland east coast. Monitoring and enforcing TEDs in these critical areas would enable fisheries managers to measure progress towards the stated target of the 95% reduction in sea turtle by-catch and contribute to the sustainable management of the fishery. The use of TEDs in non-critical areas should also be monitored, but because of the lower contribution of these areas to sea turtle by-catch, monitoring and enforcement could take place with less intensity. Critical areas for monitoring the effective use of TEDs may change if the intensity of fishing effort changes and may become unnecessary should it be demonstrated that most fishers comply fully with TED regulations.

Dissertação de mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2016<br>The present study assessed bycatch in Algarve grid dredge fisheries and estimated fishing gear inflicted damage and mortality, with the purpose of formulating mitigation measures, specifically fishing gear modifications. Bycatch using this dredge has been shown to surpass target species catch and, although it would not be a major problem if the discarded individuals survive, it nonetheless creates an issue of concern for fishers. Fishing surveys were conducted bimonthly onboard commercial fishing vessels in the same coastal areas near Olhão, throughout six months, in order to ascertain seasonal variation. Fishing targeted commercially valuable clam species, either Donax trunculus, using the DDredge, or Spisula solida and Chamelea gallina, using the SDredge. All individuals captured were attributed scores from a damage table ranging from 1 to 4, where 1 or 2 equate organism survival and 3 or 4 mortality. Results showed significant differences between fisheries regarding total catch composition, confirming dredge capacity to maximize target catch, but none for bycatch, demonstrating similar benthic communities in all sampled sites. Bycatch reached a maximum of 57.5% in abundance, and was significantly higher using the DDredge. Damage and mortality, although overall low, varied as a result of the morphological characteristics of the taxa itself, as such Echinodermata was presented as most subject to damage. Higher percentages of bycatch in the DDredge indirectly led to higher mortality rates as well. Seasonality analysis indicated the influence of spring on an increase of bycatch abundance in the DDredge. The implementation of a BRD and net bag in the grid dredge are proposed to reduce bycatch, as well as its damage and mortality, while maintaining fishing yield. Comparative studies are advised as to evaluate BRD effects on catch composition, bycatch amount, mortality, and discard rates. Additionally, the re-evaluation of the damage table through survival experiments is recommended.<br>A pesca acidental ou acessória é geralmente definida como a captura não intencional de organismos que não se enquadram na definição de captura alvo, por exemplo, indivíduos de espécies sem importância comercial ou juvenis das espécies alvo. A captura acessória inclui todos os indivíduos que são descartados para o mar, as rejeições e aqueles que, apesar de não serem considerados captura alvo, por qualquer outra razão sejam retidos e desembarcados. A pesca acessória é, assim, a diferença entre a captura total e a captura alvo. Portugal é um pequeno país com a terceira maior Zona Económica Exclusiva (ZEE) da União Europeia. As comunidades costeiras portuguesas dependem da pesca e de atividades com ela relacionadas como meio de subsistência, sendo estas uma forte componente do património cultural português. Apesar de a atividade pesqueira ser regulada por legislação própria, continua a ser um elemento perturbador dos ecossistemas e das comunidades marinhas. Este projecto focou-se na frota pesqueira que se dedica à captura de amêijoa branca (Spisula solida), pé-de-burrinho (Chamelea gallina) e conquilha (Donax trunculus) com ganchorra de grelha. A ganchorra de grelha é utilizada na pesca de bivalves ao longo da costa algarvia e em especial na área do presente estudo. Esta ganchorra é composta por uma boca com um pente de dentes na barra inferior, acoplada a uma armação de grelha metálica onde a captura é retida. Os indivíduos de pequenas dimensões, incluindo juvenis da espécie alvo, isto é, abaixo dos 25 mm de tamanho mínimo legal, escapam por entre as barras da grelha, enquanto a captura alvo e indivíduos maiores da captura acessória são mantidos e trazidos a bordo. Encontra-se demonstrado para o uso desta ganchorra uma redução da captura de juvenis da espécie-alvo e uma rápida recuperação dos indivíduos que