Though the water in eastern Georgian Bay is oligotrophic, some of the coastal embayments and wetlands have begun to show signs of water quality impairment that is thought to be related to human development along the shoreline. The primary objective of my thesis is to provide environmental agencies with the resources to effectively manage water quality in the coastal zone of eastern Georgian Bay. First, I evaluate the ability of the Lakeshore Capacity Model (LCM), developed for inland Precambrian Shield lakes, to predict the trophic status of coastal embayments. Finding that the LCM does not accurately predict trophic status, I develop the Anthro-geomorphic Model (AGM), which uses the level of human development and the degree of mixing between the embayment and open waters of Georgian Bay to predict embayment trophic status. Second, I explore the spatial association between densities of building, dock and road development and Water Quality Index (WQI) scores, an index designed to evaluate wetland condition, for wetlands in the Township of Georgian Bay. I found an inverse relationship between WQI scores and the density of these stressor variables inside wetland catchments, which indicates that these stressors have a negative impact on wetland water quality. I then created a series of mapping products that present building, dock and road densities, along with WQI scores for 61 wetlands in the Township of Georgian Bay, to determine how wetland water quality is spatially associated with densities of these stressor variables. I found that regions with high densities of building, dock and road development were associated with wetlands of lower quality, whereas wetlands in areas that had low densities of development were of higher quality. I used this information to identify areas of conservation priority for management in the Township of Georgian Bay. The results from this thesis will provide environmental managers with resources to protect the valuable coastal waters of eastern Georgian Bay. / Thesis / Master of Science (MSc) / A number of coastal embayments and wetlands of eastern Georgian Bay show signs of water quality impairment thought to be caused by cottage development. The objective of my thesis is to develop and evaluate models designed to measure the impact of human development on water quality in these coastal zones. First, finding that the Ontario Lakeshore Capacity Model, developed for Muskoka lakes, does not accurately predict trophic status in embayments, I develop the Anthro-geomorphic Model, which uses building density and basin morphometry to predict embayment trophic status. Second, I explore the appropriateness of using development densities (building, dock and road) to quantify anthropogenic stress in coastal wetlands. This thesis provides the scientific basis for choosing management practices to protect the coastal waters of Georgian Bay.

Anthropogenic disturbances can alter the abiotic composition of freshwater systems. These compositional changes can act as physiological stressors towards system inhabitants. However, little is known about how these altered abiotic factors influence stress hormones (corticosterone) in larval amphibians. Throughout the following chapters, I examined the effects of several abiotic factors on baseline and stress-induced corticosterone levels in the larvae of four amphibian species: Jefferson salamander (Ambystoma jeffersonianum), spotted salamander (A. maculatum), wood frog (Rana sylvatica), and grey treefrog (Hyla versicolor). Chapter II examined corticosterone level differences throughout development in A. jeffersonianum and R. sylvatica larvae under field, mesocosm, and laboratory venues. Baseline corticosterone levels in R. sylvatica increased near metamorphic climax in all venues, but not in A. jeffersonianum. Rather, baseline corticosterone levels differed with respect to venue throughout development in A. jeffersonianum. Chapter III examined corticosterone level differences among free-living A. jeffersonianum populations and possible abiotic factors underlying these hormone differences. Corticosterone levels significantly differed across populations. Increased baseline corticosterone levels significantly correlated to low pH. There was also a trend for increased baseline corticosterone levels to be positively correlated with chloride levels and negatively correlated with conductivity. Chapter IV examined the effects of laboratory manipulated pH on corticosterone levels in A. jeffersonianum, A. maculatum, R. sylvatica, and H. versicolor. There was a significant correlation between increased baseline corticosterone levels to low pH in all four species. Prey consumption (in both Ambystoma species) and survival (in A. jeffersonianum, A. maculatum, and R. sylvatica) were also negatively correlated to low pH. Chapter V examined the effects of increased conductivity on corticosterone levels in A. jeffersonianum, R. sylvatica, and H. versicolor. Increased conductivity exposure significantly correlated to increased baseline corticosterone levels in A. jeffersonianum and R. sylvatica. Prey consumption in A. jeffersonianum was also negatively correlated to increased conductivity. My dissertation shows that abiotic factors, such as pH and conductivity, can influence corticosterone levels in larval amphibians. These results suggest that corticosterone levels in larval amphibians may be a suitable biomarker reflective of altered freshwater habitat quality. However, my results also suggest that one should use a high degree of caution when using corticosterone levels in larval amphibians as a means to infer the health status of a population. / Ph. D.

