Elucidation of habitat and resource use patterns is important for facilitating sustainable management of fisheries. Discrete habitats in large aquatic ecosystems may offer distinct resources and differentially affect performance. Movement of organisms and organic materials links these habitats and potentially leads to spatially complex trophic pathways between basal resources and consumers. Habitat and resource use are commonly explored via two common methods: stable isotopes and morphometric analysis. The first research chapter of this thesis employed both methods to investigate seasonal habitat use of yellow perch <i>Perca flavescens</i>in eastern Lake Michigan and connected waterbodies known as drowned river mouth (DRM) lakes. Landmark-based geometric morphometrics was used to compare shape differences among habitats. Stable isotopes of ambient water, otoliths, and soft tissues were compared to differentiate among habitats. Both methods provided evidence of resident nearshore Lake Michigan fish, resident DRM lake fish occupying the littoral zone, and transient Lake Michigan fish occupying the profundal zone of DRM lakes. The majority of transient Lake Michigan fish moved into the profundal zone of DRM lakes in the fall. These results support previously published genetic data of distinct populations of yellow perch in eastern Lake Michigan and connected waterbodies. The second research chapter of this thesis also employed stable isotopes and morphometric analysis, but to investigate the consistency of resource use of age-0 yellow perch in Saginaw Bay, Lake Huron. These methods served as long-term diet indicators, as compared to short-term stomach contents analysis. Both stable isotopes of soft tissues and morphometric analysis showed spatial consistency in variation among sites. Fish from the two sites closer to the tributary input had higher δ¹⁵N values and more fusiform bodies, while fish from the third site further away from the tributary had lower δ¹⁵N values and were deeper-bodied. This spatial variation supports stomach content analysis of age-0 yellow perch from a previously published study. δ¹³C ratios displayed annual variation, and while inconsistent with stomach content analysis, was consistent with available prey items. The findings from this study suggest that young yellow perch in Saginaw Bay have limited movement and forage in a similar area to where they were collected. Previous studies have found discrepancies among indicators and have cautioned generalization of trophic relationships when only relying on a single metric. Agreement between complementary techniques provided additional support to previously-published genetic results and stomach content data, and thereby helped more fully describe habitat use by yellow perch in these systems.

A study of the aquatic invertebrate communities from two locations (Location 1 and Location 2) within the Matapouri catchment in Northland, New Zealand, was conducted to assess community structure in differing local-scale habitats. Four data collection methods were utilised generating 33,058 adult or larval invertebrates. The sampling methods comprised benthic kick-sampling, sticky trapping, light trapping, and emergence trapping. For the sticky trapping and light trapping, sampling was carried out at three different sites (Sites 1–3) within each location. The sites were situated within three habitat types; native forest, native forest-fringe, and raupo wetland. Emergence trapping also commenced within the three sites, at both locations, but was discontinued after two months, due to the equipment being destroyed by consecutive flooding events (method described in Appendix 1). Benthic sampling was carried out within the Forest and Forest-fringe habitats. Benthic sampling, sticky trapping, and light trapping were carried out following a monthly schedule between June and November 2005. Conductivity, pH, and water temperature measurements were taken concurrently with benthic sampling on a monthly basis, while water velocity and substrate measurements were taken once to assist in habitat characterisation. Overall, 71 taxa were recorded by benthic sampling over the six month period, with a mean of approximately 30 taxa per site per month. In comparison with similar studies elsewhere in New Zealand, a figure of around 30 taxa per sample was high. The benthic macroinvertebrate fauna at all sites was dominated by Trichoptera (19 taxa), Diptera (16 taxa) and Ephemeroptera (10 taxa). This pattern of diversity is similar to that reported in other New Zealand studies. However, in contrast to previous studies, the leptophlebiid mayfly genus Deleatidium was not numerically dominant over the rest of the community, and other leptophlebiid genera (Acanthophlebia, Atalophlebioides, Mauiulus and Zephlebia) were equally represented, possibly reflecting niche partitioning between the groups. The genus Nesameletus was not recorded at any site, despite being one of the core mayfly species in New Zealand streams. The rare mayfly Isothraulus abditus was recorded at one of the forest locations. There are no published records of this species from Northland. Although acknowledged as another of the core New Zealand benthic taxa, the hydropsychid caddisfly Aoteapsyche was not recorded during the study. However, another hydropsychid, Orthopsyche, was commonly recorded, and these may be filling a similar niche to the Aoteapsyche genus. In contrast to the Trichoptera, Diptera, and Ephemeroptera, the Plecoptera fauna was relatively depauperate, probably reflecting the warmer climate of the region and lack of temperature-buffered spring-fed streams. Surprisingly, Zelandobius, a core New Zealand genus, was absent but is regularly recorded in Northland. A species of conservation interest, Spaniocercoides watti, currently recognised as a Northland endemic, was recorded in low numbers. There were no apparent trends in diversity or abundance of benthic invertebrates over time. Also, there were no significant differences in species diversity between the two locations. However, in many cases, taxa were more abundant at Location 2. This may have been due to steeper gradients at Location 2, and the consequent effects on substrate size and streambed stability, as all other physical factors appeared similar between locations. Although several significant differences of individual benthic taxa were recorded, no broad effect of habitat (sites) on species diversity was observable. However, at Location 2, abundances were significantly higher at Site 3 (Forest) compared to Site 2 (Forest-fringe). The reasons were uncertain, but may be attributed to higher retention of allochthonous organic materials, trapped by in-stream cover and larger substrates. Investigations of adult stages by sticky traps supported benthic results recording community compositions and abundances dominated by Trichoptera and Diptera. Plecoptera were poorly represented. Location 2 recorded higher abundances of taxa, particularly Ephemeroptera and Plecoptera. Investigations of adult stages by light traps however did not produce any statistically significant differences in abundances between sites, between locations, or between sites across locations, and it is believed to be due to limited sampling replication combined with some biases of light trapping. This study indicates that the aquatic invertebrate community at Matapouri is diverse but also reasonably representative. Several rare or uncommon insects inhabit the catchment. It is therefore important that Iwi and the local Landcare Group, who invited and supported this research, together with the Department of Conservation, continue their efforts in protecting these areas. The resident fauna have the capacity to restock areas downstream, which are intended to be improved and restored through sediment control and riparian management.

