Tese(doutorado) - Universidade Federal do Rio Grande, Programa de Pós-Graduação em Oceanografia Biologica, Instituto de Oceanografia, 2011. / Submitted by Cristiane Gomides (cristiane_gomides@hotmail.com) on 2013-10-17T11:56:21Z No. of bitstreams: 1 Silvina.pdf: 4416418 bytes, checksum: 6765a88870d703ca47d4c0d7e6eafe23 (MD5) / Approved for entry into archive by Sabrina Andrade (sabrinabeatriz@ibest.com.br) on 2013-10-17T16:29:22Z (GMT) No. of bitstreams: 1 Silvina.pdf: 4416418 bytes, checksum: 6765a88870d703ca47d4c0d7e6eafe23 (MD5) / Made available in DSpace on 2013-10-17T16:29:22Z (GMT). No. of bitstreams: 1 Silvina.pdf: 4416418 bytes, checksum: 6765a88870d703ca47d4c0d7e6eafe23 (MD5) Previous issue date: 2011 / O objetivo geral desta tese foi identificar unidades populacionais (estoques ecológicos) e determinar padrões de uso de habitat de pequenos cetáceos no Atlântico Sul Ocidental por meio de traçadores químicos. A análise de isótopos estáveis foi utilizada como ferramenta para identificar estoques ecológicos de botos-cinza (Sotalia guianensis) e toninhas (Pontoporia blainvillei) e o uso do habitat de delfinídeos. Adicionalmente, as razões de Ba/Ca, Sr/Ca e Ba/Sr foram utilizadas, pela primeira vez, para caracterizar os padrões de uso de habitats por espécies de cetáceos ao longo de gradientes de salinidade. As análises químicas foram realizadas em dentes, utilizando um espectrômetro de massa acoplado a um analisador de elementos, no caso dos isótopos e a técnica de ablação a laser seguida da análise num espectrômetro de massa e plasma indutivamente acoplado, no caso do Ba e Sr. Quatro estoques ecológicos de botos-cinza foram identificados ao longo da costa do Brasil:(1) grupo Norte composto por animais de áreas costeiras adjacentes ao estuário do Amazonas (AmE) e indivíduos do Ceará (CE); (2) botos do Espírito Santo (ES); (3) animais do Norte do Rio de Janeiro (NRJ); e (4) indivíduos coletados na Baia da Babitonga (SC). Os animais coletados no Sul de São Paulo/Norte do Paraná (SP/PR) não constituíram um grupo separado. Os valores médios de 13C e 15N das toninhas sugeriram a existência de ao menos cinco estoques ecológicos habitando as seguintes regiões: (1) ES; (2) NRJ; (3) Norte de São Paulo (NSP), SP/PR e SC; (4) Rio Grande do Sul e Uruguai (RS e URU); e (5) Sul de Buenos Aires e Norte da Patagônia (ARG). Com base nos valores de 15N encontrados em ambas as espécies foi comprovada a existência de um gradiente latitudinal de enriquecimento em 15N nas costa Atlântica da América do Sul, provavelmente influenciado pelas contribuições diferenciais de nutrientes das distintas massas d'água que operam ao longo da mesma. A análise de isótopos estáveis de sete espécies de delfinídeos revelou valores altamente relacionados ao habitat e a ecologia trófica. As espécies apresentaram valores de 13C decrescentes entre espécies costeiras>de plataforma média e externa>oceânicas. Por outro lado, as espécies conformaram guildas tróficas evidenciadas pelos seus valores de isótopos de C e N. As razões Ba/Ca e Ba/Sr tiveram valores dez vezes mais altos em espécies de água doce (Inia geoffrensis e Sotalia fluviatilis) do que nas espécies marinhas. Os valores de Sr/Ca não variaram entre elas. Nas espécies marinhas, populações de toninhas, botos-cinza e Tursiops sp. residentes em áreas tipicamente estuarinas (p.ex. AmE, URU e ARG) apresentaram