La surexploitation des prédateurs de haut niveau trophique (HTLP) peut déclencher des cascades trophiques qui souvent conduisent à une simplification des réseaux trophiques marins en réduisant leur résistance aux impacts humains. Les aires marines protégées (AMP) peuvent favoriser des augmentations d’abondance et biomasse des HTLP, mais la complète restauration des interactions trophiques, lorsque cela est possible, nécessite des délais importants. Cette thèse vise à proposer des outils intégrés de gestion pour évaluer le retour des HTLP et la restauration des interactions trophiques dans les AMP méditerranéennes, et à évaluer l’efficacité de ces outils pour estimer les impacts de la pêche sur les HTLP et le réseau trophique associé. Deux approches souvent éloignées ont été combinées : les suivis de terrain et la modélisation des réseaux trophiques. Pour échantillonner la communauté de poissons, nous avons proposé d'améliorer la technique traditionnelle de recensement visuel sous-marin en recourant à des transects de taille variable, adaptée à la mobilité des poissons. Cette méthode a alors permis d'augmenter la précision des estimations de densité et de biomasse des HTLP dans les trois AMP méditerranéennes suivies. Ensuite, nous avons évalué l'apport de la modélisation trophique avec les approches EwE et EcoTroph comme outil de gestion écosystémique pour les AMP méditerranéennes. Une structure standard de modèle a été proposée comme étant le meilleur compromis entre la complexité du modèle, la faisabilité de sa construction et la fiabilité de ses sorties. / The overexploitation of high trophic level predators (HTLP) may trigger trophic cascades, often leading to a simplification of marine food-webs and reducing their resilience to human impacts. Marine protected areas (MPAs) can foster increases of HTLP abundance and biomass, but long time frames are needed to observe a recovery, when possible, of lost trophic interactions. This PhD aimed to propose integrated management-tools to monitor HTLP recovery and the restoration of trophic interactions in Mediterranean MPAs, and to evaluate the effectiveness of these tools at assessing fishing impacts upon HTLP and the associated food-web. Two often distant approaches were combined: field monitoring and food-web modelling. First, to survey the fish assemblage, we proposed to improve the traditional underwater visual census technique of one size-transects with variable size transects adapted to fish mobility. This improvement increased the accuracy of density and biomass estimates of HTLP at three Mediterranean MPAs. We then evaluated the potential of food-web modelling with the Ecopath with Ecosim and Ecotroph approach as a tool to inform ecosystem-based management in Mediterranean MPAs. We proposed a standard model structure as the best compromise between model complexity, feasibility of model construction in terms of data collection, and reliability of model outputs. Key functional groups for which local accurate biomass data should be collected in priority in order to get reliable model outputs were identified.

A growing number of scientists are investigating applications of landscape ecology principles to marine studies, yet few coral reef scientists have examined spatial patterns across entire reefscapes with a holistic ecosystem-based view. This study was an effort to better understand reefscape ecology by quantitatively assessing spatial structures and habitat arrangements using remote sensing and geographic information systems (GIS). Quantifying recurring patterns in reef systems has implications for improving the efficiency of mapping efforts and lowering costs associated with collecting field data and acquiring satellite imagery. If a representative example of a reef is mapped with high accuracy, the data derived from habitat configurations could be extrapolated over a larger region to aid management decisions and focus conservation efforts. The aim of this project was to measure repeating spatial patterns at multiple scales (10s m2 to 10s km2) and to explain the environmental mechanisms which have formed the observed patterns. Because power laws have been recognized in size-frequency distributions of reef habitat patches, this study further investigated whether the property exists for expansive reefs with diverse geologic histories. Intra- and inter-reef patch relationships were studied at three sites: Andavadoaka (Madagascar), Vieques (Puerto Rico), and Saipan (Commonwealth of the Northern Mariana Islands). In situ ecological information, including benthic species composition and abundance, as well as substrate type, was collected with georeferenced video transects. LiDAR (Light Detection and Ranging) surveys were assembled into digital elevation models (DEMs), while vessel-based acoustic surveys were utilized to empirically tune bathymetry models where LiDAR data were unavailable. A GIS for each site was compiled by overlying groundtruth data, classifications, DEMs, and satellite images. Benthic cover classes were then digitized and analyzed based on a suite of metrics (e.g. patch complexity, principle axes ratio, and neighborhood transitions). Results from metric analyses were extremely comparable between sites suggesting that spatial prediction of habitat arrangements is very plausible. Further implications discussed include developing an automated habitat mapping technique and improving conservation planning and delimitation of marine protected areas.