escapam através das barras da grelha. No entanto, a sua utilização acarreta consequências, já que esta arte de pesca não é tão seletiva como seria desejável, promovendo capturas acessórias e, consequentemente, rejeições. O presente trabalho tem como objetivo avaliar a importância das capturas acessórias na pesca de bivalves com ganchorra de grelha no Algarve, determinar o dano e mortalidade causados por esta arte de pesca à captura total, aferir a existência de sazonalidade e propor medidas que minimizem a pesca acidental. Tais objetivos foram alcançados através da quantificação das capturas acessórias obtidas com ganchorras de grelha com diferentes espaçamentos entre as barras paralelas, 8 mm para a captura de D. trunculus (DDredge) e 12 mm para S. solida e C. gallina (SDredge). A amostragem decorreu duas vezes por mês, entre Fevereiro e Julho, a bordo de embarcações de pesca comercial na costa algarvia perto de Olhão. A determinação da mortalidade de cada indivíduo foi calculada através da atribuição de uma escala de dano de 1 a 4, em que 1 ou 2 implicam a sobrevivência do organismo rejeitado e 3 e 4 a sua morte. Foram encontradas diferenças significativas entre a composição das capturas totais das duas ganchorras, confirmando a capacidade de cada ganchorra maximizar a captura da sua respectiva espécie alvo. Porém, nenhuma diferença foi encontrada entre a composição da captura acessória, demonstrando a presença de comunidades bentónicas semelhantes em todos os locais de amostragem. A captura acidental atingiu um máximo de 57.5% em abundância e 35.1% em biomassa e foi significativamente maior usando a DDredge, devido à menor abundância da espécie alvo. Dano e mortalidade, embora baixos, variaram em resultado das características morfológicas de cada taxa. As espécies alvo mostraram, em geral, baixas mortalidades devido à natureza resistente das conchas destas espécies de bivalves, com S. solida como mais resistente e D. trunculus mais susceptível a dano. Tanto na pescaria de S. solida e C. gallina como na de D. trunculus, Echinodermata foi o phylum com maior mortalidade e dano, em particular a classe Echinoidea, devido à sensibilidade a dano mecânico das placas fundidas que compõem estes organismos. Elevadas percentagens de capturas acessórias na DDredge causaram, assim, indiretamente taxas de mortalidade significativamente maiores, já que se verificou menor abundância de espécies resistentes a dano. Análises de sazonalidade indicaram o aumento da abundância das capturas acessórias na DDredge desde o Inverno até à Primavera. Não foram observadas diferenças significativas entre o Verão e as restantes estações, presumivelmente devido ao baixo tamanho da amostra causado pelo fecho da pesca durante esses meses. Porém, visto que outros autores indicaram também a presença de sazonalidade na abundância das capturas da ganchorra de grelha, especificamente durante o Outono, torna-se evidente a necessidade de estudos adicionais que explorem estas variações. Recomenda-se a implementação de um aparelho que reduza a proporção de rejeições (BRD) na ganchorra de grelha. Este BRD consiste numa grelha articulada diagonalmente posicionada na armação metálica da ganchorra e na criação de uma abertura no topo da mesma. O espaçamento entre as barras da grelha do BRD deverá ser largo o suficiente para a permitir a entrada e retenção da espécie alvo, mas estreito de modo a prevenir a entrada de indivíduos da captura acessória de maiores dimensões, excluindo-os através da abertura mencionada. No entanto, é indispensável que esta alteração à ganchorra não cause redução no rendimento de pesca. Propõe-se, assim, que a grelha posterior da ganchorra seja eliminada e um saco de rede acoplado. Desta forma evita-se a perda de captura alvo pela abertura no topo da armação metálica durante a recolha da ganchorra, o único momento da operação de pesca em que esta se encontra numa posição vertical. Prevê-se que, com estas alterações, as rejeições sejam reduzidas, bem como o dano e mortalidade causados pela ganchorra de grelha, visto que a imediata exclusão de organismos lhes permitirá rápida recuperação de atividade e menor risco de predação. Estudos comparativos que avaliem o efeito das modificações propostas são aconselhados. Deste modo, deverá proceder-se ao arrasto simultâneo de ganchorras com e sem BRD, de modo a avaliar os efeitos do mesmo no rendimento de pesca, composição das capturas, proporção de capturas acessórias, mortalidade e taxas de rejeição. Recomenda-se também a reavaliação da tabela de danos usada através de experiências de sobrevivência.

