The self-sustaining status of Georgian Bay’s trophy muskellunge (Esox masquinongy) fishery is owed in part to the widespread distribution of high quality coastal wetlands used as nursery habitat. The specific wetland features that promote the recruitment of young-of-the-year (YOY) muskellunge in Georgian Bay have not been clearly defined, and without such information, it is unclear to what extent an unprecedented period of sustained low water-levels (c. 1999), and/or shoreline modifications, will continue to degrade the suitability of nursery habitats used by muskellunge throughout Georgian Bay. In this thesis, I use data from two years of intensive sampling in two embayments of northern Georgian Bay to statistically differentiate between wetlands that were found with and without YOY muskellunge. By doing so, I have provided the first quantifiable definition of suitable nursery habitat for muskellunge in Georgian Bay. Muskellunge nurseries have a structurally complex community of submersed aquatic vegetation (SAV; e.g. Potamogeton richardsonii) within the water column (≤ 1-m depth) and a fish community that had abundant suitable prey (e.g. Cypinid species) and a scarcity of early-life predators (e.g. Perca flavescens). Some key aspects of the SAV community were governed by wetland's bathymetry, and this relationship makes it possible to model the effect of changing water-level scenarios on habitat suitability. I translated these results into a management tool for fish management agencies by creating an Index of Nursery Habitat Suitability (INHS) that can be applied to other embayments in Georgian Bay to identify high quality early-life habitats for muskellunge. I developed two INHS models and applied them to an independent dataset from other regions of Georgian Bay, and found them to differentiate between sites that were known to be used by YOY muskellunge and those where YOY were absent. These were also able to track deterioration in habitat quality associated with the recent decade of low water levels. Both INHS models rely on variables based on robust ecological relationships known to favour YOY survivorship that can be readily collected by fish management agencies, and one INHS model does not require detailed information of the aquatic plant community. Both models were also designed to minimize the frequency of false negatives (suitable nursery sites misidentified as unsuitable) and false positives (unsuitable nursery sites misidentified as suitable). These INHS models should become an important tool that will complement harvest regulations to promote this economically and ecologically valuable, self-sustaining muskellunge population in Georgian Bay. / Thesis / Doctor of Philosophy (PhD) / The following Ph.D. describes how a period of sustained low water levels and shoreline modifications in Georgian Bay, Lake Huron, have impacted the coastal wetland habitat used by muskellunge during their early life. To counteract these adverse effects, the thesis provides a definition of the wetland features that promote the survival of young-of-the-year muskellunge in Georgian Bay. Included is a proposed management tool in the form of an Index of Nursery Habitat Suitability (INHS) for muskellunge that can be used to identify high-quality, early-life habitat of muskellunge. Furthermore, the INHS can be used to predict how the quality of this habitat responds to different water-level scenarios and to shoreline modification in Georgian Bay, and to guide rehabilitative efforts of degraded wetland habitat.