This study presents a detailed investigation into size, density and community structure of temperate marine reef fish in the medium-sized Goukamma Marine Protected Area (Goukamma MPA) and adjacent fishing grounds on the south coast of South Africa. The oceanographic conditions, the spatial distribution of the benthic community and the prevailing fishing effort are also described. Life history traits and per-recruit (PR) models for the principle target species, roman (Crysoblephus laticeps) are compared between the protected and exploited area. From the study results, various strategies are proposed for the use of MPAs in the conservation and management of linefish species along South Africa’s south coast. The distribution and topography of reefs in the protected and exploited sections of the study area were found to be comparable. Atmospheric pressure ranged from 992 to 1,032 mb, being significantly lower in summer. Wind speeds ranged from 0.7 to 71.3 km/h. Water temperatures ranged between 9.0 and 22.2 ºC and turbidity between 0.3 and 45.8 NTU. Water temperature and clarity were uniformly low in winter. In summer the water was generally warm, clear and stratified, with a thermocline at around 20 m, although intermittent upwelling events caused water temperature to decrease and clarity to deteriorate. Current speeds ranged between 0.11 and 2.59 km/h and were significantly higher in spring and autumn. Easterly currents prevailed in spring, summer and autumn and westerly and southerly currents in winter. Hake (Merluccius capensis), various resident reef fish and kob (Argyrosomus japonicus) were most frequently targeted by the local linefishery. A significant amount of illegal fishing was found to occur in the protected area. Fishing effort was found to be highest around the border of the MPA (2.7 boats/km²) and lowest in the core of the MPA (0.2 boats/km²). If law enforcement remains poor it may be necessary to adapt the management strategy to extend the reserve, thereby mitigating against illegal fishing and ensuring a core area of no exploitation. Various other alternatives were investigated and it was demonstrated that the amount of fish caught of legal size could be increased by about 23% and post-release mortality of undersized fish reduced by 50% through the introduction of a suit of restrictive measures. Randomly stratified underwater visual census (UVC) and controlled fishing were used to investigate the ichthyofauna and benthic community at protected and exploited sites in the study area. Resulting density and size data from 273 fishing sites and 177 point counts were analyzed using generalized linear models (GLMs). Fish communities were found to vary significantly, depending on the level of exploitation. Roman, the principle reef fish species targeted by the fishery had significantly higher densities within the protected parts of the study area (CPUE: 4.3 fish/anglerhour; UVC: 2.2 fish/point-count) as compared to the exploited part (CPUE: 3.4 fish/anglerhour; UVC: 1.8 fish/point-count), correlating strongly with the observed fishing effort. Also mean sizes were significantly higher in the protected area (299 mm from fishing survey and 233 mm from diving estimates) as compared to the exploited section (283 mm from fishing survey and 198 mm from diving estimates). Although other fish species also had significantly higher mean sizes at protected sites in most cases their densities were significantly lower. This suggests a top-down control of the fish community by the dominant predator (roman). The results of the UVC showed the diversity of the ichthyofauna to be significantly higher inside the protected area. Interestingly this did not apply to the results of the controlled fishing experiment where the diversity of fish in the catch was lower in the protected area - a result that may be explained by the selectivity of fishing for the most aggressive species – and a reminder of the limitations of controlled fishing experiments. Possibly the most important finding of the study revolved around the benthic community. These were significantly different at exploited and protected sites, with algae and crinoids more abundant at exploited sites. Crinoids are the principle food of roman and were low in abundance where roman abundances were high, suggesting that the dominant top predator reduced crinoids. Furthermore, it substantiates the correlation of roman abundance with fishing effort, since habitat preferences can be ruled out by the observed causal predator-prey distribution pattern. Low algae abundances at protected sites correlated with high strepie (Sarpa salpa) frequencies within the fish communities encountered there. Strepie, a shoaling and abundant benthic grazer, does not compete for food with roman, suggesting a high potential for coexistence of the two species. As expected, and found by other studies, life history traits of roman differed between protected and exploited sample-sites. With a significantly lower age-at-maturity and age-atsex- change, the exploited population showed a typical response to fishing effort. The sex ratio of this protogynous hermaphrodite was found to be sustained at healthy levels by phenotypic plasticity. However, one important additional factor was highlighted by the study; the average condition factor of the protected population was significantly lower (0.0283 g/cm³) compared to the exploited population (0.0295 g/cm³). This was probably due to the higher intra-specific competition for lower food abundance in the protected area. Interestingly the diving and fishing survey methods yielded similar mortality results for roman. Total mortality rate estimates derived from length frequency analysis from the diving and fishing survey were not different (0.32 and 0.29 y⁻¹, respectively) as were natural mortality rate estimates (0.24 and 0.19 y⁻¹, respectively). Natural mortality rate (M) estimates indicated by Pauly’s and Hoenig’s relationship were similar (0.25 and 0.23 y⁻¹, respectively). Detailed yield-per-recruit (Y/R) and spawner biomass-per-recruit (SB/R) analyses were presented for different levels of M, varying age-at-recruitment (tR) and fishing mortality (F). Current tR (7.60 y) and F (0.16 and 0.25 y⁻¹, from the diving and fishing dataset, respectively) suggests an optimal exploitation of the population in the exploited part of the study area. However, a separate SB/R analysis of the male part of the population showed their vulnerability to over-exploitation, even at reduced age-at-sex-change from fishing. There therefore remains a high risk of recruitment failure for the roman population. Of course MPAs can be used to measure stock status directly if the influence of factors such as cachability, habitat and sampling method on CPUE assessments can be limited or reduced. The experimental design in this study allowed for contemporary CPUE comparisons across the border of the Goukamma MPA. Results were similar to those obtained by the SB/R analyses. CPUE extrapolations therefore, using small MPAs, can provide reliable and consistent estimates, and offer a practical alternative to conventional assessment strategies. This study has highlighted the importance of ensuring a well structured and comprehensive survey design when undertaking a comparison of protected and exploited marine areas. The results provide a comprehensive framework for future management of the Goukamma MPA and other protected areas along the temperate coastline of South Africa.

