Complex nonlinear and chaotic responses have been recently observed in various compliant ocean systems. These systems are characterized by a nonlinear mooring restoring force and a coupled fluid-structure interaction exciting force. A general class of ocean mooring system models is formulated by incorporating a variable mooring configuration and the exact form of the hydrodynamic excitation. The multi-degree of freedom system, subjected to combined parametric and external excitation, is shown to be complex, coupled and strongly nonlinear. Stability analysis by a Liapunov function approach reveals global system attraction which ensures that solutions remain bounded for small excitation. Construction of the system's Poincare map and stability analysis of the map's fixed points correspond to system stability of near resonance periodic orbits. Investigation of nonresonant solutions is done by a local variational approach. Tangent and period doubling bifurcations are identified by both local stability analysis techniques and are further investigated to reveal global bifurcations. Application of Melnikov's method to the perturbed averaged system provides an approximate criterion for the existence of transverse homoclinic orbits resulting in chaotic system dynamics. Further stability analysis of the subharmonic and ultraharmonic solutions reveals a cascade of period doubling which is shown to evolve to a strange attractor. Investigation of the bifurcation criteria obtained reveals a steady state superstructure in the bifurcation set. This superstructure identifies a similar bifurcation pattern of coexisting solutions in the sub, ultra and ultrasubharmonic domains. Within this structure strange attractors appear when a period doubling sequence is infinite and when abrupt changes in the size of an attractor occur near tangent bifurcations. Parametric analysis of system instabilities reveals the influence of the convective inertial force which can not be neglected for large response and the bias induced by the quadratic viscous drag is found to be a controlling mechanism even for moderate sea states. Thus, stability analyses of a nonlinear ocean mooring system by semi-analytical methods reveal the existence of bifurcations identifying complex periodic and aperiodic nonlinear phenomena. The results obtained apply to a variety of nonlinear ocean mooring and towing system configurations. Extensions and applications of this research are discussed. / Graduation date: 1992

Resolving diversity patterns and their underlying drivers has application for both ecological theory and ocean management. Because seafloor characteristics are often used to assess bottom habitat, I examined the relationship between deep-sea benthic (bottom-living) diversity and multi-scale topographic heterogeneity. Most work occurred on the Canadian Pacific continental shelf at Learmonth Bank with additional sites in Strait of Georgia (BC) and Gulf of Maine (Atlantic shelf). High-resolution species distribution and seafloor data were annotated from remotely operated vehicle benthic imagery surveys while large-scale seafloor data were derived from multibeam sonar. New method development to address problems of current methods and to facilitate comparison among ecosystems is a major outcome. My new MiLS method (microtopographic laser scanning) can profile the deep seafloor at a resolution of ~1-2 cm with high accuracy and precision. I also developed a new ACR (arc-chord ratio) rugosity index as a measure of 3-D topographic heterogeneity that is simple, accurate and highly versatile. Model systems and scales vary among my studies but results consistently yield a positive relationship between diversity and topographic heterogeneity and identify bottom hydrodynamics as an important underlying driver. Rockfish Sebastes spp. associate with higher seafloor rugosity non-randomly and select for deep-sea corals and sponges over inert substrata alone. Data indicate that degradation of biogenic structures is a long-term detriment to rockfish species. Gorgonian coral- and sponge-dominant biotopes strongly associate with a single substratum type. These relationships were used to map coral and sponge distributions. This work, which collectively adds new information on the ecological relevance and distribution of corals and sponges, is pertinent to the conservation and management of fish stocks and vulnerable marine ecosystems. Epibenthic community variables abundance, richness, and Shannon diversity positively correlated with both the local microtopographic heterogeneity on a scale of 10 m2 and with the surrounding regional large-scale topographic heterogeneity on scales of 25 to 250,000 m2. Relationships were strongest between epibenthic community variables and the largest scale rugosity and were used to generate and test predictive diversity models. Where management strategies rely on surrogate measures in data-poor areas, mapping benthic diversity using ACR rugosity will provide good indicators. Although bottom hydrodynamics is consistently identified as an underlying driver of epibenthic patterns related to topographic heterogeneity, data suggest the nature of the relationship varies across spatial scales. At small scales, high topographic heterogeneity likely increases diversity by increasing the number of available niches (including hydrodynamic gradients; e.g., the abrupt vertical rugosity created by tall corals and sponges provides rockfish refuge from currents) while at large scales, high topographic heterogeneity increases local diversity less directly through distant hydraulic events that alter bottom flow hydrodynamics. / Graduate / 0329 / 0416 / 0799 / cdupreez@uvic.ca