The goals of this thesis are to assess the use of remote sensmg and Geographic Information Systems (GIS) to map and classify coastal wetland habitat along the entire coast of eastern Georgian Bay, Lake Huron. Little mapping has been completed in this region where there is potentially the largest concentration of coastal wetlands in the Great Lakes. In chapter 1, we developed a method that uses high-resolution IKONOS imagery (1-m resolution) with an object-based approach to classify wet meadow vegetation in these coastal wetlands, and assessed the transferability of classification rulesets developed independently for 3 different satellite scenes. We showed that 4 different classes (meadow/shrub, emergent, senescent vegetation, and rock) can be mapped with an overall accuracy of 76%. When classification rulesets developed for individual scenes were transferred to other scenes without gathering additional field information for those scenes, we found a difference in accuracy of about 5%. This difference in accuracy is acceptable considering the trade-off in costs associated with field surveys. We recommend that managers use IKONOS in fine-scale habitat mapping and that rulesets only be developed for geographically distinct areas. In Chapter 2, we conducted a study to test the feasibility of using this mapping approach to complete the field surveys required in Ontario Wetland Evaluation System (OWES). In addition, we determined empirically how inclusion of vegetated deep-water habitat below 2 m can affect relevant OWES component scores, because the current system does not consider any vegetated habitat below 2 m, even though this portion of coastal wetlands is known to provide critical habitat for many Great Lakes fishes. We sampled 16 wetlands that varied in size and inundation characteristics and grouped them into 4 categories: small aquatic, small terrestrial, large aquatic, and large terrestrial. When the vegetated deep-water habitat was included, total wetland area and the overall score for all assessed criteria assessed increased significantly; however, this increase was not sufficiently large to make any practical difference in the overall score using existing the point-scale. This is largely because submerged aquatic habitat is not adequately represented in current evaluation protocols and is severely undervalued. In chapter 3 we developed a method to quantify and monitor change in coastal marsh habitat in southeastern Georgian Bay using multi-temporal IKONOS imagery. We detected a significant increase in the proportion of terrestrial habitat (high marsh) at the expense of the aquatic habitat (low marsh) over six years from 2002 to 2008. There did not appear to be any effect of human activities (indicated by the number of buildings within 500 m of wetlands) on habitat changes. We conclude that water levels may currently exert greater pressure on these systems than does cottage density in the region. We recommend that the approaches developed in this study be applied as quickly as possible to comprehensively map existing wetland habitat in eastern Georgian Bay to monitor responses to further water-level and human-induced disturbance. / Thesis / Master of Science (MSc)

Coastal wetlands of Georgian Bay have been virtually ignored by ecologists until recently, when these ecosystems were found to have exceptionally high biodiversity compared to other Gr,~at Lakes wetlands. To address this deficiency, we conducted a baseline survey (2002 to 2007) to determine the biotic and abiotic characteristics of 92 wetlands in 18 quatemary watersheds, using a suite of published ecological indices developed specifically for coastal wetlands (Water Quality Index (WQI); adjusted Wetland Macrophyte Index (WMiadj), and the Wetland Fish IndexBasinPAex (WFIBasinPAex)). Although a majority of the watersheds are located in remote eastern and northern parts of the Bay and therefore receive minimal human disturbance, one watershed, Sturgeon River, located in southern Georgian Bay receives relatively high urban, recreational and agricultural disturbance. Mean scores of WQI and WMiadj varied significantly across the watersheds, ranging from 0.48 to 2.15, and from 2.29 to 3.77, respectively. Mean WFIBasinPAex scores, however, were less variable and only ranged from 3.53 to 3.86. Of the 88 macrophyte species identified, the most common were hardstem bulrush. (Schoenoplectus acutus), water celery (Vallisneria americana), richardson's pondweed (Potamogeton richardsonii), slender waternymph (Najasjlexilis) and Canadian waterweed (Elodea canadensis). Six non-native macrophytes, Purple loosestrife (Lythrum wlicaria), narrow-leaf cattail (Typha angustifolia), hybrid cattail (Typha x glauca), Eurasian milfoil (Myriophyllum spicatum), curly pondweed (Potamogeton crispw) and frogbit (Hydrocharus morsus-ranae) were also recorded, the most common ofwhieh was Eurasian milfoil. Sago pondweed (Stuckenia pectinata), a native species that can be invasive, and is tolerant of poor water-quality, was present in about half of the watersheds. Ofthe 51 fish species, pumpkinseed (Lepomis gibbosus) bluntnose minnow (Pfmephales notatus), brown bullhead (Ameiurus nebulosus), rock bass (Ambloplites rupestris), and yellow perch (Percajlavescens) were the most widespread and abundant. Three non-native species, common carp (Cyprinus carpio), alewife (Alosa pesudoharengus), and round goby (Neogobius melanostomus) were present but not dominant. WMI scores were highly correlated with WQI scores, and as expected, wetlands in the most disturbed southern watershed were associated with the lowest WQI and WM[ scores, and had the greatest number of exotic species. However, WMI scores of wetlands in a few exposed sites located at the tip of the Bruce Peninsula were similarly low, even though these sites are not yet impacted by human activities. There was no significant relationship between WFIBasinPAand WQI scores, although the WFIBasin PA did not seem to be affected by exposure. We recommend that the WQI and WMiadj be used in long-term monitoring programs of Georgian Bay to track negative impacts of human disturbance on these valuable ecosystems. / Thesis / Master of Science (MS)

