Typescript. Includes vita and abstract. Bibliography: Includes bibliographical references (leaves 79-83). Description: viii, 83 leaves : ill., map ; 29 cm.

Using an instrumented water quality network in Morro Bay Estuary, California from 2007 to 2010 (15 min sampling frequency), this study addressed the two objectives of constructing a nitrate budget and assessing the influence of sampling frequency on water quality parameters. These two objectives led to the submission of an original report of research (Appendix A) and a note (Appendix B) to peer-reviewed journals. The first objective was to characterize the high spatial and temporal variation in physical parameters and nitrate concentrations and to construct a nitrate budget quantifying sources and sinks of nitrate from the ocean, streams, and groundwater, as well as biological processes in the Estuary. Morro Bay Estuary was found to be a non-eutrophic system and a mean net exporter of nitrate, 327.15 t yr-1. Fifty-four percent of the nitrate export was attributed to nitrate sources and internal biological processing. Nitrate loading from streams contributed 37 % to the export of nitrate (124.01 t yr-1), while groundwater nitrate loading supplied a conservative estimate of 46 % of the exported nitrate (153.92 t yr-1), with a neap tide enhancement of the discharge. Denitrification, Zostera marina, and benthic macroalgae assimilation of nitrate were the dominant internal biological processes for removal and retention, but were only 35% of the total nitrate budget. The second objective was to investigate the impact of sampling frequency and sampling location on understanding dynamics in water quality by degrading a year time series of seven parameters from three water quality monitoring stations to sampling frequencies ranging from 15 minutes to 28 days. In Morro Bay Estuary, the semi-diurnal tidal cycle was the maximum component frequency driving the variability of temperature, turbidity, and dissolved oxygen concentrations. For these parameters, asymptotes were reached and sampling frequencies greater than six hours did not explain the additional variation in the parameters sampled. Whereas, salinity, turbidity, and nitrate concentrations lacked an asymptote, and decreased sampling frequencies led to increased estimated error. Sampling water quality parameters every 28 days can lead to mean annual difference of 30 – 140 % from 15 minute sample annual mean. We recommend sampling frequencies should be selected to oversample the tidal signal to at least hourly frequencies to capture diel cycles and episodic events that contribute significantly to understanding the variability in the estuarine physical and biological dynamics.

L'influence de la diversité génétique sur la stabilité démographique des populations constitue un paradigme de l'écologie évolutive. Au sein des populations naturelles, l'étude de cette relation est complexifiée par l'influence réciproque de la stabilité sur la diversité, et leur degré d'interconnexion. Ces interrelations ont été explorées chez la plante marine Zostera marina et les coraux d'eau froide Lophelia pertusa et Madrepora oculata, des espèces partiellement clonales. Ce trait d'histoire de vie, influençant profondément la dynamique démographique et la trajectoire évolutive des espèces, a constitué le fil d'Ariane de ce travail. L'échantillonnage dans l'espace (échelle régionale) et le temps (un pas de trois ans) d'herbiers de Zostère a permis de mieux comprendre la dynamique clonale de ces plantes. L'architecture et la diversité clonale apparaissent comme la résultante de l'équilibre entre dispersion/recrutement de nuages de graines dispersées collectivement, et la compétition pour l'espace entre clones. Les perturbations affectent localement l'équilibre de l'herbier. Cette dynamique originale rend impossible l'identification des contours populationnels. En revanche, nos résultats semblent indiquer que la diversité génétique au sens strict (hétérozygotie et nombre d'allèles) des herbiers de Zostères constitue un facteur de stabilité démographique, via sa potentielle influence sur les capacités de résistance aux perturbations saisonnières. Les coraux d'eau froide, quant à eux, présentent des patrons biogéographiques en accord avec l'hypothèse d'une extinction dans le Golfe de Gascogne, lors des derniers épisodes glaciaires. Les marques visibles des activités de pêche posent la question des capacités de résilience de ces écosystèmes, qui dépendent entre autres du potentiel de dispersion de ces espèces. L'absence de structure génétique observée chez L. pertusa suggère, au moins pour cette espèce, un fort degré d'interconnexion entre les récifs, tandis que M. oculata montre davantage de structure régionale. La sensibilité de ces espèces aux variations climatiques et à la pression des activités anthropiques souligne la nécessité d'études approfondies, pour leur conservation.Les résultats obtenus pendant cette thèse permettent de mieux comprendre la dynamique populationnelle des herbiers et récifs profonds, le taux de clonalité et la connectivité des populations. Ces informations sont essentielles pour avancer vers une meilleure compréhension de la dynamique et la résistance de ces espèces structurantes, et sont donc primordiales pour la conservation de ces écosystèmes clé.

Eelgrass, Zostera marina L. (Zosteraceae), is a flowering marine plant in coastal regions in the Northern hemisphere. Apart from its significance as habitat for a diversity of marine organisms, it has been a direct resource in European and American economies, and once was a food source for people along the Pacific Coast of North America. This interdisciplinary study documented protocols and specifics of the Kwakwaka’wakw ts’áts’ayem (eelgrass) harvesting tradition in British Columbia, and how their methods of harvesting affected the remaining plants’ growth. Through interviewing 18 traditional eelgrass harvesters and participating in six harvesting sampling events, I documented the detailed protocols of the Kwakwaka’wakw eelgrass harvesting tradition. Based on the protocols of traditional ts’áts’ayem harvesting, I developed harvesting removal experiments in a dense Z. marina populations on Quadra Island (2005) and at Tsawwassen (2006) to examine the effects that traditional harvesting of eelgrass would have had on a shoot production and rhizome internode volume, within a growing season. At the Quadra site, a June treatment of between approximately 15 and 56% shoot removal corresponded with shoot regeneration above original numbers. An approximate 60% removal corresponded with the highest new shoot production after treatment, indicating the strong capacity of eelgrass meadows to promote new shoots after removal disturbance. Based on fieldwork with traditional knowledge holders, I estimate that traditionally harvesting would have been between 10-30% removal within areas the size of the experimental plots. Shoot regeneration, net shoot production and rhizome production results at the Quadra site supported the theory that a light amount of harvesting removal such that was conducted by Kwakwaka’wakw harvesters would have been within a level for full regeneration, and possibly even enhanced shoot population and rhizome production (measured by internode volume). Tsawwassen experiment treatment was applied too late in the season to show an effect of harvest, but the design provided efficient methodology for future experiments. Ecology literature substantiated many of the traditional eelgrass protocols documented in this study, strongly supporting the theory that eelgrass harvesting was a sustainable practice. Scientific literature about pollution also corroborated and explained the observations of elders on the state of today’s eelgrass: few locations yielded ts’áts’ayem fit to eat, as specimens were small, had heavy epiphytic growth and dark rhizomes that Kwakwaka’wakw consultants had not seen in their youth. The combination of traditional ecological knowledge and scientific inquiry holds much potential for providing a better understanding of eelgrass ecology and dynamics, and for defining concepts of sustainability and conservation of this important resource.