Bycatch and discards are a cause of great concern in commercial world fisheries, with important ecological, economic and conservation implications. With the recent inclusion of a discards ban (‘landing obligation’), in the reform of the EU CFP, these issues have gained a tremendous attention from the economic, scientific, political and social point of view. Demersal trawl fisheries off the southern coast of Portugal capture an extraordinary diversity of species and generate considerable amounts of bycatch and discards. Bycatch includes commercially valuable target-species and bycatch species with low or no commercial value, but the great majority consists of unmarketable species, that are discarded. Bony fishes are dominant in bycatch and discards and the most discarded are of low or no commercial value. The reasons for discarding are fundamentally economic in nature (lack of commercial value) for bycatch species, and legal and administrative (legal minimum landing size) for commercially important species. The study of the reproductive biology of Galeus melastomus, discarded by crustacean trawls, suggests that a minimum landing size should be established for this species, and explains the importance of such a study in the assessment and management of fisheries. The discovery of a new species of the ray Neoraja iberica n. sp. contributes to the knowledge of the local marine biodiversity in Portuguese waters and of the global marine biodiversity. The three cases of abnormal hermaphroditism recorded in Etmopterus spinax, are the first cases known to date of hermaphroditism in this species. There is a need to find solutions to the problem of bycatch and discards of trawl fisheries in the Algarve coast. A combination of technical, regulatory and economic measures to minimize bycatch and reduce discards, before implementing a ‘landing obligation’, is thought to be the best approach to apply in the southern Portuguese multispecies trawl fisheries.

Marine mammals, particularly cetaceans and pinnipeds, are killed as incidental bycatch in fisheries around the world. Management measures to reduce this bycatch and improve the conservation outcomes of affected bycatch species include the implementation of temporal and spatial fishery closures, operational protocols and the use of technical mitigation measures, such as the installation of devices or adjustments to operational gear. In my thesis, I first undertake a global review and assessment of technical mitigation measures used to reduce the bycatch of marine mammals, particularly cetaceans and pinnipeds, in commercial trawl, purse seine, longline, gillnet and pot or trap fishing gear. For some gear types and taxa, there are currently limited technical options that show strong evidence for effectively reducing bycatch. Research and development is urgently needed into effective measures to reduce small cetacean bycatch in trawl nets, the bycatch of some small cetacean and pinniped species in gillnets and the entanglement of large baleen whales in pot or trap buoy-lines. While there are promising results from options such as loud pingers to deter dolphins from trawls and rope-less pot or trap systems, continued research and development in these areas should be a high priority. Few technical mitigation measures have undergone robust testing to determine their effectiveness in reducing mortality of the bycatch species while maintaining operational efficiency and target catch quality and quantity. Examples of effective measures include acoustic devices (pingers) that have reduced the bycatch of some small cetacean species, particularly harbour porpoise Phocoena phocoena, in gillnets, and appropriately designed exclusion devices which have reduced pinniped bycatch in some trawl fisheries. As a case study, my thesis focused on a ‘Sea Lion Exclusion Device’, or SLED, developed to reduce bycatch of the endangered New Zealand (NZ) sea lion (Phocarctos hookeri) in trawl fisheries. The SLED, installed before the trawl codend, has a stainless steel upwardly inclined grid that directs entrapped sea lions to a top-opening escape hole covered with a backward-facing hood. Target species are able to pass through the grid and into the codend. Research, development and implementation of the SLED was undertaken to reduce NZ sea lion bycatch in the squid trawl fishery operating near the Auckland Islands in sub-Antarctic New Zealand. Observed bycatch has been greatly reduced following SLED implementation. However, there has been scepticism and concern that significant ‘cryptic’ or unaccounted mortality may be occurring, particularly sea lions actively exiting the net but exceeding their breath holding capabilities before they reach the surface. I assessed the effectiveness of SLEDs by reviewing and evaluating trials and tests of sea lion interactions with SLEDs in trawl nets. I complemented this assessment by developing and fitting population models for the two largest NZ sea lion populations on the Auckland Islands and Campbell Island to evaluate the impact of fisheries bycatch on population growth, particularly after bycatch mitigation implementation. The available evidence shows SLEDs are effective in reducing NZ sea lion bycatch, sea lions are able to escape via SLEDs and are unlikely to sustain life-threatening injuries, and SLEDs contribute to reduced rates of observed sea lion mortality in trawl fisheries. Sea lion carcasses are also unlikely to passively drop out from a SLED top-opening escape hole. Further compelling evidence that cryptic mortality is unlikely to be significant is provided through NZ sea lion demographic parameters, population viability assessments and current population trajectories. Modelling of both the Auckland Islands and Campbell Island populations showed that current bycatch estimates from relevant trawl fisheries are sustainable following effective bycatch mitigation, and population growth rates are positive although slow. Modelling also indicated that disease events causing reduced pup production may greatly impact the population growth at the Auckland Islands, and management actions that reduce pup mortality would lead to increased growth rates for both populations. The development, refinement and testing of the SLED is an example of effective mitigation resulting in encouraging bycatch reduction and conservation outcomes. The conservation of NZ sea lions over the past decade should be regarded as a ‘good news’ story, with fisheries bycatch effectively mitigated, the population decline observed at the Auckland Islands halted, all other breeding populations increasing or stable, and the species breeding range expanded. While effective bycatch mitigation implementation has significantly improved the conservation status of the NZ sea lion, the focus should remain on addressing other threats, such as disease, which appear to be slowing population recovery.