Thesis (MScConEcol)--UnStellenbosch University, 2011. / ENGLISH ABSTRACT: The privilege of utilising resources from the globe's marine ecosystems is threatened. Adequate regional and global conservation efforts are vital. Understanding species' distributions and the environmental variables influencing community structures are important for instigating optimum conservation plans. A major threat facing marine ecosystems is the introduction and proliferation of alien invasive species. The distribution and geographical expansion of marine alien invasive species, along with environmental variables driving their increase is also critical for drawing up conservation plans. In response to this point, this study addresses gaps in our knowledge regarding intertidal marine invertebrate species distributions particularly that of marine alien species in the Kogelberg Biosphere Reserve (KBR) and adjacent Betty's Bay Marine Protected Area (MPA) in the Western Cape of South Africa, a prime area for south-coast marine conservation. Species identifications were done in September 2010. Two marine alien invertebrate species were identified along the coastline. These were the invasive mytilid Mediterranean mussel Mytilus galloprovincialis and the bryozoan Watersipora subtorquata. A quantitative systematic survey of the intertidal region, consisting of seven rocky shore sites was then undertaken from October 2010 to December 2010. The abundance of all focal marine invertebrate species, within six selected habitat types was assessed. Environmental variables were also recorded. Statistical tests were done to investigate for significant interaction in mean abundance and mean species richness among intertidal zones and protection status (MPA and non-MPA), and among intertidal sampling units (SU‟s) and protection status. There was also investigated for significant difference in mean abundance and mean species richness across intertidal zones and habitat types where protection status was not taken into account, and to test for significant differences in mean abundance and mean species richness between the intertidal zones and habitat types. Correspondence analyses were used to illustrate relationships between species composition and the defined environmental variables. Tests were done to investigate for significant differences in mean abundance of the identified marine alien species between the MPA and non-MPA, study sites, SU's, and wave exposures. These results indicated that vertical and horizontal stress gradients along the shore mainly influence abundance and species richness. The significantly higher abundance of M. galloprovincialis outside the MPA is due to its preference for wave-exposed areas. The reason for the difference in the total abundance of W. subtorquata in the different habitats is not clear, although it appears that the higher abundance of this species in the MPA is because the sheltered nature of the MPA. M. galloprovincilais displaces indigenous species. W. subtorquata does not cause any significant harm along the coast of South Africa. This study indicates that the abundance of M. galloprovincialis and W. subtorquata in the MPA is relatively low. The MPA is therefore in good condition with regards to intertidal alien species. It is important that the MPA and adjacent KBR's coastline maintain its current pristine status. / AFRIKAANSE OPSOMMING: Die voorreg om mariene hulpbronne te benut, word bedreig. Voldoende nasionale en globale mariene bewaring is krities. 'n Deeglike kennis van spesies verspreiding en omgewingsveranderlikes wat gemeenskapstrukture beïnvloed is noodsaaklik vir optimale bewaringspogings. Mariene indringerspesies en verspreiding van indringerspesies bedreig mariene ekosisteme. Dit is belangrik om basiese kennis in te win oor die geografiese verspreiding van indringerspesies saam met die omgewingsveranderlikes wat hierdie verspreiding beïnvloed. Hierdie studie fokus dus daarop om die kennis met betrekking tot intergety ongewerwelde spesiesverspreiding, veral dié wat uitheems is langs die kus van die Kogelberg Biosfeer Reservaat (KBR) en aangrensende Bettys Baai Mariene Beskermde Gebied (MBG) in die Wes-Kaap in Suid-Afrika uit te brei. Hierdie streek word beskou as gesog vir mariene bewaring in Suid-Afrika. Identifikasie van spesies is in September 2010 gedoen. Twee intergety uitheemse ongewerwelde spesies is langs die kus geïdentifiseer; die indringer 'mytilid' Mediterreense mossel - Mytilus galloprovincialis en die 'bryozoa' Watersipora subtorquata. 'n Kwantitatiewe sistematiese oorsig van die intergety rotsagtige streek, bestaande uit sewe lokaliteite, is gedoen. Steekproefneming is vanaf Oktober 2010 tot Desember 2010 uitgevoer. Alle fokale intergety ongewerwelde spesies, in ses geselekteerde habitattipes is getel. Omgewingsveranderlikes is aangeteken. Daar is statisties getoets vir verskille in die talrykheid en spesiesrykheid tussen die intergety zones en beskermingsstatus (MBG en nie-MBG), en tussen die intergety habitattipes en beskermingsstatus. Daar is ook getoets vir verskille in talrykheid en spesiesrykheid tussen die intergety zones en habitattipes waar beskermingsstatus nie in ag geneem is nie. Ooreenstemmende analises is gedoen om die verhoudings tussen die spesiesamestelling en die gedefinieerde omgewingsveranderlikes te illustreer. Daar is statisties getoets vir verskille in die talrykheid van die geïdentifiseerde uitheemse spesies tussen die MBG en nie-MBG, die verskillende lokaliteite, die verskillende habitattipes en tussen die verskillende golf blootstellings. Hierdie studie dui aan dat vertikale en horisontale stresgradiënte die hoofoorsaak is wat talrykheid en spesiesrykheid beïnvloed. Die aansienlik hoër talrykheid van M. galloprovincialis buite die MBG is van die gebied se hoër golfblootstelling. Die beduidende verskil in talrykheid van W. subtorquata is onduidelik. Dit kan egter afgelei word dat die beskutte aard van die MBG 'n rol speel by die aansienlik hoër talrykheid van hierdie spesie binne die MBG. M. galloprovicialis verplaas inheemse spesies. Geen beskikbare bewys dui daarop dat W. subtorquata enige beduidende skade langs die kus van Suid-Afrika aanrig nie. Die lae talrykheid van beide hierdie spesies binne die MBG dui daarop dat hierdie unieke area steeds in goeie toestand ten opsigte van intergety uitheemse spesies is. Dit is noodsaaklik dat die huidige status van die MBG en aangrensende kuslyn gehandhaaf word.