Située au coeur du golfe de Gascogne, La Rochelle fut dès sa naissance au début du XIIe siècle une communauté de pêcheurs. La ville s’affirme comme une cité marchande, devenant l’une des plus dynamiques de l’Ouest français. Son port de commerce se déplace sur un nouveau site en 1890, libérant le vieux port au centre-ville pour la pêche. De nombreux voiliers viennent déjà y vendre leur pêche sur un marché aux poissons attractif, que le chemin de fer relie à l’intérieur du pays en 1857. Une nouvelle page s’ouvre, celle du chalutage industriel qui fait une percée majeure en Grande-Bretagne. A La Rochelle, après l’échec d’une tentative de l’anglais Craggs d’y implanter le chalutage à vapeur en 1871, de grands armements à la pêche industrielle sont fondés de 1904 à 1920. Une première période d’essor de ces armements fait de la cité le deuxième port de pêche de France, le premier de l’Atlantique. Après le marasme des pêches françaises et la crise de la flottille de chalutiers à vapeur rochelais, un nouvel essor du port s’affirme après la Seconde guerre mondiale. La Rochelle redevient le quatrième port de pêche de France dans les années 1960. Mais l’année 1965 marque une rupture de la pêche industrielle rochelaise et un déclin s’ensuit qui conduit à la disparition des derniers grands chalutiers en 1994. De nombreux travaux menés jusqu’ici ont porté sur d’autres ports de pêche de France. Cette étude a l’ambition de contribuer à la connaissance de plus d’un siècle d’histoire de pêche industrielle du port de La Rochelle, de ses dimensions économiques, sociologiques, politiques et écologiques, dans le cadre d’une étude comparative, en analysant les caractéristiques et les raisons de cet essor et celles d’un déclin précoce et rapide. / Situated in the heart of the bay of Biscay, La Rochelle, right from its foundation, at the beginning of the XIIth century, was a community of fishermen. It then became one of the most dynamic cities in western France. In 1890 the commercial port moved to a new site, liberating the old port in the city centre for fishing activities. Many sailing ships came to sell their fish on an attractive fish market boosted by the railway connection to the inland part of the country in 1857. A new era started with industrial trawling, a major innovation in Great Britain. In 1871, the English shipowner Craggs tried to introduce steam-powered trawling but suffered a setback . However from 1904 to 1920 important armaments in industrial trawling were created, making La Rochelle, in this early period of expansion, the second fishing port in France and the first one on the Atlantic coast. After the stagnation of French fisheries and a crisis of Rochelais steam-powered trawlers, a new expansion of the port occured after WWII. In the sixties, La Rochelle became the 4th fishing port in France, until in 1965 a break in industrial fishing activities resulted in the loss of the last big trawlers in 1994. There have been numerous documents about other fishing ports in France. This study aims to concentrate on the history of industrial fishing in the port of La Rochelle over a century, highlighting its economic, sociological, political and ecological dimensions. For this purpose a comparative study has been made, analysing the characteristics and the reasons of this expansion as well as the ones of a rapid and premature decline.

The chemicals produced by biological systems, whether proteins, peptides, or terpenes, will always provide an intriguing topic for researchers. Invisibly controlling every aspect of nature, these molecules are responsible for life, evolution, and death. Specifically, here is described the secondary metabolites produced by Antarctic marine organisms as well as others, and how they are used to defend or attract other animals while potentially providing health benefits to mankind. This is done through collection, extraction, and separation of individual specimens. The respective mixtures of compounds after isolation are then analyzed via spectroscopic methods such as nuclear magnetic resonance spectroscopy, mass spectrometry, and X-ray crystallography. Once identified, these compounds are tested in biological assays to provide a hypothesis for their use in nature or evidence that there may be a use for them in medicine. For this thesis, the Antarctic organisms described are an alga, Pocamium cartilagineum, an amphipod, Paradexamine fissicauda, a sponge, Dendrilla membranosa, and one undescribed and two known deep sea coral species, Briareopsis aegeon and Plumarella delicatissima. Beyond these specific specimens, their chemistry as well as natural products from other origins were combined to create a diverse compound library for biological screening against human pathogens. This was done using computational modeling and statistical analysis of the compound library and its comparison to other known chemical libraries. The diversity and impact of these molecules are assessed.