<p>Mismatches in the spatiotemporal variability of resource, resource users and management actions breeds inefficiency in the management of marine resources. To date, the spatiotemporal resolution and extent of fisheries management has been largely dictated by logistical and political constraints, and secondarily by the geographic range of the species or meta-population dynamics. Management units are rarely smaller than 1000 km2 in developed coastal fisheries, and management measures generally occur at resolutions larger than 100 km2. From a temporal perspective, the finest resolution of management measures is at best a month but more generally a year. As such, attempts to manage processes and patterns at sub-10 km, sub-1 month resolution often involve some level of spatiotemporal mismatch. To address the obvious spatiotemporal mismatch between a dynamic ocean and static management, to allow for a comprehensive implementation of ecosystem-based fisheries management, and to minimize inefficiency in our management of marine resources, we must seek to develop more dynamic management measures that allow managers to address scales, processes and patterns occurring under ten kilometers.</p><p>In this dissertation I apply point pattern processes, cumulative distribution functions, receiver operator characteristic curves, simulated annealing tools, regression models and clustering techniques to develop examples of two dynamic management measures and to compare the efficiency of static versus dynamic management measures. I show that autocorrelation analysis can inform the distances and times used in real-time closures based on move-on rules. Further, I identify optimum bottom temperature threshold values to separate individual species within the Northeast Multispecies Fishery from Atlantic cod. Results demonstrate that dynamic spatiotemporal management measures are widely applicable, and more effective and more efficient than static time-area closures. Unexpected trends in some results due to a changing climate indicate possible increasing thermal overlap between Atlantic cod and many other species in the fishery. Implications of scale in fisheries management and the importance of coarse scale (1 - 10km) ecological patterns to fisheries are discussed.</p><br>Dissertation

Os jardins de coral e corais de águas frias (CWCs) são definidos como agregados relativamente densos de uma ou de várias espécies de coral que fazem parte de vários grupos taxonómicos, incluindo escleractínios (Scleractinia), corais negros (Antipatharia), corais moles (Alcyonacea) e penas-do-mar (Pennatulacea). Muitas destas espécies são engenheiros de ecossistemas, pois para além de criarem habitat, tais organismos também são capazes de alterar fatores bióticos e abióticos, possibilitando assim a colonização dos habitats bentónicos por outros organismos o que faz com que sejam muito importantes. Os corais também representam habitat essencial para muitas espécies de peixes e crustáceos que, em alguns casos, são explorados comercialmente. Outro dos serviços que estes habitats nos dão é relativo a materiais, para joias como é o caso do coral vermelho (Corallium rubrum) ou mesmo a nível da medicinal como a espécie Sarcodictyon roseum, em que alguns dos seus compostos estão a ser usados em ensaios clínicos para combater o cancro. Infelizmente, estes magníficos ecossistemas enfrentam imensas ameaças associadas às atividades humanas. Desde 2004, os jardins de coral e CWCs são considerados ecossistemas marinhos vulneráveis (VMEs). Os VMEs são definidos como espécies ou habitats que são raros ou únicos e que apresentam uma complexidade estrutural e funcional significativa, enquanto apresentam uma probabilidade limitada de recuperação aos impactos a que estão sujeitos. Tais atividades humanas incluem derrames de petróleo, acidificação dos oceanos e o impacto causado pelas pescas. Este último é, sem dúvida, o impacto mais preocupante e mais devastador principalmente por causa dos arrastos de fundo. Apesar de já existirem muitos estudos efetuados sobre os impactos da pesca em jardins de coral e CWCs, a sua maioria foca-se na pesca industrial como o caso dos arrastos. Como resultado, sabe-se muito pouco sobre os impactos causados pelas pescas artesanais (i.e. armadilhas, covos e redes de tresmalho e de emalhar) nestes habitats, apesar de representar 84% e 90% da frota pesqueira na Europa e mundo, respetivamente. Para