Le sanctuaire Agoa est une aire marine protégée dans la zone économique exclusive (ZEE) des Antilles françaises qui fut créée en 2010 pour la conservation des mammifères marins et de leurs habitats. Il est connu que le rorqual à bosse fréquente les eaux des Antilles de décembre à mai pour la reproduction et la mise bas. Par contre, peu d’information existe sur l’abondance, le comportement, la distribution et les pressions anthropiques sur cette espèce aux Antilles et encore moins dans le sanctuaire. Cette maîtrise s’intéresse principalement à connaître cette espèce dans un secteur précis de cette aire marine et les liens qu’elle entretient avec certains utilisateurs humains de son habitat. Le tout vise à informer les intervenants en place, autant institutionnels qu’utilisateurs, vers une mise en place de mesures de conservation adaptées. Un suivi terrestre hivernal de plus de 300 heures, en 2012 et 2013, a permis de déterminer l’utilisation de l’habitat et les pressions anthropiques sur une population de rorquals à bosse fréquentant le sud de la péninsule de la Pointe-des-Châteaux en Guadeloupe. Il s’agit du premier suivi terrestre de cette espèce aux Antilles françaises et un des premiers dans l'arc caribéen. La zone d’étude couvre environ 264 km2 et serait une des zones les plus fréquentées de l’archipel guadeloupéen par l’espèce. À l’aide d’un théodolite, la trajectoire de 107 groupes différents (137,8 heures, 699 remontées) a été décrite. Les résultats montrent que la zone d’étude est principalement fréquentée en mars et avril, avec une abondance maximale au début du mois d’avril. La forte présence de baleineaux, particulièrement au mois de mars, pousse à croire que cette zone est utilisée comme pouponnière. Le comportement n’est pas aléatoire dans la zone d’étude et les trajectoires convergent vers certaines zones ayant possiblement un lien avec la bathymétrie. De plus, la zone marine à proximité de la Pointe-des-Châteaux pourrait potentiellement être un lieu de convergence des groupes. Ceux-ci se déplacent à vitesse réduite en direction ENE en général, à l’exception des femelles accompagnées de baleineaux qui prennent une orientation tout autre, c’est-à-dire vers le ONO, et ce à plus grande vitesse. Bien que la pression d’observation soit considérée comme modérée, une forte proportion des remontées se trouve dans les corridors de navigation présents dans la zone d’étude. De plus, le corridor de navigation des navettes entre Saint-François et La Désirade comporte le plus grand risque relatif de collision mortelle. Une réduction de vitesse des embarcations fréquentant le corridor des navettes diminuerait significativement le risque de collision mortelle. Ces pistes de réflexion mèneront sans doute à d’autres études plus poussées afin de continuer à en apprendre sur l’écologie de cette espèce fascinante. / The Agoa sanctuary, a marine protected area (MPO) covering the exclusive economic zone (EEZ) in the French Caribbean, was created in 2010 to protect marine mammals and their habitats. It is known that the Caribbean islands are used from December to May by humpback whales (Megaptera novaeangliae) as a reproductive area. However, sparse information exists on the abundance, the behaviour, the distribution and the anthropogenic pressures on this species in the Caribbean and even less in the sanctuary. This thesis focuses on increasing scientific knowledge about this species’ use of a part of the Agoa Sanctuary and their interactions with human users of the MPO. Such knowledge may inform stakeholders’ (institutional and individual) decision-making towards implementation of appropriate conservation measures. A land-based survey of more than 300 hours, in 2012 and 2013, was carried out to determine the habitat use of, and anthropogenic pressures on, a population of humpback whales frequenting the surrounding water of the Pointe-des-Châteaux peninsula in Guadeloupe. This is the first land-based survey of this species in the French West Indies and one of the first in the Caribbean. The study area of approximately 264 square kilometres is one of the most visited areas by this species in the Guadeloupe archipelago. Using a theodolite, 107 trajectories (i.e. groups of whales) were recorded, representing 137.8 hours and 699 surfacings. Results show that the abundance was higher in March and April with a peak in the first week of April. The high proportion of calves in this population, mainly in March, suggest that the study zone is a nursing area. Overall movement patterns are not random and may possibly be dictated by the bathymetry. Furthermore, trajectories seem to converge close to the Pointe-des-Châteaux. The average movement is slow and oriented in the same direction as the dominant current to the west of the Pointe-des-Châteaux (i.e. ENE), except for mother and calf groups that swim faster in the opposite direction (i.e. WNW). Even if the anthropogenic pressure may be consided as moderate, a high proportion of surfacing is located in some of the main maritime traffic corridors. In addition, the shuttle corridor between Saint-Francois and Désirade island has the greatest relative risk of fatal collision. A reduced speed for the shuttle corridor would lower significantly the collision risk. These findings may lead to more extensive studies to better understand the ecology of this fascinating species.