Analysis of animal movement has been integrated into a framework of four components: internal state, motion capacity, navigation capacity, and external factors (Nathan et al., 2008). We used this framework to enhance understanding of movement behavior in the 15 West Indian rock iguana (Cyclura) taxa and to inform conservation management. Our review found that adult female Cyclura large-scale movement is primarily driven by nesting and migrations. Nest site selection also influences hatchling dispersal, but few studies identify preferred habitats for nesting females. Anthropogenic impacts on nesting ecology are largely unexplored, especially in Cyclura carinata. We studied C. carinata nesting ecology in a threatened population, aiming to identify habitat preferences and assess human impact on nesting success. This research fills gaps by addressing both proximate causes of movement and ultimate outcomes of movement decisions, essential for developing effective conservation strategies. Understanding both aspects is crucial for mitigating threats to Cyclura populations.

Testing ecological theory at macroecological scales may be useful for disentangling abiotic influences from anthropogenic disturbances, and thus provide insights into fundamental processes that structure ecological communities. In tropical coral reef systems, our understanding of community structure is limited to small-scale studies conducted in moderately degraded regions, while larger regional or ocean scale analyses have typically focused on identifying human drivers of reef degradation. In this thesis, my collaborators and I combined stable isotope specimens, underwater visual censuses, and remote sensing data from 43 Pacific islands and atolls in order to examine the relative roles of natural environmental variation and anthropogenic pressures in structuring coral reef fish and benthic communities. First, at unexploited sites on Kiritimati Atoll (Kiribati), isotope estimates indicated that trophic level increased with body size across species and individuals, while negative abundance ~ body size relationships (size spectra) revealed distinct energetic constraints between energy-competing carnivores and energy-sharing herbivores. After demonstrating size structuring of reef fish communities in the absence of humans, we then examined evidence for size-selective exploitation impacts on coral reefs across the Pacific Ocean. Size spectra 'steepened' as human population density increased and proximity to market center decreased, reflecting decreases in large-bodied fish abundance, biomass, turnover rate, and mean trophic level. Depletion of large fish abundances likely diminishes functions such as bioerosion by grazers and food chain connectivity by top predators, further degrading reef community resilience. Next, we considered the relative strengths of abiotic, biotic and anthropogenic influences in determining reef benthic state across spatial scales. We found that from fine (0.25 km2) to coarse (1,024 km2) grain scales the phase shift index (a multivariate metric of the relative cover of hard coral and macroalgal) was primarily predicted by local abiotic and bottom-up influences, such that coral-dominated reefs occurred in warm, productive regions at sites exposed to low wave energy, irrespective of grazing or human impacts. Our size- based analyses of reef fish communities revealed novel exploitation impacts at ocean-basin scales, and provide a foundation for delineating energetic pathways and feeding interactions in complex tropical food webs. Furthermore, we demonstrate that abiotic constraints underpin natural variation among fish and benthic communities of remote uninhabited reefs, emphasizing the importance of accounting for local environmental conditions when developing quantitative baselines for coral reef ecosystems. / Graduate / 0329