Muskellunge (Esox masquinongy) and Northern Pike (E. lucius) are ecologically and economically important fish species that rely on coastal habitats in Georgian Bay, especially coastal marshes. These habitats have adapted to the high natural water-level fluctuations of Lake Huron but are threatened by changing water-level conditions associated with global climate change. The overall goals of this thesis were to identify important esocid habitats and understand how their suitability will be affected by changing water levels. First, I used tracking information from radio telemetry studies of esocid populations in spatially distinct regions of Georgian Bay to identify important habitats during breeding and non-breeding seasons. I documented the strong affinity of Muskellunge to re-use specific spawning grounds close to known nursery habitat in coastal marshes. Both Muskellunge and Northern Pike used coastal marshes during the non-breeding season, and physical habitat structure was a more important driver of habitat use in the summer months than water temperature. Next, I created a GIS model using only hydrogeomorphic features (depth, slope, and wave exposure) to map the extent of coastal marshes throughout eastern and northern Georgian Bay to assess how habitat would shift under a range of possible lake elevations scenarios (175.5 – 177.5 m). The geomorphology at low lake levels favoured large areas of shallow (< 0.5 m) habitat at the expense of deeper habitats (0.5 – 1.5 m) that can support an aquatic vegetation community more suitable for young esocids. I used a similar approach to develop a Resilience Index to rank coastal marshes according to their resilience/vulnerability to stable low water levels, for use as a regional screening tool to identify critical esocid habitat. This research advances the understanding of the effects of water levels on coastal marshes and provides applicable tools to assist in conservation and management of these important recreational fisheries. / Thesis / Doctor of Philosophy (PhD) / This Ph.D. thesis describes how changes in water levels may affect habitats used by Muskellunge and Northern Pike, two important species of sport fish, in Georgian Bay (Lake Huron). Coastal wetlands were identified as critical habitats, especially for early-life stages, and are directly influenced by water levels of the Great Lakes. I developed several tools to assist in identification, evaluation, and management of coastal wetlands in Georgian Bay, a relatively undisturbed coastal region in Ontario. These tools use physical features of the landscape to predict how wetlands will respond to different lake-level conditions and influence habitat suitability for Muskellunge and Northern Pike, as well as Great Lakes fish communities in general. My thesis provides tools for environmental agencies to adaptively manage important fish habitat in a period of unpredictable water levels associated with global climate change.

Cumulative effects, often minor individually but collectively significant, are continually being grappled with by researchers, policy makers and practitioners. Despite this the Canadian approach to cumulative effects assessment is thought by many to be ineffective. In this thesis I investigate the literature that surrounds cumulative effects and uncovered three distinct themes that occur chronologically: genesis, project-based approach and integration. During the genesis phase cumulative effects nomenclature, ideas and frameworks was created. The main theme of this era was to asses these effects at a large scale and to have a strong understanding of a systems ecology prior to the assessment. This approach was found to be too complex and so a more narrow project-based approach was implemented and still remains today. This approach is heavily criticized and as such researchers are now trying to find an approach that integrates these two divergent themes into a regional level assessment. I have found there to be several frameworks but an absence of effective regional methodologies. There is a need for regional metrics if this approach is to ever be institutionally supported. Food web structure can be evaluated at multiple scales and has been shown to be responsive to environmental variation; thus, it has potential for application as a metric for cumulative effects. Here, using stable isotope analysis, I field test integrative measures of food web structure (food chain length, habitat coupling, trophic omnivory) at sites of varying degrees of anthropogenic stressors in Georgian Bay, Ontario to evaluate the use of food webs as a metric for cumulative effects assessment. I found that food web structure varied significantly among sites. Sites with high levels of stress displayed structural characteristics reflective of human activities such as shorter food chain lengths, increased trophic omnivory, and reduced habitat coupling relative to the non-stressed sites. These results indicate that food web structure as an ecosystem level metric may provide insight into anthropogenic activities, and may be applied routinely as a metric for doing Cumulative Effects Assessment. / University of Guelph, Saugeen Ojibway Nation, Georgian Bay Forever