Understanding the movement behavior and foraging strategies of individuals across multiple spatial and temporal scales is essential not only for understanding the biological requirements of individuals but also for linking individual strategies to population level effects. Glacial fjords scattered throughout south-central and southeastern Alaska host some of the largest seasonal aggregations of harbor seals (Phoca vitulina richardii) in the world, and an estimated 15% of the harbor seal population in Alaska is found seasonally at these glacial ice sites. Over the last two decades, the number of harbor seals has declined at two of the primary glacial fjords, in Aialik Bay in south-central Alaska and in Glacier Bay in southeastern Alaska, thus raising concerns regarding the viability of seal populations in glacial fjord environments. From 2004-2009, the foraging ecology, diving behavior, and migration patterns of harbor seals from Glacier Bay National Park, Alaska were examined in relation to prey availability and oceanographic features in Glacier Bay and the surrounding regions of southeastern Alaska. Time-depth recorders, very high frequency transmitters, and satellite-linked transmitters were used to quantify the vertical and horizontal movement patterns of harbor seals in the marine environment. Specifically, (1) I characterized the diving behavior, foraging areas, and foraging strategies of female harbor seals from terrestrial and glacial ice sites relative to prey availability during the breeding season (May-June) in Glacier Bay, (2) I quantified the intra-population variation in at-sea post-breeding season (September-April) distribution and movement patterns of female harbor seals in relation to oceanographic features, (3) I quantified the post-breeding season migration patterns of female harbor seals relative to the boundaries of the marine protected area of Glacier Bay National Park, and (4) I characterized the use of the continental shelf region of the eastern Gulf of Alaska by female harbor seals from Glacier Bay, both as a foraging area and as a migratory corridor in relation to oceanographic features. During the breeding season, there was a substantial degree of intra-population variation in the diving behavior and foraging areas of juvenile and adult female seals from glacial ice and terrestrial sites in Glacier Bay. The presence of multiple diving strategies suggests that differences in the relative density and depth of prey fields in glacial ice and terrestrial habitats in addition to seal age and reproductive status may influence diving and foraging behavior of harbor seals. During the post-breeding season, juvenile and adult female harbor seals ranged extensively beyond the boundaries of the marine protected area of Glacier Bay National Park, throughout the northern inshore waters of southeastern Alaska and the continental shelf region of the eastern Gulf of Alaska between Cross Sound and Prince William Sound, Alaska (up to 900 kilometers away). Seals exhibited a relatively high degree of intra-population variation in their at-sea post-breeding season distribution patterns that may be a function of extrinsic factors such as oceanographic characteristics, which can influence prey availability as well as intrinsic factors including previous experience with foraging areas and seal condition and age. Use of the continental shelf region of the eastern Gulf of Alaska by harbor seals as a foraging area may be due to enhanced biological productivity which may be associated with ephemeral hydrographic and/or static bathymetric features. Despite extensive migrations of seals from Glacier Bay during the post-breeding season, there was a high degree of inter-annual site fidelity of seals to Glacier Bay the following breeding season after seals were captured. / Graduation date: 2012

The dusky grouper Epinephelus marginatus (Lowe 1834), is a protogynous sequential hermaphrodite and is considered to be one of the most important fish species in the Mediterranean Sea. It is a K-strategist, being slow growing and late maturing, and this, coupled with its reproductive biology and relatively sedentary behaviour, has made it extremely sensitive to overexploitation, leading it to be classified by the IUCN as an endangered fish species. Wild dusky grouper have suffered from disease outbreaks in the past decade, leading to mass mortalities across the Mediterranean Sea, including Libyan coastal waters. These mortalities have mostly been attributed to Nodavirus infections. In Europe and Brazil, efforts are in place to culture this fish for commercial grow-out and stock enhancement programmes. In Libya, the dusky grouper is consumed regularly and is considered a prime-eating fish. Its importance for the Libyan internal market, as well as its potential for export, makes it an ideal candidate for future Libyan aquaculture activities. Given the scarce literature regarding the dusky grouper in Libya, this study aimed first to assess dusky grouper fisheries, spawning seasons and to identify the main threats that the fishing sector poses for wild stocks. Second this study aimed to determine the health status of wild dusky grouper offered at a local fish market in the capital Tripoli, in order to identify pathogens, pathologies or other health issues that might pose a hazard to cultured populations but also to remaining wild dusky grouper stocks. To achieve these aims, twelve field surveys spanning the period of 2013-2015 were conducted. From these surveys, it was established that the dusky grouper is captured throughout the year, including the spawning season. Fish sizes offered for sale ranged between 20-92 cm