Thesis (M.Sc.)--Memorial University of Newfoundland, 2005. / Includes bibliographical references.

Thesis (M.S.)--Western Washington University, 2008. / CD-ROM in back pocket. Includes bibliographical references (leaves 114-121). Also available online.

Thesis (Ph.D. (Zoology & Entomology)) - Rhodes University, 2009.

Eelgrass (Zostera marina) is a critical nearshore marine habitat for juvenile Pacific salmon (Oncorhynchus spp.) as they depart from their natal streams. Given the poor marine survival of Coho (O. kisutch) and Chinook (O. tshawytscha) salmon juveniles in recent decades, it is hypothesized that deteriorating eelgrass habitats could contribute to their low survival. The primary goal of this research was to investigate the possible long-term spatial-temporal trends in eelgrass habitat in the Salish Sea and was addressed by two main objectives: (1) Define a methodology for mapping eelgrass habitats using UAV imagery to create a baseline for long-term mapping; and (2) Assess changes in eelgrass area coverage and fragmentation over the period of 1932-2016 using historic aerial photographs and Unmanned Aerial Vehicle (UAV) imagery, and assess the relationship between eelgrass and residential housing density and shoreline activities. Three study sites in the Southern Gulf Islands of the Salish Sea were chosen for analysis. The overall accuracies of eelgrass delineation from UAV imagery were 95.3%, 88.9%, and 90.1% for Village Bay, Horton Bay, and Lyall Harbour, respectively. The UAV method was found to be highly effective for this size of study site, however results were impacted by the environmental conditions at the time of acquisition, namely: sun angle, tidal height, cloud cover, water clarity, and wind speed. The results from the first objective were incorporated into a long-term dataset of historic aerial photography and used to evaluate changes in eelgrass area and fragmentation. All three eelgrass meadows showed a deteriorating trend in eelgrass condition. On average, eelgrass area coverage decreases by 41% while meadow complexity as indicated by the shape index increases by 76%. Shoreline activities (boats, docks, log booms, and shoreline armouring) and residential housing density increased markedly at all sites over the study period. By using a linear correlation model, it was revealed that eelgrass areal coverage and fragmentation (Shape Index) were, in general, very strongly correlated to these landscape-level coastal environmental indicators. While this correlation model is not meant to show a direct causative impact on eelgrass at these sites, these results suggest an overall deterioration of coastal environmental health in the Salish Sea due to a dramatic increase in the use of the coastal zone, as well as likely declines in water quality due to urbanization. / Graduate

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. / The influence of genetic diversity on the demographic stability of populations constitutes a paradigm in evolutionary ecology. The complexity of this relationship within natural populations is enhanced by the reciprocal effect of stability on diversity, and the degree of interconnection among populations. This interaction was explored within the seagrass Zostera marina and the cold-water corals Lophelia pertusa and Madrepora oculata, three partially clonal species. This life history trait, deeply influencing the population dynamics and evolutionary trajectory of species, constituted the underlying theme of this work.The sampling in space (regional scale) and time (a three-years step) of eelgrass meadows allowed us to better understand the clonal dynamics of these plants. The clonal architecture and diversity may result from the equilibrium between dispersal/recruitment of collectively dispersed clouds of seeds, and the competition for space among clones. Perturbations locally affect the equilibrium of meadows. This original dynamic makes impossible the identification of population contours. Yet, our results suggest that the genetic diversity sensu stricto (heterozygosity and number of alleles) represents a factor of demographic stability, through its putative influence on resistance capacity for seasonal disturbances. Cold-water corals show biogeographic pattern in line with the hypothesis of glacial extinction, within the Bay of Biscay. The noticeable footprints of fishing activities question the capacity of resilience of these ecosystems, depending on dispersal potential of the structuring species, which showed low levels of clonality. The lack of genetic structure observed for L. pertusa suggest, at least for this species, a high degree of interconnection among reefs at large scale, while M. oculata revealed a stronger regional structure. Sensitivity of these two species to climatic variations and the pressures of human activities highlight the need of thorough studies for their conservation. Results obtained during this thesis allow a better understanding of the populations dynamics of both seagrass and deep reefs and their levels of clonality and connectivity. This information constitutes the first step toward a better understanding of dynamics and resistance of these structuring species, and is also primordial for the conservation of their key ecosystems.

