This thesis investigates the influence of predator movements upon habitat selection and foraging success. It deals with two very distinct datasets one from a marine system, the snow crab (Chionoecetes opilio) fishery, and the second from a freshwater system, an experimental rainbow trout (Oncorhynchus mykiss) aquaculture operation. Deriving a standardized measure of catch from logbook data is important because catch per unit effort (CPUE) is used in fisheries analysis to estimate abundance, but it some cases CPUE is a biased estimate. For the snow crab fishery, a relative abundance measure was developed using fisher movements and logbook data that reflected commercially available biomass and produced an improved relative abundance estimate. Results from the aquaculture dataset indicate that escaped farmed rainbow trout continue to use the cage site when waste feed is available, while native lake trout do not interact with the cage. Once access to waste feed is removed, both lake trout and escaped rainbow trout do not use the cage site. This thesis uses methods to identify patterns and behaviours using movement tracks to increase our understanding of predator habitat usage.

This thesis investigates the influence of predator movements upon habitat selection and foraging success. It deals with two very distinct datasets one from a marine system, the snow crab (Chionoecetes opilio) fishery, and the second from a freshwater system, an experimental rainbow trout (Oncorhynchus mykiss) aquaculture operation. Deriving a standardized measure of catch from logbook data is important because catch per unit effort (CPUE) is used in fisheries analysis to estimate abundance, but it some cases CPUE is a biased estimate. For the snow crab fishery, a relative abundance measure was developed using fisher movements and logbook data that reflected commercially available biomass and produced an improved relative abundance estimate. Results from the aquaculture dataset indicate that escaped farmed rainbow trout continue to use the cage site when waste feed is available, while native lake trout do not interact with the cage. Once access to waste feed is removed, both lake trout and escaped rainbow trout do not use the cage site. This thesis uses methods to identify patterns and behaviours using movement tracks to increase our understanding of predator habitat usage.