Coral reefs have one of the highest levels of biodiversity of all ecosystems in the world and are important for both human livelihood and food security throughout many tropical countries. However, due to increased anthropogenic pressure on marine ecosystems, especially during the last couple of decades, coral reefs have become critically over-fished, and many reefs are now in a degraded state and are facing additional future threats due to further over-exploitation, chemical pollution, sedimentation, and effects of climate change. The main aim of this PhD thesis was to understand effects of anthropogenic disturbances on tropical coastal ecosystems and fish connectivity for coastal management purposes. Therefore, linkages between anthropogenic disturbance and corals were investigated (Paper I), as well as interactions between coral reef habitat and associated fish assemblage (Paper II). Furthermore, connectivity between coral reefs and other tropical coastal ecosystems was explored (Paper III), as well as fish migration to reproduction sites (Paper IV), and evaluations of spatial ecology methods (Paper V). The result showed that coral reefs that are already exposed to disturbances, such as freshwater and nutrient run-offs, may be more sensitive to climate change, in terms of increased sea surface temperatures (Paper I). In addition, there were also clear linkages between coral reef quality, in terms of coral coverage, and fish assemblages, which displayed high spatial variability and suggesting patchy recovery after the 1997/1998 bleaching and subsequent coral mass mortality event (Paper II). This highlights the importance of understanding effects of disturbances on corals, especially in terms of synergistic effects between increased water temperatures and other coastal stressors such as decreased salinity and increased nutrients; and the indirect effects of habitat degradation on the fish community. Linkages between fish and different coastal habitats were further explored. The results showed that coral reefs were strongly connected with mangrove and seagrass beds, through ontogenetic migration of fish (Paper III). Migrations to spawning sites of groupers were related to lunar activities when thousands of fish gather for reproduction purposes during new moon, which increases the risk of over-exploitation (Paper IV). The results emphasises the importance of protecting key areas such as nursing grounds and reproduction sites. Furthermore, acoustic telemetry has become an increasingly common method in studies of fish movement, and the results showed that efficiency of acoustic arrays may increase depending on deployment strategies and habitat characteristics (Paper V). In conclusion, the results from this PhD thesis emphasises the importance of protecting coral reef habitats, as well as identifying related susceptible tropical coastal areas, such as nursing grounds and reproduction sites. Indeed, a better scientific understanding of coral reef ecology and indirect and direct effects on fish assemblages are needed for efficient and accurate coastal management decisions. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 5: Manuscript.</p>

Sperm whales (Physeter macrocephalus) are nomadic species typically studied across broad (>100km) spatial scales. In this study, I model fine-scale (or submesocale) habitat preferences, determine how organization into distinctive units of associating female and juveniles influences habitat use, and describe how movements change across the 24-hour cycle. This study concerns a well-studied population of sperm whales off Dominica in the Eastern Caribbean. Statistical models suggest that overall habitat use is rather homogenous, and social behaviour is best predicted by the presence of mature males. Variation among social units in the amount of time spent, and space occupied, within the study area indicates habitat preferences at the level of the social unit. Finally, movements are influenced by the diurnal cycle, as whales tend to move from inshore to offshore at dusk. This study betters our understanding of sperm whale habitat decisions over fine-scales, and has implication for conservation and management strategies.

