Longline fishing is the most common elasmobranch capture method in the world, both for commercial fishing, and to a lesser extent for scientific surveys. The capture of an animal on a longline initiates a series of physiological responses designed to promote survivorship in the short term, but if unchecked, can cause reduced individual fitness and/or mortality in the long term. Given widespread declines in shark populations, an improved understanding of the physiological costs of longline capture is needed. The aim of this thesis was to investigate the physiological response of sharks to capture and restraint, to assess novel, non-invasive alternatives to scientific longline surveys, and to generate scientific insight into poorly understood elasmobranch populations in The Bahamas. The results presented herein suggest that some species of shark are able to recover from the physiological stress of capture despite the presence of persistent negative stimuli. Tonic immobility was assessed as a means of generating baseline blood chemistry data, but was found to be inappropriate given that it increases the magnitude of physiological perturbation in the short term. To avoid the stress of capture altogether, Baited Remote Underwater Video Surveys (BRUVS) were considered as a non-invasive alternative to capture based surveys, however, it was concluded that they lack the resolution necessary to answer fine scale demographic questions. For the Caribbean reef shark, longline surveys yielded high resolution data allowing the identification of fine scale spatiotemporal shifts in demographic population structure with minimal cost (mortality). Nevertheless, the ethics of using capture based surveys on sensitive species are questionable when alternative techniques are available. Deep water sharks caught on longline surveys exhibited high mortality rates, however, for these very poorly understood species moribund specimens have great scientific value which in some cases can offset the high ecological costs of the surveys. The results presented in this thesis highlight the on-going need for improved biological and ecological research into the majority of elasmobranch populations, particularly with regards to anthropogenic interactions such as capture. Given the tenuous conservation status of many species, the acquisition of applied, management focused data should remain the priority of elasmobranch scientists.

L’estimation de la diversité et de l’abondance des espèces de poisson est fondamentale pour comprendre la structure des communautés et la dynamique des récifs coralliens. Les observations sont généralement obtenues par des recensements visuels en scaphandre autonome (UVC). Ces informations peuvent également être obtenues de manière originale grâce aux observations issues des techniques vidéo sous-marines modernes sans plongeur qui permettent des couvertures spatiales et temporelles accrues.La première phase de ce travail de thèse synthétise l’ensemble des travaux ayant été effectués avec des techniques vidéo entre 1952 et 2012. La seconde phase, présente deux systèmes vidéo rotatifs complémentaires, utilisés pour étudier la diversité de l’ichtyofaune et des habitats marins dans le lagon de Nouvelle-Calédonie : le STAVIRO (pour « STAtion VIdéo ROtative ») et le MICADO (pour « Module d’Imagerie Côtier, Autonome pour le Développement de l’Observation sous-marine »). La troisième phase de ce travail consiste à comparer ces systèmes vidéo aux UVC puis à examiner l’effet « observateur » inhérent aux techniques vidéo rotatives. Il résulte de cette étude que : (i) les observations des communautés de poissons par UVC et STAVIRO différaient significativement, (ii) la richesse spécifique etla densité des espèces de grande taille n'étaient pas significativement différentes entre les techniques, (iii) la diversité et la densité des espèces de petite taille étaient plus élevés avec les UVC; (iv) la densité des espèces pêchées était plus élevée avec les STAVIRO et (v) seuls les UVC ont détecté des différences de structure des assemblages en fonction du type de récif. L’étude de l’effet « observateur » a montré que sur une liste d’espèces définie, les dénombrements et les identifications des individus peuvent être considérées comme similaires entre observateurs ayant une expérience suffisante (> 6 mois). La dernière phase de ce travail a permis d’appliquer la technique MICADO à l’étude des variations temporelles del’ichtyofaune d’un site corallien à l’échelle de la journée. Elle a permis de mettre en évidence des variations cycliques journalières en fonction de l’heure et de la marée et des « profils type » de variations ont pu être identifiés pour certains groupes d’espèces. Ce travail de thèse permet ainsi de participer au développement de nouvelles techniques d’observations complémentaires des techniques traditionnelles afin d’enrichir les connaissances du fonctionnement et de la dynamique des écosystèmes coralliens. / Estimating diversity and abundance of fish is fundamental for the understanding of community structure and dynamics of coral reefs. Observations are generally gathered using Underwater VisualCensus (UVC). These informations can also be collected by underwater video techniques involving no diver and allowing a high spatial and temporal coverage. The first part of this PhD thesis is a review ofpublications using underwater video techniques between 1952 and 2012. The second part present two rotating video systems used to study the diversity of ichthyofauna and habitats in the lagoon of NewCaledonia: the STAVIRO (for "STAtion VIdeo ROtative") and the MICADO (for "Module d’Imagerie Côtier, Autonome pour le Développement de l’Observation sous-marine"). The third part of this work is acomparison of these techniques with UVCs and an analysis of the “observer effect” for the rotating video techniques. The comparison between rotating video systems and UVC showed that: (i) fish communitydata collected by UVC and by STAVIRO differed significantly; (ii) species richness and density of large species were not significantly different between techniques; (iii) species richness and density of smallspecies were higher for UVC; (iv) density of fished species was higher for STAVIRO; and (v) only UVC detected significant differences in fish assemblages structure across reef type. The comparison of fishcounts obtained from the same videos by different observers showed that for a defined list of species, estimates of species richness and total abundance can be considered as similar between observers withsufficient experiences (> 6 months). The last part of this PhD is an application of rotating video techniques to the study of daily temporal variations of the ichthyofauna. Daily variations were observed depending onthe time of day and the tidal state and typical patterns of variations have been described for some species groups. The outcomes of this work bring original insights of new techniques complementary to traditionaltechniques in order to enhance our understanding of the functioning and dynamic of coral reef.