Seagrass ecosystems are some of the most productive in the world and provide a variety of ecosystem services but are facing global decline chiefly due to anthropogenic disturbance. Mechanical disturbances to seagrass meadows from anchoring, propeller scars, and mooring scars result in losses or damage to both shoots and the underlying rhizome. I conducted a literature synthesis on the extent of, recovery from, and ecological impacts of these mechanical disturbances to seagrass meadows. The literature suggests that anchoring damage tends to be worst in deeper water where larger vessels anchor and can cause large (>100m2) loss per anchoring and recovery may take decades to over a century. Propeller damage is of largest concern in shallow (<2m) areas experiencing heavy boat traffic because propeller damage can only occur where the propeller can come close to the seagrass. Mooring damage is highly variable depending on the type of mooring used (>10m2 to >1000m2 scoured per mooring). Seagrass patches experiencing these mechanical disturbances have, in some studies, been found to have lower seagrass percent cover and shoot density than reference areas. This indicates scars can have "halos" of impacted seagrass meadow. Some seagrass systems cannot recover within a century (e.g. Posidonia oceanica meadows at the extent of their depth tolerance) while others recover annually from some disturbances (e.g., anchor scars <1m2). Systems face altered species composition when scars are preferentially recolonized by certain species and patterns of recovery are affected by altered biogeochemical conditions following disturbances. Additionally, mooring, anchoring, and propeller scarring frequently alter meadow density, cover, patch size, patch shape, patch isolation, edge area, and ratios of edge to interior meadow leading to changes in faunal community structure. Correlations between these disturbances and faunal abundances, densities, and richness in seagrass ecosystems are complex, vary temporally (sometimes on the scale of days), and may result in species showing positive, negative, or no responses to a wide range of disturbance regimes. To explore the connections between mooring scarring, the surrounding seagrass meadow condition and epifaunal community, in the second part of this thesis I measured 30 mooring scars to determine average scar size. To explore any potential "halo" effect around mooring scars for seagrass or epifauna and to seek any difference in epifaunal community between mooring and reference sites I also sampled paired sites at eight locations in Nantucket Harbor, Massachusetts three times each in the summer of 2015. Each location consisted of a meadow site actively experiencing mooring scarring and a reference site without moorings. My conservative sampling methods of the 30 sampled mooring scars found scars to average 21.1m2. Across my paired sites, seagrass was found to have lower cover and lower canopy height in mooring versus reference sites. Seagrass cover and canopy height were lower in the first few meters (typically 2-3m) surrounding each scar in comparison to paired reference quadrats indicating a "halo" effect of each scar. I did not detect a difference in epifaunal community composition or density per blade between mooring and reference sites; however, the relatively constant per blade concentration of epifauna combined with the differences in seagrass biomass between the mooring versus reference sites indicate an overall increase in the total amount of epifauna in areas with less disturbance. Epifaunal community composition was different and between locations and sampling dates indicating these factors are more important than proximity to mooring scarring in determining epifaunal abundance and richness. When considering scar area and the "halo" of each scar I estimate that at least 32ha (2%) of Nantucket Harbor was impacted by mooring scarring. Given that the estimates of seagrass do not include areas previously denuded of this plant and that my measurements were conservative, likely a larger portion of this harbor's potential seagrass habitat is impacted. Combined with the findings of loss due to these direct boat-related physical disturbances of seagrass meadows worldwide across regions, this halo effect is likely to also be found for moorings globally. I encourage management of the issue by employing and fine-tuning mooring methods (such as deploying moorings with anchor connections that do not drag on the sea floor) to minimize these unintentional but strong effects of mooring on the recipient habitat.

The Tay estuary is situated on the east coast of Scotland. The estuary is dominated by sediment biotopes, including mudflats which support sparse beds of two nationally scarce seagrass species, Zostera marina var. angustfolia (Hornem.) and Z. noltii (Hornem.). Seagrasses have been described as ecosystem engineers, shaping their sediment environment, and this may increase sediment deposition and stability. In this thesis the ecosystem engineering characteristics of seagrass habitats are explored. In 2008, the distribution of Zostera spp. in the Tay estuary was surveyed and mapped for the first time. Sediments within beds of Z. marina and Z. noltii were compared to investigate the influence of seagrasses on sediment characteristics. To explore the role of seagrass in sediment deposition and erosion, and coastal stability, sediment depth measurements were made in patches of Z. noltii, Z. marina and bare sediment over one year. The role of the root/rhizome system on sediment retention over winter was also considered. Sediment deposition in Z. noltii beds, and the influence of the plants on near-bed flow dynamics was further explored in the laboratory, using an 8 m seawater flume. In the field the retention of particles over 2 and 14 tides was measured, and the results of this experiment led to a study of the influence of leaf and sediment biofilms on particle retention, using the novel method of magnetic particle induction (MagPI). The efficacy of artificial seagrass beds and Z. noltii transplantation as habitat restoration techniques were compared over one year. During the trial, sediment deposition and changes in sediment characteristics were determined, and the protection given to saltmarsh cliffs fringing the study plots was assessed. Mechanisms underlying the results are suggested and the findings discussed. This study provides an insight into the ecology of seagrass in the Tay estuary and its role as an ecosystem manager. It may offer valuable data which could be utilised for future conservation policies, habitat restoration schemes and management planning of the area.