The deep-sea is the largest habitat on earth, containing over 90 percent of the world’s oceans and home to over 20,000 species. Deep-sea ecosystems are increasingly impacted by human activities including fishing and oil extraction. To understand potential impacts on deep-sea food webs, it is crucial to gather baseline data in these systems. I quantified the trophic interactions of three groups of deep-water animals across a range of trophic levels living in the northern and eastern Gulf of Mexico using stable isotope analysis. First, I propose methods for correcting δ15N values for the presence of nitrogenous metabolic waste products (e.g., urea) in muscle tissue using chemical extractions and/or species-specific mathematical normalizations. Significant differences in δ15N, %N, and C:N values as a result of extractions were observed in eight of ten shark and all three hagfish species. The δ15N values increased, but shifts in %N and C:N values were not unidirectional. Mathematical normalizations for δ15N values were successfully created for four shark and two hagfish species. I then describe the trophic interactions of three consumer assemblages. Carbon isotopic values indicate a heavy reliance on allochthonous nutrient inputs from surface waters. Nitrogen isotopic values reveal somewhat atypical taxa as top predators in the deep sea. Shark, teleost, and invertebrate species across a wide range of body sizes are feeding at a similar trophic level. This apparent lack of size structuring could be the result of a high degree of opportunistic scavenging or perhaps feeding at many trophic levels simultaneously in an oligotrophic system. There was a high degree of isotopic niche overlap among species within each consumer assemblage, perhaps the result of limited nutrient resources in the deep-sea. In general, individuals from the northern sampling stations displayed higher δ13C and δ15N values than those from the eastern sites. With the exception of a few species, there were no strong relationships between body size and isotopic values. The present study is among the first characterizations of the trophic structure of deep-sea organisms in the Gulf of Mexico and establishes system baselines for future studies describing deep-water systems and investigating anthropogenic impacts.

Nos connaissances sur la diversité virale associée aux micro-organismes présents dans les sources hydrothermales océaniques profondes restent encore limitées. Seules quelques études concernant l’abondance virale et l’impact de ceux-ci sur la mortalité microbienne dans ces écosystèmes sont disponibles. En effet, seuls 6 bactériovirus et 2 archéovirus provenant de ces écosystèmes ont été caractérisés à l’heure actuelle. Les deux archéovirus infectent des archées anaérobies hyperthermophiles appartenant à l’ordre des Thermococcales et ont été décrits au laboratoire.Afin d’étendre nos connaissances sur la diversité virale associée aux micro-organismes colonisant ces environnements, il a été décidé d’élargir les recherches à l’ordre bactérien des Thermotogales. Cet ordre bactérien est composé de bactéries chimio-organotrophes anaérobies en majorité thermophiles ou hyperthermophiles. De nombreux transferts latéraux de gènes ont contribué à l’histoire évolutive des Thermotogales supposant une forte implication des virus dans celle-ci. Ces travaux de thèse ont permis la caractérisation fonctionnelle et génomique de deux nouveaux siphovirus, MCV1 et MCV2, infectant deux souches de Marinitoga camini. Ces souches ont été isolées de deux sites hydrothermaux profonds (Menez Gwen et Lucky Strike) au niveau de la dorsale médio-atlantique. Ces virus mettent en oeuvre un cycle lysogénique avec une production basale sans induction relativement haute (>107 virions/ml). Une comparaison de ces deux génomes viraux à celui de MPV1, virus précédemment isolé de Marinitoga piezophila, a été réalisée, révélant la présence de nombreuses similarités. Un core genome de 35 ORFs partagé par ces trois génomes a été identifié, incluant des protéines impliquées dans le métabolisme de l’ADN, l’assemblage des virions et le cycle lysogénique. Des protéines hypothétiques ont aussi été identifiées parmi ces gènes communs, elles portent donc probablement des fonctions importantes pour ces bactériovirus. Par ailleurs, 60% des gènes de ces virus ayant une correspondance dans les bases de données, après exclusion des Thermotogales, partagent des similarités avec lesFirmicutes et les bactériovirus qui leurs sont associés. Le génome d’une autre Thermotogales, Thermosipho sp. AT1244-VC14 a été étudié ainsi que son système CRISPR-cas. Ces résultats indiquent que cette souche, qui porte un système CRISPR-cas qui semble complet et fonctionnel, a probablement déjà été infectée par MCV1, MCV2 ou un virus similaire. Ces travaux permettent d’étendre nos connaissances sur les virus portés par les bactéries du phylum Thermotogae, encore peu décrits à ce jour. Les éléments génétiques mobiles associés à ce phylum sont particulièrement intéressants car ils ont probablement eu un impact important dans l’évolution de ces communautés microbiennes ainsi que dans leur adaptation aux conditions physico-chimiques extrêmes et fluctuantes présentes dans les