combater os diversos impactos que afetam os ecossistemas de coral, já foram implementadas várias medidas, tais como criação de áreas marinhas protegidas (MPAs), o fecho temporário da pesca em algumas zonas e outras medidas relacionadas com as pescas, como a proibição de arrastos a profundidades inferiores a 800m instituída na Europa. Visto que os jardins de coral e CWCs são tão importantes ecologicamente e são hotspots de biodiversidade, o interesse em implementar medidas de conservação e recuperação de habitats têm crescido nos últimos tempos. No entanto, o número de trabalhos desenvolvidos até ao momento com o objetivo de restaurar habitats de corais circalitorais e profundos é limitado, pois este tipo de restauração é monetariamente dispendioso uma vez que no geral requer o uso de tecnologia subaquática especializada visto que estes habitats ocorrem maioritariamente a profundidades abaixo dos 50m de profundidade. Como tal, os objetivos deste trabalho são: 1) documentar o impacto causado por redes de emalhar usadas pela pesca artesanal nos jardins de coral e CWCs ao largo de Sagres (Portugal); 2) identificar hotspots de biodiversidade de corais e de capturas acidentais pela pesca artesanal que possam constituir áreas de gestão prioritárias, assim como melhorar o conhecimento sobre a biodiversidade de corais que existem ao largo de Sagres; 3) testar a viabilidade de usar corais de zonas profundas apanhadas acidentalmente pela pesca artesanal para ações de recuperação de habitats pouco profundos; e 4) testar o efeito da densidade e da composição de espécies em transplantes de corais de modo a fornecer indicações para projetos de recuperação de corais futuros. Este estudo foi dividido em duas componentes científicas: a documentação do impacto causado por redes de emalhar ao largo da costa de Sagres (Capítulo 2) e o estudo piloto de recuperação de habitats de corais usando biomassa apanhada nas redes de emalhar (Capítulo 3). Para o Capítulo 2, foi seguida a atividade de uma embarcação pesqueira durante 42 dias, onde foi documentado todos os corais recolhidos, assim como os seus tamanhos e algumas variáveis adicionais como a profundidade, malhagem, localização das redes lançadas, espécie alvo e número de indivíduos capturados. Em 118 redes documentadas, foram recolhidos 4,326 fragmentos/colónias de coral pertencentes a 22 espécies, o que representa 13% das espécies conhecidas para esta área. Em média, foram recolhidos 31.1 (±2.7) corais em cada rede, onde o máximo observado foi de 144 corais numa única rede. Adicionalmente, em média foram recolhidas 4.31 (±0.2) espécies de coral em cada rede, atingindo um máximo de 10 espécies numa só rede. Os resultados, mostram que as comunidades de corais recolhidas, tal como as suas quantidades, estão relacionadas com a profundidade a que as redes foram lançadas. Foram ainda identificadas 4 áreas com grande biodiversidade e abundância de corais e que foram designadas de hotspots. Os resultados deste estudo indicam que o impacto causado por redes de emalhar em jardins de coral e CWCs é muito superior ao que se pensava anteriormente, e revela a necessidade de novas medidas de conservação e o uso de artes de pesca alternativas. Além destas medidas, o desenvolvimento de protocolos de captura acidental excessiva de corais em águas nacionais que imponha a obrigatoriedade de pescar noutra zona pode também ser uma alternativa de gestão viável. Globalmente, este estudo revela a grande biodiversidade de espécies de coral que existe nos jardins de coral e CWCs ao largo de Sagres, bem como o impacto potencialmente significativo que a pesca artesanal pode ter em certas áreas. Para o Capítulo 3 de recuperação de habitats de coral, foram utilizados 12 recifes artificias construídos com blocos de alvenaria para replantar um total de 90 colónias de coral provenientes de descartes da pesca artesanal e que foram instala 20m de profundidade. O desenho experimental incluiu 4 tratamentos diferentes, de acordo com os dois fatores definidos para o estudo, nomeadamente a densidade dos transplantes (10 colónias por m2 vs. 20 colónias por m2) e composição de espécies (mono-específico vs. multi-específico). A espécie Eunicella verrucosa foi usada para os tratamentos mono- e multi-específico e as espécies Leptogorgia sarmentosa e Paramuricea grayi para o tratamento multi-específico. Em média 78% (±4%) dos corais transplantados sobreviveram até 8 meses