total length (TL), with the fish being sold from local fishing grounds around Tripoli, but also from as far as Benghazi, 1300 km to the east of Tripoli. The dusky grouper is principally caught in artisanal fisheries and by spearfishing, with approximately 300 spear-fishermen serving one particular fish market in Tripoli that was a focus in this study, and with dusky grouper being one of their main targets. Over the period of the survey, 267 landed dusky grouper were inspected for visible lesions prior to sampling. A total of 50 dusky grouper with sizes ranging from 27- 66 cm TL including the gonads from a further five fish measuring 66-92 cm TL that were sampled separately and examined to assess the stage of sexual maturity and to look for the presence of parasitic infections mainly affecting the gills, skin and gonads. The spawning season was found to extend from May to early September, with females ranging between 39-68 cm TL, males measuring 57-92 cm TL, and transient fish measuring 58-68 cm TL. From otolith readings of 8 fish, the youngest fish was a 3 year old juvenile of 28 cm TL and the oldest was an 8-9 year old 56 cm TL female. Whilst the highest prevalence of parasitic infection was found to be monogenean infection of the gills, with 100% prevalence, followed by gnathiid isopods infecting the oral cavity with 92% prevalence, it was the nematode Philometra sp. infecting post-spawning ovaries at 52% prevalence, that gave the highest apparent pathological impact. Necrosis potentially attributed to Philometra sp. in one particular ovary, was at a level likely to have caused complete parasitic castration, while others showed varying levels of probable functional reduction. The pathologies described need further investigation, especially in relation to possible synergies between Philometra sp. and bacteria in causing the necrosis. From the 267 inspected dusky grouper, 55 fish ranging in size from 42-92 cm TL were observed to be affected by external skin lesions of unknown aetiology. Twenty-six of these fish were sampled, having lesions at various stages of severity, and 5 further unaffected fish were used for histological assessment of the skin as negative controls. Histopathologically, the lesions comprised a multifocal, unilateral or bilateral dermatitis, involving the epidermis, superficial dermis and scale pockets, and sometimes, in severe cases, the hypodermis. Severe lesions had marked epidermal spongiosis progressing to ulceration. Healing was observed in some fish. Bacteria and fungi could be isolated from severe lesions, although they were not seen histopathologically in early-stage lesions. By contrast, metazoan parasite eggs were observed in the dermis and epidermis of some fish with mild and moderate dermatitis. Unidentified gravid digenean trematodes, carrying similar eggs, were also seen within the blood vessels of the deep and superficial dermis. The newly described condition was termed dusky grouper dermatitis (DGD). DGD’s geographical distribution along the Libyan coastline was investigated using a novel application of the social media network Facebook. Using Facebook, it was possible to document skin lesions of dusky grouper in Libyan waters from images attached to the entries of spear-fishermen. Thirty two Facebook accounts and 8 Facebook groups posting from 23 Libyan coastal cities provided a retrospective observational dataset comprising a total of 382 images of dusky grouper caught by spearfishing from December 2011-December 2015. Skin lesions were observable on 57 / 362 fish, for which images were of sufficient quality for analysis, giving a minimal prevalence for lesions of 15.75%. Only dusky grouper exceeding an estimated 40 cm total length exhibited lesions. The ability to collect useful data about the occurrence and geographical distribution of pathological conditions affecting wild fish using social media networks, demonstrates their potential utility as a tool to support epidemiological studies and monitor the health of populations of aquatic animals. The gravid digenean trematode described from mild lesions of five fish was identified using reconstruction through histological sectioning as belonging to the Family Aporocotylidae Odhner, 1912. This is the first description of a blood fluke from the dusky grouper, as well as from dermal blood vessels. The parasite was relatively long; the longest section of the parasite that could be measured was 1500 µm and 20-80 µm in width, while the total length of the parasite was estimated at 1500-2000 µm. Minute tegumental spines, possibly covering only a few parts of the parasite, were seen from some cross-sections. The parasite had one post-testicular ovary, which might overlap the testis, a pre-ovarian ascending uterus, and a post-ovarian descending uterus. It also possessed an oesophagus surrounded by oesophageal glandular cells and a pre-ovarian and pre-testicular extension of the vitelline cells, mostly at the level of the ascending uterus. The parasite was observed to be intra-vascular, the uterine lumen varies in size to accommodate between 1-7 eggs. The uterine eggs were embryonated and observed to span several stages of maturation. Eggs were also found in the dermal blood vessels, in the dermis, and in the epidermis, with the latter appearing to provide a potential route of egress of eggs into the environment. The extra-uterine eggs were 23.5 to 37.52 µm long and contained a ciliated miracidium. The eggs seemed to elicit a mixed inflammatory reaction, with degranulation of eosinophilic granular cells attached to the external surface of some of the eggs within the blood vessels but also the dermis. From observations made