Made available in DSpace on 2017-07-10T17:48:23Z (GMT). No. of bitstreams: 1 Julio_Cesar_Juvenal.pdf: 1051867 bytes, checksum: a4731ec908b451f5eadcb37ef14cedfe (MD5) Previous issue date: 2010-11-17 / This study was developed in two areas in the southern portion of the Ilha Grande National Park (23 º 59 'and 24 º 04' S and 54 º 09 'to 54 º 15' W) in Guaira, Parana. The objective was to compare and analyze the bird communities in these two areas between the months of April 2009 and March 2010. The first area is formed by the Pacu Island and three small islands in its adjacency (total area of 97.34 ha) and it is closer to the center of human disturbance. In these islands were distributed 13 observation points. Already the area is formed by Robinson, Scott and San Francisco Islands (total area of 100.40 ha) and 14 observation points. For the birds sampling was used the fixed points method. During the study period, there were 20 expeditions to Area 1 (442 point samples) and 17 expeditions to Area 2 (448 point samples). We recorded 123 bird species, 99 in Area 1 and Area 2 107. Sixteen species (16.16%) were unique to one area and twenty-four (22.4%) exclusive Area 2. We recorded two endangered species in the Paraná State (Sporophila angolensis Procacicus solitarius), both with high frequency of occurrence, besides the first record of Icterus croconotus in this state. The Abundance Index changed by 0.0022 (a contact) in fourteen species in both areas and 0.6651 (294 contacts) just to Todirostrum cinereum in Area 1 and 0.5647 (253 contacts) just for thrush in leucomelas Area 2. The birds variety was 3.332 in Area 1 and 3.517 in Area 2. The equidistribution of the species was 0.725 for Area 1 and 0.752 for Area 2 with similarities between the areas of 0.80. Frugivorous and scavengers have similarity of 0.5 between the study areas, followed by insectivorous (0.46), omnivores (0.45), granivores (0.41) and carnivores (0.38). The omnivorous represent 41.46% of the 123 species recorded in the survey, followed by insectivores (30.89%), granivores (10.56%), carnivores (7.31%), piscivores (4.87%), frugivores (2.43%) and scavengers (2.43%). The low incidence of frugivores raises an alert for this ecosystem. Probably the great enterprises and intense process of deforestation in the region may have been responsible for the negative effects on bird community. The study showed no statistical difference in the results for the calculated parameters in different areas. These results are explained by the fact that the factors of human disturbance may have also affected areas, besides proximity and similarity in habitat between areas (mean distance of 8.5 km.). These results were the first systematic data about the lake avifauna after the creation of the Itaipu hydroelectric plant and the construction of Ayrton Senna Bridge and they can support studies for forecasting, mitigate and compensation for the environmental impact for future enterprises in near of the study area / O estudo foi realizado em duas áreas na porção sul do Parque Nacional de Ilha Grande (23º59 e 24º04 S e 54º09 a 54º15 W) no município de Guaíra, Paraná. Objetivou-se comparar e analisar as comunidades de aves nestas duas áreas entre os meses de abril de 2009 e março de 2010. A Área 1 é formada pela Ilha Pacu e mais três ilhotas em sua adjacência (área total de 97,34 ha) e está mais próxima do centro de perturbações antrópicas. Nestas ilhas foram distribuídos 13 pontos de observação. Já a Área 2 é formada pelas ilhas Rodrigues, Saraiva e São Francisco (área total 100,40 ha) e 14 pontos de observação. Para a amostragem de aves foi utilizado o método de pontos fixos. No período de estudo, foram realizadas 20 expedições à Área 1 (442 amostras pontuais) e 17 expedições à Área 2 (448 amostras pontuais). Foram registradas 123 espécies de aves, 99 na Área 1 e 107 na Área 2. Dezesseis espécies (16,16%) foram exclusivas da Área 1 e vinte e quatro (22,4%) exclusivas da Área 2. Foram registradas duas espécies ameaçadas de extinção no estado do Paraná (Sporophila angolensis e Procacicus solitarius), ambas com alta frequência de ocorrência, além do primeiro registro do Icterus croconotus neste estado. O