Brown bear is the largest mammal in Turkey and its main distribution lies in the Black Sea and Eastern Anatolia Regions. Its basic ecology is almost unknown in Turkey, except for a limited number of studies. This study aims to determine the spatio-temporal ecology and habitat use of brown bears in the Ka&ccedil / kar Mountains, and to estimate their population size in the &Ouml / zg&uuml / ven Valley and Yusufeli, both firsts for Turkey. The study area is primarily covered with conifer and oak stands, but sparse mixed shrubland occurs in the Mediterranean climate influenced lower parts. GPS-GSM telemetry on seven captured bears (5 males and 2 females) was the main field technique used in this study. Other methods include monitoring via camera trapping, visual direct observations, and counting cubs of the year. Bears were fitted with GPS-GSM collars and tracked for 3 to 603 days. Mean home range size (HRS) was calculated by 95% kernel and MCP estimators for three different samples sizes.95% MCP for all positions produced a home range size of 19.91 &plusmn / 8.89 sq. km. for females, and 130.68 &plusmn / 102.95 sq.km. for males. On average, males and females move at rates of 199 m/h and 129 m/h, respectively. Males hibernate around 140 days whereas females around 150 days and at lower elevations than males. According to camera trapping results, bears are generally active at twilight whereas activity data loggers produced disparate results for tracked bears. Resting patterns showed that bears may also rest at midnight. Estimated population density per 100 km2. is 24.50 &plusmn / 1.74 individual using the Fcub method and 23.85 &plusmn / 2.51 using the mark&ndash / resight method. Captured bears indicated nonrandom distribution on habitat use and selected productive croplands and shrublands than other types of vegetation. Brown bear HRS in the Ka&ccedil / kars is smaller than reported from most countries. The large female-male HRS difference is probably due to polygamous mating system, sexual dimorphism, hard mast availability, high population density, and female&rsquo / s habitat exclusivity as a result of high tolerance by the local people in contrast with most northern countries. Although primary productivity is used to explain high population density and small HRS in other countries, the low productivity in the study area cannot explain the observed density and HRS difference. These findings will construct a scientific basis for brown bear management and conservation in Turkey.