valores mais altos destas razões do que aquelas populações de áreas com menor influência de águas continentais (CE, NRJ, NSP, SP/PR e SC). O perfil de variação de Ba/Ca e Ba/Sr ao longo da vida obtido para nove indivíduos de Tursiops sp. do RS revelou três padrões temporais: perfis homogêneos e de valores baixos; perfis com variações temporais e valores mais altos do que os perfis homogêneos; e perfis com picos de valores extremamente altos, refletindo possivelmente, marcadas variações interanuais no regime de chuvas na região. / The main objective of this thesis was to identify population units (ecological stocks) and to determine the patterns of habitat use of small cetaceans in the Western South Atlantic by means of chemical tracers. Stable isotope analysis was used as tool for identifying ecological stocks of Guiana dolphins (Sotalia guianensis) and franciscanas (Pontoporia blainvillei) and for studying habitat use of delphinids. Additionally, the use of Ba/Ca, Sr/Ca and Ba/Sr ratios for characterizing habitat use patterns through aquatic salinity gradients was first assessed in cetaceans. Teeth chemical analyses using a mass spectrometer coupled to an elemental analyzer in the case of stable isotopes and with a laser ablation coupled to a mass and plasma inductively coupled spectrometer for the Ba, Ca and Sr analyses. Four ecological stocks of Guiana dolphins were identified along the Brazilian coast: (1) a northern group composed by dolphins from adjacent coastal areas of the Amazon estuary (AmE) and individuals from Ceará (CE); (2) dolphins from Espírito Santo (ES); (3) animals from northern Rio de Janeiro (NRJ); and (4) individuals collected in Babitonga Bay (SC). Guiana dolphins from southern São Paulo/northern Paraná (SP/PR) could not be grouped apart. Mean 13C and 15N values in franciscana teeth, suggested the existence of five ecological stocks inhabiting the following areas: (1) ES; (2) NRJ; (3) northern São Paulo (NSP), SP/PR and SC; (4) Rio Grande do Sul and Uruguay (RS and URU); and (5) southern Buenos Aires and northern Patagonia (ARG). Based on 15N values found in both species, a latitudinal trend in 15N enrichment along the Atlantic coast of South America was observed, probably due to varying nutrient contributions from different water masses. Stable isotope analysis of seven delphinids revealed values highly related to their habitat and trophic ecology. Mean 13C values decreased from coastal species>mid and outer continental shelf species>offshore. On the other hand, C and N isotopes values indicated the existence of trophic guilds among some species. Ba/Ca and Ba/Sr ratios were tenfold higher in freshwater species (Inia geoffrensis and Sotalia fluviatilis) than in marine species. Sr/Ca values did not differ between them. Among marine species, resident populations of franciscanas, Guiana dolphins and Tursiops sp. from typical estuarine areas (e.g. AmE, URU and ARG) presented higher ratios than populations from areas with minimal freshwater discharge (CE, NRJ, NSP, SP/PR and SC). Ba/Ca and Ba/Sr age-related profiles from nine individuals of Tursiops sp. from RS revealed three temporal patterns: low values with minimal temporal variation; intermediate values with peaks and troughs; and high values with peaks and troughs, the latter probably reflecting interannual variations in precipitation rates.