pós-transplantação. Os resultados mostraram que o tratamento multi-específico de baixa densidade teve a melhor taxa de sobrevivência (87%) apesar do efeito dos tratamentos experimentais não ter sido estatisticamente significativo. No geral, as taxas de sobrevivência para cada tratamento experimental diferiram entre espécies. A espécie com maior taxa de sobrevivência foi a E. verrucosa (82%), enquanto que a P. grayi e L. sarmentosa tiveram a mesma taxa de sobrevivência (67%). A níveis de crescimento, o estudo demonstra que em média não houve crescimento efetivo do comprimento total dos ramos dos corais (-0.32cm±5.97cm) durante os 8 meses de monitorização. Contudo, o potencial de crescimento é bastante elevado em todas as espécies estudadas com a observação de um aumento máximo do comprimento total dos ramos das colónias de 72.61cm, 21.90cm e 113.42cm para a E. verrucosa, P. grayi e L. sarmentosa, respetivamente. Estes resultados, demostram o elevado grau de dinamismo do crescimento das colónias de octocorais, que se partem e voltam a crescer com frequência e rapidez, visto que muitos dos transplantes deste estudo tiveram tal dinâmica. Os resultados também mostraram que o uso da métrica do tamanho total dos ramos parece ser melhor do que a altura máxima das colónias para detetar variações no crescimento de espécies com morfologia ramificada como é o caso dos octocorais. No geral, a metodologia usada neste estudo foi bem-sucedida, sendo que apenas 10% das colónias morreram nos primeiros 3 meses de monitorização, o que indica que a fixação das colónias não constitui uma limitação. No entanto, são necessários estudos adicionais para se perceber se o uso de recifes artificiais poderá ser usado com outras espécies, visto que a sensibilidade a manipulação e características biológicas varia de espécie para espécie. Os dois estudos apresentados aqui demonstram também a importância de colaborar com as comunidades pesqueiras, quer para melhorar o conhecimento sobre a distribuição das espécies de coral e os impactos a que estão sujeitas, quer para juntos proteger estas espécies vulneráveis.<br>Coral gardens and cold-water corals are key habitats for many marine organisms, providing several goods and services. Because of their ecological importance and susceptibility to degradation caused by human activities, these habitats are considered vulnerable marine ecosystems. Fisheries are likely the most destructive threat affecting these habitats and there is an urgent need to understand how different fishing gear affects them, as well as how to implement effective conservation and protection measures that mitigate these impacts. This study aims to provide baseline information on the impact of fisheries using bottom-set gillnet locally on coral assemblages, and to develop a time-effective and low-cost restoration pipeline for both deep- and shallow-water populations using coral bycatch. In order to assess the impact of bottom-set gillnet fisheries on coral assemblages, the fishing activity and coral bycatch of one vessel were documented over 42 days, determining coral composition, specimen size, fishing depth, location, number of fish caught, mesh size and soaking time for each net deployed. In total, 4,326 specimens of corals belonging to 22 different species of corals were collected from 118 bottom-set gillnets. Additionally, we report 4 hotspots of coral biodiversity. This study confirms anecdotal evidence on the destructive impact of bottom-set gillnets on benthic ecosystems, demonstrating that the impact is greater than previously observed. For the restoration component of the study, twelve artificial reefs were used to transplant 90 corals obtained from bycatch, which were divided in 4 treatments varying transplant density and species composition. On average, 78% of the colonies transplanted survived after 8 months. The results show that total branch length metric can detect the changes in growth of branching organisms better than maximum height metric. Additionally, this study demonstrates that octocorals grow much faster than generally assumed, but the constant dynamic of breakage and recovery that these species cope with maintains their net growth relatively low.<br>I would like to thank the fishermen community in Sagres, for all the help with the coral specimens, inside and outside of the vessel, as well as their friendship. I offer my gratitude to DOCAPESCA Baleira-Sagres for providing the warehouse where corals were measured, maintained and stored over this period, to the Autoridade Marítima Nacional for the accommodation provided in Sagres, and to the Instituto da Conservação da Natureza e das Florestas (ICNF) for providing the authorization for the deployments. Additionally, this study was co-funded by the project HABMAR- “Contribuição para potenciar a proteção e revitalização da biodiversidade marinha e de habitats especiais na costa continental portuguesa”, MAR2020 projeto MAR-01.04.02-FEAMP-0018 “HABMAR”