Concern over recent declines in many wetland-dependent bird species has led to a need to monitor marsh bird populations in response to anthropogenic activities. I conducted point counts and vegetation surveys at 26 coastal wetlands in the Laurentian Great Lakes Region of Canada from 2006-2008 to determine 1) effective methods to monitor marsh birds, and 2) the impacts of land use surrounding coastal wetlands on marsh bird communities. The first part of this dissertation showed that call-broadcasts are effective tools for monitoring marsh birds and that point counts for marsh birds should be conducted from both the shoreline and from the interior of large marshes. Because of the species-area relationship for wetland birds in southern Ontario, sampling effort should increase proportionally with wetland area to attempt the detection of all species present. In the second part of this thesis, I showed that marsh obligate-nesters preferred wetlands in rural areas as opposed to urban areas, while generalist marsh-nesting species showed no apparent difference in use. The Index of Marsh Bird Community Integrity (IMBCI), a biological index used to indicate wetland health, was significantly higher in rural than in urban marshes. Marsh isolation was also an important factor in predicting the marsh bird community, with more isolated wetlands containing fewer obligate species and associated with a lower IMBCI value. Wetlands of Georgian Bay were found to have quite different bird and plant communities than wetlands of Lake Ontario. Even though wetlands of Lake Ontario were considerably more degraded than those in Georgian Bay (according to land use alteration and degree of water quality impairment), these two regions produced similar IMBCI scores, and this draws into question the applicability of some indicators on a basin-wide scale. The results of this thesis indicate how survey protocols in existing wetland bird monitoring programs should be modified and support current literature that urbanization negatively affects the marsh bird community. </p> / Thesis / Doctor of Philosophy (PhD)

<p> This report is the only detailed study concerning the fresh water cobble beaches of the Georgian Bay Islands. It includes extensive studies on the morphological characteristics, especially the platform development and profile configuration, and the sedimentary provenance of the cobbles. </p> <p> It was found that the platform configuration (step topography) acts as a substrate control for the cobble beaches. The presence of two cobble generations, angular and well-rounded, indicate that t he shore platform is the source for these cobble beaches. </p> <p> The roundness values of these cobble generations depends on t heir mode of transport. Evidence indicates that longshore movement of cobbles increases their roundness values, but their angular shape i s indicative of their lack of transport. </p> <p> Very little proof was found within this study to correlate relict cobble beaches with any specific stage of the Lake Huron Basin, although it was possible to generalize and state that the relict cobble beaches were generated by high-energy wave events during the transition from the Algoma stage to Lake Huron. </p> <p> Clast analysis determines the relationship between the length of the wave fetch and its related energy environment. It was found that high-energy coastal environments have oblate cobbles with a high roundness and low sphericity. In each case, the samples were associated with a large fetch. Those cobbles of a low-energy coastal environment have a high sphericity, low roundness, and are associated with smaller fetches. </p> <p> The steepness of the beach profile results from the increase in wave height, generated by an increase in shallowness. It also depends upon the volume of backwash. The backwash is reduced by the increased percolation rates through the cobbles, thus reducing the combing down effect of the backwash. </p> <p> This study also provides a discussion on the minor morphological features such as sinkholes and imbrication. </p> / Thesis / Bachelor of Arts (BA)

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.