The aim of this research was to assess three hierarchical aspects of alga-grazer interactions in intertidal communities on a small scale: spatial heterogeneity, grazing effects and spatial stability in grazing effects. First, using semivariograms and cross-semivariograms I observed hierarchical spatial patterns in most algal groups and in grazers. However, these patterns varied with the level on the shore and between shores, suggesting that either human exploitation or wave exposure can be a source of variability. Second, grazing effects were studied using manipulative experiments at different levels on the shore. These revealed significant effects of grazing on the low shore and in tidal pools. Additionally, using a transect of grazer exclusions across the shore, I observed unexpected hierarchical patchiness in the strength of grazing, rather than zonation in its effects. This patchiness varied in time due to different biotic and abiotic factors. In a separate experiment, the effect of mesograzers effects were studied in the upper eulittoral zone under four conditions: burnt open rock (BOR), burnt pools (Bpool), non-burnt open rock (NBOR) and non-burnt pools (NBpool). Additionally, I tested spatial stability in the effects of grazing in consecutive years, using the same plots. I observed great spatial variability in the effects of grazing, but this variability was spatially stable in Bpools and NBOR, meaning deterministic and significant grazing effects in consecutive years on the same plots. Both the significance in grazing effects and spatial stability depended on the level of resolution (species, functional, biomass) at which the algal assemblage was evaluated, suggesting hierarchical variability. In order to be able to predict spatial variability in the effects of grazers in the upper eulittoral zone using biotic and abiotic micro- and macrofactors, a conceptual model was proposed, based on data from several multiple-regressions. This linked the interactions among three elements: idiosyncratic heterogeneity, micro and macrofactors. This suggests that spatial variability can be a product of these factors, while spatial stability can be caused by the same or different combinations of factors. In conclusion, grazing and other ecological phenomena must be studied hierarchically, not only through spatiotemporal scales, but also at different levels of resolution, as these also influence our perception of patterns.

Most of what is known about the ways in which strongly interacting species affect ecological communities stems from changes to community structure revealed in contemporary research. However, trophic downgrading has limited the temporal extent to which inferences can be drawn. The aim of my Dissertation was to expand on the strongly interacting species concept by examining species interactions at a historical scale, in a textbook example of a strongly interacting and keystone predator. The sea otter, Enhydra lutris, was driven to near-extinction but is recovering in parts of its range, providing a mosaic of areas with and without sea otters. This mosaic allowed for a series of natural experiments, which I conducted using behavioural observations, genetic tools, and archaeological methods, to examine sea otter effects spanning contemporary (last ~40 yrs.), and late-Holocene (~3500-150 yrs. ago) timeframes, and on an evolutionary scale that inferred middle-Pleistocene interactions. In Chapter 2, my coauthors and I found that sea otter use of clam-based niches increased as occupancy-time increased, and that bachelor groups of male otters primarily inhabited these niches, findings that informed and inspired subsequent questions. In Chapter 3, we found that where sea otters were established for 20-30 years, the disturbance to eelgrass (Zostera marina), caused by sea otters digging for clams and other infaunal prey, was correlated with ~25% greater eelgrass allelic richness than where otters were present <10 yrs, or absent. We posit that sea otter digging has long-influenced the genetic diversity and resilience of eelgrass – perhaps since the middle Pleistocene. In Chapter 4, we asked how two strongly interacting species – people and sea otters – co-existed for millennia where they both consumed clams. We used assemblages of live and otter-cracked butter clams (Saxidomus gigantea), to confirm the ecological effects that sea otters exert today. We measured clams from archaeological assemblages in areas densely populated with clam gardens – terraced beaches that enhance clam habitat and productivity – and found that sea otters reduced the sizes of ancient clams, acting as ecologically effective predators in the mid-to-late Holocene. However, clam harvests were stable for thousands of years, with or without otters. We suggest that clam gardening supported coexistence of people and otters in the past, and could function the same way today. Collectively, we found that a few, perhaps long-forgotten, interactions increased the breadth of the strongly interacting species concept. In Chapter 5, I suggest that such rediscoveries could occur in other systems. Many large vertebrates have suffered population declines, but the most insidious losses accompanying these, are the losses of ecological interactions that become unknowable, and thus cannot be intentionally restored. By searching out ancient interactions, long-forgotten relationships have the potential to be recovered, and to inform our understanding of contemporary systems. / Graduate / 2022-09-10

The objectives of the present study are to: (1) Describe the macro-invertebrate species composition and seasonal changes in abundance of the benthic infauna within an eelgrass bed; (2) Observe what immediate effects occur to the benthic community as a result of experimental removal of eelgrass plants from plants within the Zostera bed; (3) Measure the seasonal variation of eelgrass turion length over an annual cycle and determine its correlation to biomass (dry weight); (4) Examine, by means of field experiments, the importance of incident solar irradiation in affecting the seasonal growth of Zostera; and (5) Determine the relationship, if any, between the abundance of major invertebrate species and the abundance of eelgrass as determined by mean turion length.