Dissertação(mestrado) - Universidade Federal do Rio Grande, Programa de Pós–Graduação em Oceanografia Biológica, Instituto de Oceanografia, 2013. / Submitted by Cristiane Gomides (cristiane_gomides@hotmail.com) on 2013-11-19T11:38:07Z No. of bitstreams: 1 elisa.pdf: 1223620 bytes, checksum: b663448fea1aa40da19e4272a5aab6d2 (MD5) / Approved for entry into archive by Angelica Miranda (angelicacdm@gmail.com) on 2013-11-20T21:35:09Z (GMT) No. of bitstreams: 1 elisa.pdf: 1223620 bytes, checksum: b663448fea1aa40da19e4272a5aab6d2 (MD5) / Made available in DSpace on 2013-11-20T21:35:09Z (GMT). No. of bitstreams: 1 elisa.pdf: 1223620 bytes, checksum: b663448fea1aa40da19e4272a5aab6d2 (MD5) Previous issue date: 2013 / A vulnerabilidade dos mamíferos marinhos a ameaças que comprometam a manutenção de suas populações é uma das razões que os levam a ser alvo de pesquisas que visam sua conservação. A baleia-franca-austral, Eubalaena australis, é uma dessas espécies, sendo que a caça foi uma forte ameaça a todas as suas populações. No Brasil, sua principal concentração reprodutiva ocorre no litoral de Santa Catarina, onde indivíduos da espécie são observados anualmente entre os meses de julho e novembro. Esses indivíduos pertencem a uma população compartilhada entre Brasil e Argentina e que se recupera a taxas significativas. Esforços vêm sendo realizados a fim de preservar essa importante área para a espécie, porém faz-se necessário um melhor conhecimento acerca do seu uso de habitat na região, bem como de fatores que podem influenciar a taxa relativa de nascimentos de indivíduos, a qual possui forte relação com a recuperação populacional. O objetivo do presente trabalho foi testar a influência de variáveis temporais e ambientais na distribuição da espécie no litoral sul de Santa Catarina e avaliar a influência de anomalias climáticas em sua taxa relativa de nascimentos através de Modelos Lineares Generalizados e correlação cruzada, respectivamente. Os resultados sugerem que tanto grupos de fêmeas com filhotes quanto de adultos desacompanhados preferem enseadas amplas, com declive suave e parecem evitar enseadas com grandes ângulos de inclinação quando ventos intensos da direção leste atuam sobre elas. O sucesso reprodutivo dos indivíduos parece influenciado por anomalias climáticas, relacionadas principalmente à temperatura superficial da água do mar, que afetam a disponibilidade de alimento em sua área de alimentação, no entorno das ilhas Geórgias do Sul. / Vulnerability to threats that can compromise population maintenance is one of the reasons why many marine mammal species are targeted for conservation research. The southern right whale, Eubalaena australis, is one such species, and hunting was a strong threat to all of their populations. On the Brazilian coast, its main reproductive site is located along the Santa Catarina State, where individuals of the species are observed annually between July and November. These individuals belong to a population shared between Brazil and Argentina, which recovers at significant rates. Efforts have been made to preserve this important area for the species, but the habitat use of right whales in the region needs to be better known, as well as factors that may be influencing their relative birth rates, which are strongly related to population recovery. The objective of this study was to test the influence of temporal and environmental variables on species distribution at the southern coast of Santa Catarina and whether climate anomalies influence their relative birth rate using Generalized Linear Models and cross correlation, respectively. Our results suggest that both cowcalf and unaccompanied adult groups prefer large bays with gentle slope and they seem to avoid bays with great inclination angles when strong east winds are acting on them. The reproductive success of individuals appears to be influenced by climate anomalies, mainly the ones related to sea surface temperature, which affect food availability on the species feeding area, in the vicinity of South Georgia Islands.

Les prédateurs marins supérieurs, ici les cétacés et les oiseaux marins, doivent développer des stratégies optimales d’utilisation des ressources et des habitats. Notre objectif était d’explorer leurs habitats en fonction de leurs coûts de vie. Nous avons postulé que les prédateurs coûteux étaient contraints d’occuper les habitats de meilleure qualité alors que les prédateurs plus économes pouvaient occuper les habitats de qualité moindre. Nous nous sommes basés sur des guildes de cétacés et oiseaux définies selon leurs coûts de vie et les observations de survols aériens dans trois régions tropicales (l’Atlantique Ouest tropical, le Sud Ouest de l’Océan Indien et la Polynésie française). Nous avons construit des modèles additifs généralisés à partir de variables physiographiques (ex : profondeur), océanographiques (ex : activité tourbillonnaire) et biologiques (ex : chlorophylle et micronecton) pour décrire la qualité des habitats. Nous avons d’abord modélisé les habitats des cétacés et oiseaux à l’échelle régionale. Les