Le déclin du thon rouge de l'Atlantique nord-est et de Méditerranée (ABFT, Thunnus thynnus) qui faisait suite à une forte surexploitation a été largement médiatisé au cours de la dernière décennie. Pour contrer cette tendance et reconstituer ce stock, d’importantes mesures de gestion ont été mises en place à partir de 2007. En dehors des difficultés liées à leur mise en œuvre et à leur contrôle, la gestion des pêcheries thonières est aussi limitée dans les capacités à suivre précisément les variations d’abondance de ces espèces dont les observations reposent principalement sur les données de pêche. Le manque d’indice d’abondance fiable fait que l’évaluation du thon rouge, comme celle des autres espèces de poissons grands pélagiques, est entachée d’importantes incertitudes. Cependant, les suivis aériens pourraient permettre de fournir un indice d’abondance du thon rouge. Ils sont en effet fréquemment utilisés pour l'évaluation de l'abondance des mammifères marins et aussi par les pêcheurs pour détecter les poissons épipélagiques, comme les thons. Dans ce contexte général, cette thèse a pour objectifs : (i) d'évaluer des facteurs qui affectent potentiellement la détectabilité des thons pendant les suivis aériens, (ii) d’analyser leur comportement horizontal et vertical et les facteurs environnementaux qui l’influencent, et (iii) d’intégrer les connaissances acquises pour développer un indice abondance robuste du thon rouge en Méditerranée Nord Occidentale. Les analyses reposent sur des suivis aériens conduits depuis 2000 dans le golfe du Lion, une zone de nourricerie importante pour le thon rouge. Une modélisation des données basée sur le « distance sampling » montre des effets significatifs des observateurs, de la taille des bancs de thons et de l'état de la mer sur l’estimation d’abondance. Cette étude confirme par ailleurs une augmentation importance des abondances entre 2003 et 2009, probablement en réponse aux mesures de gestion mises en œuvre depuis 2007 (notamment la taille minimale de débarquement de 30 kg). Pour évaluer les effets du comportement sur les estimations d'abondance, une étude a porté sur les trajectoires de thons issues du marquage électronique. Ces analyses montrent une disponibilité des thons rouge ainsi qu’une présence en surface dans la zone et la période (Août-Octobre) des suivis aériens ; résultat confortant la fiabilité de l’indice d’abondance. On note également des changements saisonniers du comportement, avec un approfondissement des thons à partir de mi-Novembre correspondant à la dé-stratification de la colonne d’eau. Le comportement de plongée profonde était particulièrement fréquent pendant les mois de forte productivité biologique (février-Mai), mais des plongées profondes ont également été observées à la fin de l'été en relation avec des fronts thermiques. La variabilité des schémas migratoires sur l’horizontale et du comportement sur la verticale indique une forte composante opportuniste, probablement liée à la disponibilité des ressources alimentaires. Les résultats obtenus durant cette thèse démontrent la faisabilité d’obtenir un indice d’abondance de thon rouge robuste à partir des suivis aériens (donc indépendants des données de pêche) et fournissent un cadre théorique et méthodologique pour une extension de ce type de suivi afin de diminuer les incertitudes autour de l’évaluation de ce stock. Outre le thon rouge, les suivis aériens ont également permis un suivi du rorqual commun (Balaenoptera physalus) et des dauphins rayés (Stenella coeruleoalba). La présence des mammifères marins semble également être liée à la productivité élevée et l'activité méso-échelle de la zone d'étude. Si les dauphins présentent une distribution spatiale en partie corrélée à celle du thon rouge, les rorquals ne présentent pas de forte co-occurrence avec le thon rouge, résultat qui confirmerait une certaine proximité des régimes alimentaires des thons et des dauphins. / Declines in Atlantic bluefin tuna stocks (ABFT, Thunnus thynnus), due to extensive over-fishing, have been widely publicized in recent decades. To counteract this trend, regulatory measures have been introduced by the fisheries managers, aiming at the rebuilding of ABFT stocks. However, apart from difficulties in controlling the implementation of these measures, fisheries management is limited in its capabilities to track their efficiency due to major uncertainties in the stock assessment. Indeed, there is a general need of reliable indicators of ABFT abundance. Aerial surveys may provide a helpful tool for the abundance monitoring of this highly exploited fish species. They are frequently used for the abundance assessment of marine mammals and also by fishermen to detect epipelagic fish, such as tunas. The aim of this thesis was to address these issues and to create a robust fishery-independent abundance index for ABFT through aerial surveys. To achieve this goal, the focus was set on (i) the assessment of factors that potentially affect the detectability of ABFT during the aerial surveys, (ii) the habitat use of ABFT, i.e. their horizontal and vertical behaviour as well as the factors driving it, and (iii) the integration of the knowledge gained through these analyses in the development of a robust index of ABFT abundance. Surveys were conducted from 2000 onwards in the Gulf of Lions, an important nursery ground for ABFT in the Northwestern Mediterranean Sea. Line transect modelling of the sighting data revealed significant effects of detectability changes on abundance estimates, related to the observer teams employed, the size of detected ABFT schools and the sea state during the aerial surveys. Derived estimates of ABFT abundance confirmed a significant increase from 2003 to 2009, likely reflecting the success of recently implemented management measures (e.g. minimum landing size of 30 kg since 2007). To assess behavioural effects on abundance estimates, auxiliary archival tagging experiments, conducted since 2007, focused on the presence and surface availability of ABFT during the aerial surveys, and aimed to identify factors influencing these variables. The data gained from these experiments demonstrated seasonal changes in the migratory behaviour of ABFT, but also a high area and surface presence of ABFT in the study zone during the survey period (August–October), supporting the reliability of the abundance index. Surface presence of ABFT decreased with the breakdown of the thermal stratification of the water column (mid-November), when the fish left the survey zone and moved South. By contrast, deep diving behaviour was particularly frequent during months of high biological productivity (February--May), although deep and unusual long spike dives were also observed during late summer in relation to thermal fronts. However, the variability in the migration patterns indicates a strong opportunistic component in both, the horizontal and vertical behaviour of ABFT, probably related to the availability of food resources. Apart from ABFT, the aerial surveys also allowed an abundance monitoring of fin whales (Balaenoptera physalus) and striped dolphins (Stenella coeruleoalba) as well as an analysis of their co-occurrence with ABFT. In fact, similar to ABFT, the presence of these species appeared to be related to the high productivity and mesoscale activity of the study zone, improving our understanding of their habitat use, essential for the conservation of these much less abundant and endangered species. Regarding the stock assessment of ABFT, the results gained through this thesis prove the feasibility to derive robust fishery independent abundance indicators for ABFT through aerial surveys, providing the theoretical and methodological background for an extension of these efforts for a more sustainable management of the stocks of this species.

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) / 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 / CAPEs / 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. / 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.