Índice Pontual de Abundância apresentou variação de 0,0022 (1 contato) em quatorze espécies em ambas as áreas e 0,6651 (294 contatos) apenas para Todirostrum cinereum na Área 1 e 0,5647 (253 contatos) apenas para Turdus leucomelas na Área 2. A diversidade da avifauna foi de 3,332 na Área 1 e 3,517 na Área 2. A equidistribuição das espécies foi de 0,725 para Área 1 e 0,752 para Área 2 com similaridade entre as áreas de 0,80. Os frugívoros e necrófagos tiveram similaridade de 0,5 entre as áreas de estudo, seguidos dos insetívoros (0,46), onívoros (0,45), granívoros (0,41) e carnívoros (0,38). Os onívoros representam 41,46% das 123 espécies registradas no levantamento, seguido por insetívoros (30,89%), granívoros (10,56%), carnívoros (7,31%), piscívoros (4,87%), frugívoros (2,43%) e necrófagos (2,43%). A baixa incidência de frugívoros levanta um alerta para este ecossistema. Provavelmente os grandes empreendimentos e o intenso processo de desmatamento na região podem ter sido responsáveis pelos efeitos negativos sobre a comunidade de aves. O estudo não demonstrou diferença estatística nos resultados para os parâmetros calculados nas diferentes áreas. Estes resultados são explicados pelo fato que os fatores de perturbações antrópicas podem ter afetado igualmente as áreas, além de semelhança nos habitats e proximidade entre as áreas (distância média de 8,5 Km). Esses resultados foram os primeiros dados sistematizados sobre a avifauna após a criação do lago da usina hidrelétrica de Itaipu e a construção da ponte Ayrton Senna e podem subsidiar estudos para a previsão, mitigação e compensação de impacto ambiental para futuros empreendimentos nas proximidades da área de estudo

Coastal marine ecosystems are among the most impacted globally, attributable to individual and cumulative effects of human disturbance. Anthropogenic nutrient loading is one stressor that commonly affects nearshore ecosystems, including seagrass beds, and has positive and negative effects on the structure and function of coastal systems. An additional, previously unexplored mechanistic pathway through which nutrients may indirectly influence nearshore systems is by driving blooms of benthic jellyfish. My dissertation research, conducted on Abaco Island, Bahamas, focused on elucidating the role that benthic jellyfish have in structuring systems in which they are common (i.e., seagrass beds), and explored mechanistic processes that may drive blooms of this taxa. To establish that human disturbances (e.g., elevated nutrient availability) may drive increased abundance and size of benthic jellyfish, Cassiopea spp., I conducted surveys in human-impacted and unimpacted coastal sites. Jellyfish were more abundant (and larger) from human-impacted areas, positively correlated to elevated nutrient availability. In order to elucidate mechanisms linking Cassiopea spp. with elevated nutrients, I evaluated whether zooxanthellae from Cassiopea were higher from human-disturbed systems, and whether Cassiopea exhibited increased size following nutrient input. I demonstrated that zooxanthellae population densities were elevated in human-impacted sites, and that nutrients led to positive jellyfish growth. As heightened densities of Cassiopea jellyfish may exert top-down and bottom-up controls on flora and fauna in impacted seagrass beds, I sought to examine ecological responses to Cassiopea. I evaluated whether there was a relationship between high Cassiopea densities and lower benthic fauna abundance and diversity in shallow seagrass beds. I found that Cassiopea have subtle effects on benthic fauna. However, through an experiment conducted in a seagrass bed in which nutrients and Cassiopea were added, I demonstrated that Cassiopea can result in seagrass habitat modification, with negative consequences for benthic fauna. My dissertation research demonstrates that increased human-driven benthic jellyfish densities may have indirect and direct effects on flora and fauna of coastal marine systems. This knowledge will advance our understanding of how human disturbances shift species interactions in coastal ecosystems, and will be critical for effective management of jellyfish blooms.