cétacés coûteux occupaient les habitats de meilleure qualité alors que les cétacés plus économes occupaient aussi les habitats de qualité moindre. La distribution des oiseaux reflétait principalement celle des colonies et leur dépendance à la qualité de l’habitat semblait moins claire. Nous avons ensuite mis en évidence des propriétés génériques de distribution des cétacés et fourni des prédictions circumtropicales. Cette thèse a donné un nouvel aperçu des stratégies d’utilisation des habitats des prédateurs supérieurs à la lumière de leurs coûts de vie. Ces prédictions spatiales ont des implications majeures pour la gestion de ces espèces et de leurs écosystèmes. / Marine top predators, here cetaceans and seabirds, must develop optimal strategies of resource and habitat utilization. The main goal of this dissertation was to investigate cetacean and seabird strategies of habitat utilization in relation to their energetic costs of living. We hypothesized that predators with high costs of living should be constrained to high quality habitats, whereas less active predators could cope with habitats of lesser quality. We studied the habitats of cetacean and seabird guilds defined according to their likely costs of living. We relied on sightings collected from aerial surveys in three tropical regions (the western tropical Atlantic, the Southwest Indian Ocean and French Polynesia). We built generalized additive models based on a range of physiographic (e.g. depth), oceanographic (e.g. mesoscale activity) and biological variables (e.g. chlorophyll concentration and micronekton) to describe the quality of pelagic habitats. We first modeled cetacean and seabird habitats at the regional scale. Energetically costly cetaceans appeared to be constrained to the highest quality habitats, whereas less active cetaceans exploited habitats of lesser quality. Seabird distributions primarily reflected colony locations and their dependences on habitat quality were less clear. We then highlighted generic properties of cetacean distributions and provided predictions at the circumtropical scale. This dissertation gave new insights on top predator strategies of habitats utilization in light of their costs of living. These spatial predictions have significant implications for the management of these species and of their pelagic ecosystems.

This work is mainly based on the collection of Neogene (Miocene-Pliocene) odontocetes (toothed whales) from the area of Antwerp (northern Belgium, southern margin of the North Sea Basin) preserved at the Institut royal des Sciences naturelles de Belgique (IRSNB). <p> The systematic revision of members of the long-snouted dolphin family Eurhinodelphinidae leads to the description/re-description of five species in the genera Eurhinodelphis (E. cocheteuxi and E. longirostris), Schizodelphis (S. morckhoviensis), and Xiphiacetus n. gen. (X. cristatus and X. bossi). Furthermore, the systematic status of several eurhinodelphinid species from other localities in the world is revised. A cladistic analysis with the parsimony criterion is undertaken to highlight the phylogenetic relationships of several eurhinodelphinid taxa with other fossil and extant odontocetes. Eurhinodelphinids are more closely related to the beaked whales; the latter are distinctly separated from the sperm whales. A second analysis, with a likelihood criterion, reaches nearly identical results. Then a separate parsimony analysis investigates the relationships within the family Eurhinodelphinidae; the results suggest sister-group relationships between Schizodelphis + Xiphiacetus and Ziphiodelphis + (Mycteriacetus + Argyrocetus) and a more stemward position for Eurhinodelphis. After that, anatomical, palaeogeographic, and phylogenetic data allow several suggestions about the ecological features of the eurhinodelphinids. The extinction of this family, before the end of the Miocene, is commented, related to the changes in the biodiversity of other odontocete groups and to a contemporary major sea level drop. <p>\ / Doctorat en sciences, Spécialisation biologie animale / info:eu-repo/semantics/nonPublished

This study focuses on the habitats of cetaceans in the Mid-Atlantic Bight, a region characterized by bathymetric diversity and the presence of distinct water masses (i.e. the shelf water, slope water, and Gulf Stream). The combination of these features contributes to the hydrographic complexity of the area, which furthermore influences biological productivity and potential prey available for cetaceans. The collection of cetacean sighting data together with physical oceanographic data can be used to examine cetacean habitat associations. Cetacean habitat modeling is a mechanism for predicting cetacean distribution patterns based on environmental variables such as bathymetric and physical properties, and for exploring the potential ecological implications that contribute to cetacean spatial distributions. We can advance conservation efforts of cetacean populations by expanding our knowledge of their habitats and distribution. Generalized additive