Monitoring and maintaining the health of coastal wetlands is a global concern. The greatest threat to coastal wetlands in the Great Lakes Basin are anthropogenic removal and enrichment. The coastal wetlands in Georgian Bay are relatively undisturbed by humans, but face disturbance caused by reduced annual water-level fluctuations. Since these wetlands are critical habitat for many fish, bird, amphibian, and reptile species, many efforts to accurately monitor and maintain their health have been put into place. Recently, these wetlands have been experiencing an abrupt (~1 m) transition to higher water levels, following 14 years of sustained lows, which allowed trees and shrubs to invade the meadow vegetation zone. This sustained water-level pattern has never occurred in this region before, offering the unique opportunity to study wetlands undergoing a transition, where areas of 10+ years of upland plant species growth was inundated and became part of the wetland habitat. This thesis first investigates how this change in water level affects the distribution of meadow, emergent, floating, and submerged vegetation both in physical space and area. The second chapter of this thesis presents long-term water quality, macrophyte, and fish community monitoring using ecological indices. Water quality and macrophyte indices are robust enough to monitor wetlands undergoing a transition; however, issues arise in the calculation of the wetland fish index, as the changes in macrophyte distribution described in Chapter 1 impact the ability to replicate community sampling using fyke nets. The research done throughout this thesis is highly beneficial in adding to the limited knowledge of key factors impacting macrophyte community shifting. This work also identifies water-level scenarios where managers must adjust sampling protocols to succeed in effectively sampling wetland fish communities. / Thesis / Master of Science (MSc) / The coastal wetlands in the Georgian Bay area are primarily threatened by human development and the removal of annual water-level fluctuations. From 1999-2013, the water level decreased and remained low. In 2014, the water level rose about 1 m, causing flooding of grass and trees that had grown in the meadow zone during the 14 years when the water level was low. The first goal of this thesis is to explain how and why all wetland plants are relocating during this period. The second goal is to make sure that common indicators of wetland health (water quality, plants, and fish) can still be used during a time when flooding of grasses and trees was occurring in wetlands. The findings in this thesis contribute to the ability to predict and understand how the plants will shift within a wetland during a time of flooding, as well as informing managers on appropriate sampling protocols.

Reptiles are the vertebrate taxon with the highest percentage of at-risk species in Canada, many of which exist at the northern limit of their species’ home range in Ontario. Numerous reptiles are found in the Georgian Bay area; however, factors limiting their distribution in Ontario are poorly understood. It is likely that the thermal and hydrological conditions of a reptile’s critical habitat are contributing factors. Specifically, peatlands serve as ideal hibernacula for the threatened Eastern Massasauga Rattlesnake (Sistrurus catenatus) while moss cushions may provide freshwater turtles, including the threatened Blanding’s Turtle (Emydoidea blandingii) and endangered Spotted Turtle (Clemmys guttata), with nesting opportunities on open rock barrens. Although different in their functional purpose at opposite life stages for two separate orders of reptiles, these ecosystems provide suitable conditions to meet the physiological needs of the reptiles utilizing them. This analysis characterizes the thermal and hydrological conditions of moss-dominated ecosystems from a reptile species-at-risk perspective. The interaction between the water table and the frost line is important when assessing the winter survival of Eastern Massasauga Rattlesnakes hibernating in peatland hummocks. Larger hummocks are more ideal as they have a lower chance of becoming flooded in the winter while still providing protection from the advancing frost line. Ideally, hummocks that are 30-35 cm tall provide the greatest chance of survival when snakes hibernate 20-25 cm below the surface. Subsurface temperatures in relation to snow depth, as it is influenced by tree stand characteristics, was also assessed. This resulted in the conclusion that the presence, absence, timing, and frequency of freeze and thaw events is likely more important than snow depth when it comes to winter survival. Similar to rattlesnake hibernacula, turtle nests can be inundated for extended periods of time or exposed to extreme temperatures which reduces their chance of survival. The water storage dynamics of 22 hillslope and 12 hilltop moss cushions along with the temperature dynamics at nine locations were characterized. Although it was determined hilltop locations had greater water storage capabilities, continuously monitored moss cushions responded very quickly to rainfall events whereby sites were inundated for less than 12 hours. Average subsurface temperatures decreased with depth as did temperature fluctuations, both of which were positively correlated but not significantly affected by canopy openness. However, due to their tendency to grow on flat surfaces, not all moss cushions are suitable nesting sites. Moreover, temperatures that ensure proper development and equal ratios of male-to-female turtles were not achieved suggesting that this is a potential factor limiting the northern distribution of turtles in Ontario. In order to properly asses the vulnerability of these populations to threats including habitat loss and climate change, the habitat requirements of different species at critical life stages needs to be understood. Therefore, conservationists can use this study to implement mitigation strategies that consider impacts on the thermal and hydrological dynamics within reptile habitat. / Thesis / Master of Science (MSc)