in the current study, this parasite appears to be a new species, most closely allied to none of the currently described Aporocotylidae genera. / In summary, the present study has demonstrated that the dusky grouper is extensively fished in Libya without discrimination to sizes and season, by both artisanal and spearfishing, with the latter as one of the main fishing methods, posing treats to the spawning potential and conservation of dusky grouper in Libya. The philometrid infecting the ovaries has a potential to reduce fecundity or to result in parasitic castration of wild broodstock. Gill-infecting monogeneans might represent a hazard for all stages of dusky grouper production. Dusky grouper dermatitis is a skin lesion, although there are no indications that infections may result in mortalities. Under culture conditions, however, this might change due to increase bacterial loads, which might lead to secondary bacterial infection. The presence of skin lesions would undoubtedly reduce the market value of whole fish. These findings are important for existing wild stocks, and for future plans regarding the aquaculture of dusky grouper. Future studies need to focus on the pathology of DGD, describing the disease process and aetiology using laboratory techniques such as TEM and virology as well as using morphology and molecular-based tools to describe the blood fluke and to determine their potential role in the initiation the disease. The novel approach to disease surveillance using social media Facebook posts could be further expanded by attracting citizen scientists, for future research assessing disease in wild fish, for sightings of mortality events and/or the appearance of disease outbreaks, or, for mapping marine mammal stranding’s and/or turtle nesting activity.

La compréhension des interactions liant la répartition des espèces, la biodiversité, les habitats marins et le changement climatique est nécessaire voire fondamentale pour la mise en oeuvre d’une gestion efficace de la conservation, par exemple la mise en place d’aires marines protégées. Dans cette étude, nous avons travaillé sur l’évolution de richesse de 89 espèces de poissons notées «rares» ou «exotiques» (observées en dehors de leur aire de répartition connue) lié au changement climatique. Nous avons modélisé et prédit leur distribution saisonnière par le modèle SIG en fonction de leurs niches écologiques (déterminée dans cette étude). En superposant tous les modèles en fonction du temps, cette approche permet d’identifier des zones d’occupation préférentielle de forte biodiversité (hotspots). La méthode offre une alternative pour mesurer la richesse d’espèces de façon saisonnière dans des zones peu connues, et de suivre leur mouvement au cours de temps, puis avoir information de base sur l’efficacité de positionnement des aires marines protégés liées à ces zones hotspots. La zone d’étude s’est située dans trois grands écosystèmes marins : le courant des Canaries, le plateau sud de l’Atlantique Européen et les mers celtiques. La région centrale est une zone de transition (entre les eaux tropicales et tempérés) connue pour sa sensibilité aux effets du changement climatique. De 1982 à 2012, la SST augmente constamment au fil du temps, avec des tendances et des magnitudes qui varient selon l’écosystème. Une augmentation du nombre d'espèces dans un écosystème dans une période a été généralement suivie par une tendance à la baisse ou à la hausse dans des écosystèmes adjacents. Les niches écologiques des espèces étudiées ont été estimées par l’extraction des valeurs environnementales à l’échelle mondiale au point d'occurrence au moment de l'observation. Les résultats de niches sont cohérents avec ceux obtenus à partir d’études observationnelles ou expérimentales. La flexibilité du modèle SIG nous a permis de suivre l'évolution saisonnière de distribution des espèces au fil du temps. En général, les espèces montrent une tendance à élargir leur distribution vers le nord, montrant l'effet du réchauffement de l'océan sur la distribution des poissons marins. L’approche de modèle peut être utilisée pour modéliser la distribution des espèces moins connues, ou dans des zones où les données d’occurrences sont peu nombreuses, ainsi que pour prédire le modèle de distribution future. L'analyse spatiale de la superficie des AMPs (Aires Marines Protégées) par pays appartenant à la zone d'étude, montre que le Royaume-Uni puis la France possèdent le plus grand nombre d'AMP ainsi que les superficies totales protégées les plus importantes. La fréquence à laquelle les AMPs (Aires Marines Protégées) sont touchées par les zones de hotspots est fortement influencée par les variations de l’environnement, les zones favorables évoluant alors au fil des saisons. Ainsi, il est important de prendre en compte les variations saisonnières pour la création des AMPs afin de préserver les capacités adaptative des espèces soumises au changement global. / Understanding connectivities among species distributions, biodiversity, marine habitats and climate change is necessary for the design of an effective conservation management, such as in the implementation of marine protected area (MPA). In this study, we observed the richness of 89 "rare" or "exotic" fish species (observed outside their known distribution range) related to climate change. We modeled and predicted their seasonal distributions according to the species ecological niches (determined in this study) using the GIS model. Superposing the models of all species using GIS, we determined the preferential zones or zones of high biodiversity (hotspots) over time. The GIS approach offers an alternative to measure seasonal