models (GAMs) were developed to predict the spatial distribution patterns of sperm whales (Physeter macrocephalus), pilot whales (Globicephala spp.), bottlenose dolphins (Tursiops truncatus), and Atlantic spotted dolphins (Stenella frontalis) based on significant physical parameters along the continental shelf-break region in the Mid-Atlantic Bight. Data implemented in the GAMs were collected in the summer of 2006 aboard the NOAA R/V Gordon Gunter. These included visual cetacean survey data collected along with physical data at depth via expendable bathythermograph (XBT), and conductivity-temperature-depth (CTD) instrumentation. Additionally, continual surface data were collected via the ship’s flow through sensor system. Interpolations of physical data were created from collected point data using the inverse distant weighted method (IDW) to estimate the spatial distribution of physical data within the area of interest. Interpolated physical data, as well as bathymetric (bottom depth and slope) data were extracted to overlaid cetacean sightings, so that each sighting had an associated value for nine potentially significant physical habitat parameters. A grid containing 5x5 km grid cells was created over the study area and cetacean sightings along with the values for each associated habitat parameter were summarized in each grid cell. Redundant parameters were reduced, resulting in a full model containing temperature at 50 m depth, mixed layer depth, bottom depth, slope, surface temperature, and surface salinity. GAMs were fit for each species based on these six potentially significant parameters. The resultant fit models for each species predicted the number of individuals per km2 based on a unique combination of environmental parameters. Spatial prediction grids were created based on the significant habitat parameters for each species to illustrate the GAM outputs and to indicate predicted regions of high density. Predictions were consistent with observed sightings. Sperm whale distribution was predicted by a combination of depth, sea surface temperature, and sea surface salinity. The model for pilot whales included bottom slope, and temperature at 50 m depth. It also indicated that mixed layer depth, bottom depth and surface salinity contributed to group size. Similarly, temperature at 50 m depth was significant for Atlantic spotted dolphins. Predicted bottlenose dolphin distribution was determined by a combination of bottom slope, surface salinity, and temperature at 50 m depth, with mixed layer depth contributing to group size. Distribution is most likely a sign of prey availability and ecological implications can be drawn from the habitat parameters associated with each species. For example, regions of high slope can indicate zones of upwelling, enhanced vertical mixing and prey availability throughout the water column. Furthermore, surface temperature and salinity can be indicative of patchy zones of productivity where potential prey aggregations occur. The benefits of these models is that collected point data can be used to expand our knowledge of potential cetacean “hotspots” based on associations with physical parameters. Data collection for abundance estimates, higher resolution studies, and future habitat surveys can be adjusted based on these model predictions. Furthermore, predictive habitat models can be used to establish Marine Protected Areas with boundaries that adapt to dynamic oceanographic features reflecting potential cetacean mobility. This can be valuable for the advancement of cetacean conservation efforts and to limit potential vessel and fisheries interactions with cetaceans, which may pose a threat to the sustainability of cetacean populations.

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

Projects to observe the marine biota are developed worldwide to mitigate the impacts of anthropogenic noise on marine mammals. The first chapter of this dissertation analyzes guides published by various institutions to orient the methodology to be applied in those projects, in order to ensure better efficacy in mitigating and quality of acquired data. Therefore bibliographic research was made on the internet and it was found 16 guides specific to monitoring cetaceans. The protocols were similar in methodology and mitigation measures suggested. The second chapter analyzed a set of forms utilized during daytime visual observations aboard of drilling rigs occurred in the Sergipe Basin between 2010 and 2012. The objective of the analysis was to evaluate the methodology applied in the project of sighting of marine mammals during oil and gas drilling since the guide applied has been customized from protocols to mitigate the impact of marine seismic surveys. It was proposed indicators of quality based in the content of fields of the forms. The results indicate that the data have good quality to be used in scientific studies of occurrence, distribution and abundance of cetaceans. However, the method used in the monitoring of cetaceans conducted in offshore drilling activities proved ineffective for