écosystèmes qu’elles colonisent. / Our knowledge of the viral diversity associated to microorganisms inhabiting the deep-sea hydrothermal vents is still limited. Only a few studies have focused on viral abundance and impact on microbial mortality within these ecosystems. A limited number of viruses (6 bacterioviruses and 2 archaeoviruses) were isolated from these environments and characterized. Two viruses associated to hyperthermophilic anaerobic Archaea, from the Thermococcales order, have been described in our laboratory. In order to deepen our knowledge on the viral diversity of these extreme environments, we have extended our investigation to the bacterial order of Thermotogales. This order is composed of anaerobic chemoorganotrophic bacteria that are, for the most part, hyper/thermophilic. Numerous lateral gene transfers have contributed to the evolutionary history of the Thermotogales, implying the potential involvement of viruses. Here, we will report the characterization of two new siphoviruses MCV1 and MCV2 that infect two strains of Marinitoga camini. Those bacterial strains were isolated from two deep-sea hydrothermal vents sites (Menez Gwen and Lucky strike) in the Mid Atlantic Ridge. These viruses are temperate with a high basal production of virions (>107 virions/mL). Comparative genomics with MPV1, a virus isolated from M. piezophila, was performed and show that those bacterioviruses share numerous similarities. A set of “core genes” shared by all these three viruses was identified and includes proteins involved in DNA metabolism, head and tail assembly and lysogenic cycle. Shared hypothetical proteins were also identified, suggesting that these unknown proteins probably provide important functions for these viruses. Interestingly, for genes with blastp matches in Genbank, over 60% have their top matches, outside the Thermotoga, to genes from Firmicutes and bacterioviruses associated to Firmicutes. We also analyzed the genome of Thermosipho sp. 1244 and studied his CRISPR-cas system. Our results indicated that thisThermosipho strain, with a complete and functional CRISPR-cas system, had already been infected by MCV1, MCV2 or a similar virus. The analyses presented here extend our knowledges about these newly discovered viruses in the deeply branching bacterial phylum Thermotogae. This bacterial order and associated mobile genetic elements are significant for addressing long-term evolutionary adaptation to fluctuant and extreme physicochemical conditions.

In 2010, the largest oil spill in U.S history occurred off the coast of Louisiana from April 20th to September 19th, when the well was declared officially sealed by the U.S Coast Guard, after releasing more than 4.4 million barrels of crude oil into the Gulf of Mexico (GOM) (McNutt et al., 2012). This spill was unique because it occurred in deep water approximately 1500 m below the ocean surface. Virtually nothing is known about the effects of oil spills on marine life in the deep sea, and there are limited data on mesopelagic and bathypelagic animals in the GOM before the Deepwater Horizon oil spill (DWHOS). The study presented here focuses on one of the most abundant and diverse groups of pelagic decapod crustaceans in the GOM – the family Oplophoridae and also includes one species from the family Pandalidae. Past studies on pelagic decapod crustaceans have been limited on both spatial and temporal scales. This study is unique because 1) it covers a large temporal range with data collected in 2011 and from 2015-2017, allowing for a more in-depth look at crustacean assemblage patterns, 2) it allows analysis of seasonality in reproduction, about which little is known for any deep-sea species, and 3) it assesses the potential effects of the Loop Current on species distribution and abundances, about which little is known. This information is important in understanding how the DWHOS may have affected the GOM ecosystem because pelagic decapod crustacean are intermediate components of the food web, and are in turn preyed upon by higher trophic levels. Unfortunately, there were little data on the mesopelagic ecosystem from this region before the spill, with the exception of a site in the eastern GOM (Standard Station, Hopkins et al., 1989; Hopkins et al., 1994). Therefore, these data, which incorporate samples taken one, five, six and seven years after the DWHOS, were analyzed with respect to year and season to determine if any trends were present. Results indicate that both biomass and abundance were significantly higher in 2011, than in subsequent years, indicating that the ecosystem has been declining since 2011. These two parameters were also lower in Loop Current water when compared to Common Water at all depths up to 1200 m, indicating that the Loop Current does have effects on deeper waters. The information obtained from this thesis will also act as a reference state for future studies in the GOM to monitor changes, or lack thereof, in the assemblage of deep-sea oplophorid and pandalid crustaceans.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Earth and Planetary Science, 1979. / Microfiche copy available in Archives and Science. / Bibliography: leaves 114-116. / by Daniel Allen Galson. / M.S.