species richness in poor-data areas. This approach allowed also species track movement over time. This information could be then used to measure the effectiveness of MPA positioning related to the hotspot areas. Our study area covers a wide latitudinal range of the Eastern Atlantic waters, from the warm tropical/subtropical waters to the temperate waters. This area is located in three large marine ecosystems: the Canary current, the South European Atlantic Shelf and the Celtic Seas. The transitional zone in the central region has well known for its sensitivity to the detection of climate change. From 1982 to 2012, the SST in all of studied ecosystems has increased consistently over time, with magnitude and trend varied among ecosystems. The change of number of species in each decadal period differed among ecosystems. Increasing number of species in an ecosystem was generally followed by decreasing trend in adjacent ecosystems. Species ecological niches were obtained by extracting the environmental values in the location of species occurrence at the time of observation. The environmental data and the occurrence records used were at global scale, and the methods yields coherent results with the results obtained from observational studies. The flexibility of GIS Model used in this study allowed us to follow the evolution of species seasonal distribution over time. Generally, most of the studied species showed a northbound trend in their distribution. These northbound tendencies were more evident in the middle region, confirming the effect of global warming in shifting marine species distribution. This approach provides an alternative of measuring seasonal richness of poor-known species and/or modeling in poor-data areas. The results present a complete picture of predictive number of species in an area over time. MPAs superficial analysis by country (countries lying in the study area) showed that UK has the highest number of MPA and the largest protected areas, following by France and Mauritania. Frequencies of the MPAs touched by the hotspot were strongly influenced by seasonal variations. Thus, considering seasonal variations in a conservation effort could preserve species adaptive variation under environmental changes. Overall, our works provide several alternative methods for species distribution studies and for studies poor-known species in data-poor area. The results provide evidences of ocean warming effect in shifting marine fish distribution.

La protection des ressources naturelles marines est un enjeu fort pour les décideurs publics. Le développement récent des aires marines protégées (AMP) contribue à ces enjeux de préservation. Les AMP ont pour objectifs de conserver les écosystèmes marins et côtiers tout en favorisant les activités humaines. La complexité de ces objectifs les rend difficiles à atteindre. L’objectif de cette thèse est de mener une analyse ex ante d’un projet d’une AMP aux îles Kuriat (Tunisie). Cette analyse représente une aide aux décideurs pour une meilleure gouvernance en intégrant les acteurs impliqués (pêcheur, visiteur, plaisancier) dans le processus de gestion. Pour ce faire, nous appliquons la méthode d’évaluation contingente (MEC) à des échantillons des pêcheurs et des visiteurs aux îles Kuriat. Nous nous intéressons au traitement des biais de sélection et d’échantillonnage et à l’incertitude sur la spécification des modèles économétriques lors de la mise en œuvre de la MEC. Nous faisons appel au modèle HeckitBMA,qui est une combinaison du modèle de Heckman (1979) et de l’inférence bayésienne, pour calculer le consentement à recevoir des pêcheurs. Nous utilisons aussi le modèle Zero inflated ordered probit (ZIOP), qui est une combinaison d’un probit binaire avec un probit ordonné, pour calculer le consentement à payer des visiteurs après avoir corrigé l’échantillon par imputation multiple. Nos résultats montrent que les groupes d’acteurs se distinguent par leur activité et leur situation économique ce qui les amène à avoir des perceptions différentes. Cela permet aux décideurs d’élaborer une politique de compensation permettant d’indemniser les acteurs ayant subi un préjudice. / The protection of marine natural resources is a major challenge for policy makers. The recent development of marine protected areas (MPAs) contributes to the preservation issues. MPAs are aimed to preserve the marine and coastal ecosystems while promoting human activities. The complexity of these objectives makes them difficult to reach. The purpose of this work is to conduct an ex-ante analysis of a proposed MPA to Kuriat Islands (Tunisia). This analysis is an aid to decision makers for better governance by integrating the actors involved (fisherman, visitor, boater) in the management process. To do this, we use the contingent valuation method (CVM) to samples of fishermen and visitors to the islands Kuriat. We are interested in the treatment of selection and sampling bias and uncertainty about specifying econometric models during the implementation of the CVM. We use the model HeckitBMA, which is a combination of the Heckman model (1979) and Bayesian inference, to calculate the willingness to accept of fishermen. We also use the model Zero inflated ordered probit (ZIOP), which is a combination of a binary probit with an ordered probit, to calculate the willingness to pay of visitors after correcting the sample by multiple imputation. Our results show that groups of actors are distinguished by their activity and economic conditions that cause them to have different perceptions. This allows policy makers to develop a policy of compensation to compensate the players who have been harmed.