the purposes of assessing the impacts of oil and gas drilling phase on this group of animals since that the method adopted does not emphasize the behavior exhibited by cetaceans and use forms generalized to four different vertebrate groups. / Projetos de observação de biota marinha são desenvolvidos em todo mundo como forma de mitigação de impactos de atividades produtoras de ruídos sobre os mamíferos marinhos. O primeiro capítulo dessa dissertação analisa os guias publicados por diversas instituições em nível mundial, com o propósito de garantir melhor eficácia na mitigação e na qualidade dos dados adquiridos. Para tanto foi realizada pesquisa bibliográfica na rede mundial de computadores onde foram encontrados 16 guias publicados e uma comparação entre esses protocolos. Uma das conclusões retiradas está no alto nível de padronização metodológica encontrada na aquisição dos dados de ocorrência e nas medidas mitigatórias a serem implementadas ao ser observado um animal nas proximidades da área de atividade. Como resultado geral, os guias e protocolos se assemelham substancialmente nos requisitos exigidos, orientando as mesmas medidas mitigadoras nos documentos analisados. No segundo capítulo foram analisados os formulários preenchidos durante a implementação de observações visuais diurnas, a bordo das plataformas de perfuração, realizadas durante perfurações ocorridas na Bacia de Sergipe entre 2010 e 2012. A metodologia aplicada nessas observações segue o Guia de Monitoramento da Biota Marinha publicado pelo IBAMA em 2005. As análises tiveram como objetivo a avaliação da qualidade das informações contidas nos formulários de observação de mamíferos marinhos executados em atividades de perfuração marítima, uma vez que o guia que o embasou foi publicado para atividades de aquisição de dados sísmicos. Para essa avaliação foram criados indicadores de qualidade os quais ponderaram as informações inseridas nos formulários de registro de biota preenchidos em cada ocorrência. Como resultado pode-se concluir que os dados podem ser considerados de boa qualidade para estudos de ocorrência, distribuição e abundância. Entretanto, o método utilizado no monitoramento de cetáceos conduzidos em atividades de perfuração marítima mostrou-se ineficaz para os propósitos de avaliação dos impactos dessa atividade petrolífera sobre qualquer um dos grupos de cetáceos registrados, uma vez que este não dá ênfase ao comportamento exibido, generalizando o formulário para os quatro grupos de vertebrados. Diante do exposto e afim de orientar a execução de projetos de monitoramento de mamíferos marinhos a serem executados a bordo de plataformas de perfuração foi apresentado no último capítulo, uma proposta de guia metodológico aplicável durante esse tipo de atividade de exploração e produção de petróleo.

The historical range of the Indus River dolphin has declined by 80% since the 19th century and has been fragmented into 17 river sections by construction of irrigation barrages. Dolphin sighting and interview surveys showed that river dolphins persist in six river sections, have been extirpated from ten, and are of unknown status in the remaining section. Logistic regression and survival modelling showed that low dry season river discharge was the primary factor responsible for the Indus dolphins range decline. Abundance of the three largest Indus dolphin subpopulations was estimated using tandem vessel-based direct counts, corrected for missed animals using conditional likelihood capture-recapture models. The entire subspecies was estimated to number between 1550-1750 in 2006. Dolphin encounter rates within the Guddu-Sukkur subpopulation (10.35/km) were the highest reported for any river dolphin and direct counts suggest that this subpopulation may have been increasing in abundance since the 1970s when hunting was banned. The dry season habitat selection of Indus dolphins was explored using Generalised Linear Models of dolphin distribution and abundance in relation to river geomorphology, and channel geometry in cross-section. Channel cross-sectional area was shown to be the most important factor determining dolphin presence. Indus dolphins avoided channels with small cross-sectional area &lt;700m2, presumably due to the risk of entrapment and reduced foraging opportunities. The phylogenetics of Indus and Ganges River dolphins was explored using Mitochondrial control region sequences. Genetic diversity was low, and all 20 Indus River dolphin samples were identical. There were no haplotypes shared by Indus and Ganges River dolphins, phylogenetic trees demonstrated reciprocal monophyletic separation and Bayesian modelling suggested that the two dolphin populations diverged approximately 0.66 million years ago. Declining river flows threaten Indus dolphins especially at the upstream end of their range, and it is important to determine how much water is required to sustain a dolphin population through the dry season. Fisheries interactions are an increasing problem that will be best addressed through localised, community-based conservation activities.