Over the past several decades, naturally occurring populations of Fraser fir (Abies fraseri) in the Black Mountains of North Carolina have been heavily impacted by both direct and indirect anthropogenic disturbances, including logging and logging- associated fires, and high mortality rates due to the introduction of the exotic insect, balsam woolly adelgid (BWA) (Adelges piceae). The decline in Fraser fir is particularly concern because it serves as a foundation species within the spruce-fir forests of the Southern Appalachian Mountains. Our objectives for this research were to 1) use current stand structure to infer whether Fraser fir trees are experiencing a cycle of regeneration-mortality that will lead to eventual decline of the population, 2) determine what role, if any, the site-specific geographic variables of slope, elevation, aspect, and land use history have on stand structure, mortality, and BWA infestation level, and 3) analyze repeat aerial photography to examine broad trends of spruce-fir forest cover change caused by anthropogenic disturbance and the BWA. In order to understand stand structure, mortality, and infestation levels, we conducted detailed field surveys of Fraser fir trees throughout the Black Mountains using 44, fixed-radius circular sampling plots. These plots were placed throughout a series of aspects, elevations, and disturbance types in order to understand geographic variability among these variables. An analysis of 4 repeat aerial photographs and corroborating ground photographs revealed broad spatio-temporal trends of spruce-fir regeneration and mortality from 1954 to 2006. Our results indicate that Fraser fir stands at higher elevations are currently in a state of recovery; whereas stands at lower elevations appear to be more susceptible to BWA-induced mortality. Changes in forest cover area from 1954 to 2006 were influenced greatly by direct and indirect anthropogenic disturbance. Our results call attention to the significant impact that direct and indirect anthropogenic disturbance has had on Fraser fir stand structure, but also provide evidence for the ability of an imperiled ecosystem to recover from high rates of insect caused mortality. / Master of Science

A primary focus of wildlife research is to understand how habitat conditions and human activities impact the health of wild animals. External factors, both natural and anthropogenic that impact the ability of an animal to acquire food and build energy reserves have important implications for reproductive success, avoidance of predators, and the ability to withstand disease, and periods of food scarcity. In the analyses presented here, I quantify the impacts of habitat quality and anthropogenic disturbance on indicators of health for individuals in a threatened grizzly bear population in Alberta, Canada. The first analysis relates spatial patterns of hair cortisol concentrations, a promising indicator of long-term stress in mammals, measured from 304 grizzly bears to a variety of continuous environmental variables representative of habitat quality (e.g., crown closure, landcover, and vegetation productivity), topographic conditions (e.g., elevation and terrain ruggedness), and anthropogenic disturbances (e.g., roads, forest harvest blocks, and oil and gas well-sites). Hair cortisol concentration point data were integrated with continuous variables by creating a stress surface for male and female bears using kernel density estimation validated through bootstrapping. The relationships between hair cortisol concentrations for males and females and environmental variables were quantified using random forests, and landscape scale stress levels for both genders was predicted based on observed relationships. Low female stress levels were found to correspond with regions with high levels of anthropogenic disturbance and activity. High female stress levels were associated primarily with high-elevation parks and protected areas. Conversely, low male stress levels were found to correspond with parks and protected areas and spatially limited moderate to high stress levels were found in regions with greater anthropogenic disturbance. Of particular concern for conservation is the observed relationship between low female stress and sink habitats which have high mortality rates and high energetic costs. Extending the first analysis, the second portion of this research examined the impacts of scale-specific habitat selection and relationships between biology, habitat quality, and anthropogenic disturbance on body condition in 85 grizzly bears represented using a body condition index. Habitat quality and anthropogenic variables were represented at multiple scales using isopleths of a utilization distribution calculated using kernel density estimation for each bear. Several hypotheses regarding the influence of biology, habitat quality, and anthropogenic disturbance on body condition quantified using linear mixed-effects models were evaluated at each habitat selection scale using the small sample Aikake Information Criterion. Biological factors were influential at all scales as males had higher body condition than females, and body condition increased with age for both genders. At the scale of most concentrated habitat selection, the biology and habitat quality hypothesis had the greatest support and had a positive effect on body condition. A component of biology, the influence of long-term stress, which had a negative impact on body condition, was most pronounced within the biology and habitat quality hypothesis at this scale. As the scale of habitat selection was represented more broadly, support for the biology and anthropogenic disturbance hypothesis increased. Anthropogenic variables of particular importance were distance decay to roads, density of secondary linear features, and density of forest harvest areas which had a negative relationship with body condition. Management efforts aimed to promote landscape conditions beneficial to grizzly bear health should focus on promoting habitat quality in core habitat and limiting anthropogenic disturbance within larger grizzly bear home ranges. / Graduate / 0768 / 0463 / 0478 / mathieub@uvic.ca