Conservation of elasmobranch populations is often inhibited by a lack of data, particularly in understudied regions like the Red Sea. Survey efforts in this region have been infrequent and often highly localized. Establishing a broad baseline for elasmobranch diversity and abundance along the Saudi Arabian Red Sea coast could inform both conservation efforts and a nascent ecotourism industry. In this thesis, I describe a pilot study comparing biodiversity data from baited remote underwater video stations (BRUVS), unoccupied aerial vehicle surveys (UAVs), and eDNA sequencing at five islands in the Farasan Banks region of the Saudi Arabian Red Sea. Estimates of relative abundance were also compared between the BRUVS and UAVs. Each method identified species missed by the other two, but all three techniques exhibited clear habitat- and taxa-specific biases. I was able to identify key concerns for each approach that need to be addressed before large-scale implementation. If carefully planned and executed well, a full assessment of the Saudi Arabian coastline could establish a true baseline for shallow water elasmobranchs in the eastern Red Sea. Informing best conservation practices and identifying potential ecological attractions in accordance the environmental and economic goals of Saudi Arabia’s Vision 2030.

Down Stream [Appalachia] is an immersive, interactive art installation that addresses themes of ecological preservation, conservation, and connectedness—illuminating the precarity of imperiled freshwater species in the Appalachian region. The exhibition is composed of reflective, refractive sculptures and underwater video footage, surrounded by fully-immersive spatial audio. Both the audio and visual elements react to audience presence and proximity. Species highlighted are the Candy Darter (Etheostoma osburni); the Cumberlandian Combshell (Epioblasma brevidens) and other freshwater mussels; and the Eastern Hellbender Salamander (Cryptobranchus alleganiensis alleganiensis). This paper examines the context and content of this installation, its progression and influences, and themes of ecology and the environment in the Southeast United States. / Master of Fine Arts / There are endangered species right here in the mountains of Virginia, and hardly anyone knows about them. Down Stream [Appalachia] is an immersive, interactive art installation that attempts to raise awareness and allow people to connect to these animals that otherwise go unseen. This paper examines the context, content, and themes of the installation.

Predators often have strong top-down effects on ecosystems and are considered a priority for conservation and management. Predator activity can influence prey distribution, abundance, and foraging behaviors and are likely to influence habitat by impacting ecological and environmental characteristics as well as presence of competitor species. There are knowledge gaps of the functional diversity of fish assemblages, non-consumptive predator effects, and environmental effects on fish assemblages. With this study, effects of top marine predators, such as sharks and great barracuda, on diversity and abundance of prey communities were examined in putative low (north side of South Bimini = lagoon) and high-risk (south side of South Bimini = flat) areas around South Bimini, The Bahamas. Baited remote underwater video surveys (BRUVs) deployed in the nearshore habitat captured abundance and potential predator-prey interactions. Predator and prey abundances at each site were compared to determine potential risk affect within high and low risk environments. A general baseline of predator and prey species was established throughout six months of observation (January- June 2018). Results showed a difference in prey communities between high and low risk habitats. Teleost abundance was highest on the south side of South Bimini. There were no differences in flight behavior of prey from predator (sharks vs barracuda). Longitude, depth, temperature, salinity, and dissolved oxygen were significantly linked to biotic assemblages. The identification of significant factors influencing predator-prey interaction is important in understanding community composition and for future implementation of conservation and management practices pertaining to nearby mangrove and seagrass habitats.

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