This project used a variety of genetic markers to investigate the evolution and population genetics of hydrothermal vent fauna that were recovered from the Scotia Sea, in the Atlantic sector of the Southern Ocean. The origins of one of these species, an undescribed species of Kiwa sp. found on the East Scotia Ridge (ESR) and its constituent family Kiwaidae, a group of vent and seep-associated decapod squat lobsters (infraorder Anomura) was investigated using a concatenated nine-gene dataset and key divergences were dated using fossil calibrations. These results confirm earlier research showing Kiwaidae reside in the superfamily Chirostyloidea, but form a monophyletic clade with the non-chemosynthetic family Chirostylidae and not Eumunididae. Chirostyloid families diverged in the Cretaceous, although extant Kiwaidae radiated in the Eocene, consistent with many other chemosynthetic taxa that appear recently derived. The basal tree position of Pacific species (and the Alaska location of a likely stem-lineage kiwaid fossil) suggests kiwaids originated in the East Pacific. Within a Southern Hemisphere clade, the divergence between the southeastern Pacific K. hirsuta and a non-Pacific lineage (Kiwa sp. ESR and Southwest Indian Ridge kiwaids) is no earlier than 25.9 Ma, consistent with a spread from the Pacific into the Scotia Sea and beyond via now-extinct active ridge connections or mediated by a Miocene onset of the Antarctic Circumpolar Current (ACC) through a newly-opened Drake Passage. This project also investigated the population genetics of three undescribed species found at two vent fields ~ 440 km apart at either end of the ESR: Kiwa sp., a peltospirid gastropod and Lepetodrilus sp. limpets. Lepetodrilus sp. was also found at the Kemp Caldera, a submerged part of the South Sandwich Islands (SSI). Analyses of cytochrome c oxidase subunit 1 (COI) as well as microsatellite loci developed from Roche 454 sequence libraries revealed no differentiation along the ESR for all three species consistent with panmixia, or the dominance of non-equilibrium processes between vent field colonies within a metapopulation, possibly enhanced further by cold-induced arrested larval development. Despite apparent connectivity along the ESR, both COI and microsatellites revealed differentiation between ESR limpets and Kemp Caldera limpets ~ 95 km to the east, possibly owing to the hydrographic isolation of the caldera. Both COI and microsatellite diversity patterns were consistent with recent (< 1 Ma) demographic expansions for all three species (although the influence of selection sweeps on COI cannot be discounted); a pattern observed worldwide at vent communities and may reflect demographic instability over time as a consequence of the stochastic birth and death of vent colonies within a metapopulation. Different COI bottleneck ages between the three species (excluding the influence of possible selection) as well as the absence of kiwaids and peltospirids at Kemp, have been attributed to differences in life history, in particular larval morphology and presumed dispersal strategy. These results highlight the role of larval dispersal of vent fauna along active spreading ridges, both in maintaining vent metapopulations across vent colonies prone to stochastic birth and extinction in the short term, but also in the spread of taxa globally and the formation of biogeographic provinces. The likelihood that the three species presented here exist at vents east of the ESR and SSI, prompts further exploration along ridges in the South Atlantic, in order to investigate the effect of the ACC in enhancing gene flow and delineating biogeographic provinces.

The vertical and horizontal distributions of Euphausiacea in the northern Gulf of Mexico, including the location of the Deepwater Horizon oil spill, were analyzed from 340 trawl samples collected between April-June, 2011. This study is the first comprehensive survey of euphausiid distributions from depths deeper than 1000 m in the Gulf of Mexico and included stratified sampling from five discrete depth ranges (0-200 m, 200-600 m, 600-1000 m, 1000-1200 m, and 1200-1500 m). In addition, this study encompasses the region heavily impacted by the Deepwater Horizon oil spill. Data presented here could potentially be used in ecosystem models investigating trophic effects of the spill because euphausiids are the preferred prey of a variety of higher trophic organisms. Lastly, these data represent the first quantification of euphausiid assemblages in this location after the Deepwater Horizon event and can serve as a basis of comparison against which to monitor recovery of the euphausiid assemblage after exposure to Deepwater Horizon hydrocarbons and dispersant in the water column.