The ranging behaviour, habitat preferences, genetic structure, and demographic parameters of bottlenose dolphins living in the Azores were studied using data collected from 1999 to 2004. Only 44 dolphins out of 966 identified were frequently sighted within and between years and showed strong site fidelity. The remaining individuals were either temporary migrants from within or outside the archipelago, or transients. Estimates of home range size were three times larger than previously reported for this species, possibly as a result of the lower availability of food resources. Mitochondrial DNA sequences showed very high gene and nucleotide diversity. There was no evidence of population structuring within the Azores. The Azorean population was not differentiated from the pelagic population of the Northwest Atlantic, suggesting the "unproductive" waters of the Atlantic do not constitute a barrier to dispersal. Population size, survival and temporary emigration rates were estimated using open-population models and Pollock's robust design. A few hundreds of dolphins occur in the area on a given year, though the majority should use it temporarily, as suggested by the high emigration rates. Bottlenose dolphins preferentially used shallow areas with high bottom relief. Temporal and spatial persistence of dolphin-habitat associations documented in this study further supports the idea of a close relationship between certain bathymetric features and important hydrographic processes and suggests the occurrence of prey aggregations over these areas may be, to some extent, predictable. Several results of this study suggest there are no reasons for concern about the status of this population. Yet, the resident group may be negatively affected by increasing pressure from the whale watching activity. Although the proposed Marine Park constitutes important habitat for resident dolphins, at present, the area is clearly insufficient to satisfy their spatial requirements and its conservation value may be limited.

Les cétacés grands plongeurs, cachalots Physeteridae et Kogiidae, et baleines à bec Zipiidae, sont des espèces marines rares. Leur faible densité, aire de distribution étendue et faible disponibilité en surface génèrent de faibles taux d’observations. Cette particularité constitue un défi pour la modélisation d’habitat de ces espèces, préalable à leur conservation. Les modèles doivent gérer l’abondance de zéros qui limitent leur capacité à inférer des résultats écologiquement cohérents. Cette thèse vise donc à trouver une méthodologie adaptée aux jeux de données abondants en zéros, à déterminer comment les variables environnementales influencent la distribution des grands plongeurs et à prédire les zones potentielles qu’ils utilisent. Tester la capacité de prédiction de différents modèles d'habitat confrontés à un nombre décroissant d’observations a permis de souligner la pertinence d’un modèle, même si un minimum de 50 observations est nécessaire pour fournir des prédictions fiables. Des données issues de différentes campagnes visuelles ont été assemblées afin de produire les premières cartes de densités de grands plongeurs à l’échelle de l’océan Atlantique Nord et la mer Méditerranée. Les densités les plus élevées sont prédites dans les eaux entre 1500 et 4000 m de profondeur et près des fronts thermiques, particulièrement le long des pentes continentales et à l'ouest de l'océan Atlantique Nord. Par ailleurs, l’analyse de la transférabilité des modèles a montré une variation des habitats préférentiels en fonction des écosystèmes. Finalement, cette thèse permet de discuter les défis de la modélisation statistique appliquée aux espèces rares et les applications de gestion associées. / Deep-diving cetaceans, sperm- and beaked whales Physeteridae, Kogiidae and Ziphiidae, are rare marine species. Due to their low densities, wide distribution ranges and limited presence at the water surface, visual surveys usually result in low sighting rates. This paucity of data challenges the modelling of their habitat, prerequisite for their conservation. Models have to cope with a great number of zeros that weakens the ability to make sound ecological inferences. Consequently, this thesis aimed at finding a methodology suitable for datasets with a large number of zeros, determining how environmental variables influence deep-diver distributions and predicting areas preferentially used by these species. By testing the predictive performance of various habitat models fitted to decreasing numbers of sightings, I selected the most suitable model and determined that at least 50 sightings were needed to provide reliable predictions. However, individual surveys can rarely provide sufficient deep-diver sightings thus I merged many visual survey datasets to produce the first basin-wide deep-diver density maps in the North Atlantic Ocean and the Mediterranean Sea. Highest densities were predicted in waters from 1500-4000 m deep and close to thermal fronts ; hotspots were predicted along the continental slopes, particularly in the western North Atlantic Ocean. In addition, a model transferability analysis highlighted that habitat drivers selected by the models varied between contrasted large ecosystems. Finally, I discussed challenges related to statistical modelling applied to rare species and the management applications of this thesis.