Estimating the risk associated with species and pathogen movements involves considerable uncertainty. One key uncertainty concerns the extent and frequency of human-mediated species and pathogen movements relative to the distribution of recipient ecosystems. Baitfish use in Ontario, Canada is one of many pathways with the potential to introduce and spread biota to beyond their current geographic range. To determine the biological risk associated with baitfish use, models were used to estimate the probability of species occurrences throughout pathway levels, from the commercial harvest level, to retail tank and angler purchases, to movement and release by the end-user (i.e., the angler). Vector activity, as the primary contributor of species movements and introductions associated with this pathway, was modeled within a spatial interaction framework that incorporated landscape structure (e.g., the distribution of angling populations, lake size and sportfish richness, and their physical separation via least-cost routing of transportation networks) to predict the extent of movement. Agent-based models of vector activity were used to relate vector movements to region-specific probability thresholds of risk activity. Model outputs were used to estimate the movement and introduction of species and pathogens to lake ecosystems resulting from a variety of infection scenarios. Species results identified a pronounced reduction in the probability of non-target species occurrences throughout pathway levels. However, the occurrence of biological invaders and other non-target fishes at retail levels implied incidental bycatch throughout the pathway. Relatively short, frequent vector movements associated with incidentally purchased species were very likely, yet would not contribute to species range expansions due to the homogeneity of biological communities at those levels. However, rarer, yet considerably lengthier, vector movements associated with key species and pathogens implied the potential for low-probability, long-distance species and pathogen movements resulting from human activities.

Chapter 1 Introduction. Chapter 2 Gross and microscopic visceral anatomy of the male Cape fur seal with reference to organ size and growth. Chapter 3 Age determination and growth in the male Cape fur seal: part one, external body. Chapter 4 Age determination and growth in the male Cape fur seal: part two, skull. Chapter 5 Age determination and growth in the male Cape fur seal: part three, baculum. Chapter 6 Suture age as an indicator of physiological age in the male Cape fur seal. Chapter 7 Sexual dimorphism in the adult Cape fur seal: standard body length and skull morphology. Chapter 8 Reproduction in the male Cape fur seal: age at puberty and annual cycle of the testis. Chapter 9 Diet and foraging behaviour of the Cape fur seal. Chapter 10(a) The Impact of the fur seal industry on the distribution and abundance of Cape fur seals. Chapter 10(b) South African Airforce wildlife rescue: Cape fur seal pups washed from Black Rocks, Algoa Bay, during heavy seas, December 1976. Chapter 11(a) Operational interactions between Cape fur seals and fisheries: part one, trawl fishing. Chapter 11(b) Operational interactions between Cape fur seals and fisheries: part two, squid jigging and line fishing. Chapter 11(c) Operational interactions between Cape fur seals and fisheries: part three, entanglement in man-made debris. Chapter 12 Concentrations of heavy metals (Cd, Cu, Pb, Ni & Zn) and organochlorine contaminants (PCBs, DDT, DDE & DDD) in the blubber of Cape fur seals. Chapter 13 Endoparasites of the Cape fur seal. Chapter 14(a) Preliminary investigations of shark predation on Cape fur seals. Chapter 14(b) Aggressive behaviour of an adult male Cape fur seal towards a great white shark Carcharodon carcharias. Chapter 15 Conclusions and future directions.