As habitat loss and fragmentation are major causes of decline in animal species, studying habitat requirements in these species is a key component of their recovery. I investigated the relationship between landscape composition and habitat use of Blanding’s turtles, Emydoidea blandingii, a freshwater turtle threatened by habitat loss and road mortality on most of its Canadian range. In 2010, I conducted a radio-telemetry survey of 44 Blanding’s turtles in southern Québec, Canada, and modelled their home range size from land cover proportions measured at many spatial scales. I also used data from a visual survey conducted in 2008 and 2009 to model wetland occupancy of the species at the landscape scale. Home range size of the Blanding’s turtle was significantly correlated to landscape composition, and the proportions of agriculture, open water and anthropogenic lands had the strongest relationships with home range size. However, those relationships were weak and the models were unable to predict home range size accurately. At the landscape scale, land cover and road density poorly predicted probability of occurrence, and Blanding’s turtles occupied wetlands in both disturbed and natural sites. Management of the species should focus on protecting sites of occurrence with high wetland density, low road density, and sufficient suitable habitat to cover their seasonal movement patterns.

The heterogeneous landscape of Florida Bay provides habitats for a variety of predators and prey. This dissertation examined the bottom-up transfer of affects from environmental variability through prey composition up to competition and predation affects on top predator distribution and foraging ecology in Florida Bay. Line transect surveys for bottlenose dolphins and seabirds were conducted in Florida Bay during the summer months of 2002 - 2005. Photo-identification techniques were implemented to identify individual dolphins. Synoptic with this survey effort, habitat characteristics (temperature, salinity, dissolved oxygen, turbidity, chlorophyll a, depth and bottom type) and prey composition (bottom trawl or gillnet) were sampled. Comparison of envelope maps from generalized additive models determined that predictive capacity of dolphin habitat did not improve by incorporating fish distribution data. However, models of dolphin distribution based solely on environmental proxies of fish distribution resulted in high predictive capacity. During the 2005 summer, shark distribution was sampled using a longline. The abundance of sharks was only correlated to fish catch from trawls on a regional scale. Larger sharks, of species that may threaten dolphins, were only caught in the Gulf zone of the Bay. Analysis of dolphin distribution revealed high individual site and foraging tactic fidelity. Dolphins were spatially coincident with habitat characteristics that encouraged the use of each individual's preferred foraging tactic. Depth was identified as the primary variable determining dolphin foraging tactic choice. Depth plays a significant role in the benthic composition of Florida Bay, which subsequently impacts prey communities and affects dolphin distribution, foraging and social ecology. Ordinations determined that fish distribution was also principally affected by depth and bottom type. Shallow environments frequently corresponded with mudbank habitat (depth < 1m) where the sighting rates of seabirds (cormorants, osprey, pelicans, terns) and foraging dolphins peaked. In conclusion, subtle relief in South Florida's bedrock topography dramatically affect benthic composition within Florida Bay, providing patchy habitats for prey and predators. The Florida Bay ecosystem will change with expected sea level rise, including spatial shifts of mudbank habitats. Top predator populations in Florida Bay will be forced to modify their distribution and foraging ecology accordingly. / Dissertation

In 2002, a proposal was submitted to divert water from the confluence of the Guadalupe and San Antonio Rivers to San Antonio, Texas. To investigate the potential impacts of diverting water from the Guadalupe Estuary, my research focused on the foraging ecology of the crane and population ecology of the blue crab, a documented crane food. During winters 2004-2005 and 2005-2006, I examined diets and optimal foraging patterns of territorial adult cranes at Aransas National Wildlife Refuge, Texas. To identify foods of greatest benefit to cranes, I used currencies of optimization to evaluate foraging gain, cost, and efficiency. Foraging benefit differed among foods, depending on the foraging currency used and resource targeted (e.g., energy). Wolfberry fruit, snails, and insects were consumed in the highest quantities, required the least foraging effort, and were generally associated with the highest foraging efficiency. Blue crabs and clams were important sources of protein and biomass. During September 2003-October 2005, I used novel artificial settlement substrates and modified methods of standard deployment to investigate the spatio-temporal patterns of blue crab terminal settlement and recruitment rates. Monitoring rates in shallow bay habitat and ponds of the interior salt-marsh revealed megalopal crabs were developmentally advanced when arriving to study sites and the extent to which young crabs infiltrated the salt-marsh increased with age. Such findings suggested sites represented optimal terminal settlement habitat and consequently critical nursery habitat. Model selection indicated water temperature before and during embryonic development was the best predictor of megalopal settlement, whereas juvenile recruitment was most influenced by recent precipitation. I studied the size-specific abundance patterns of blue crabs in and around mature salt-marsh. Using drop-trapping and throw-trapping methods, I collected monthly samples in several habitats during October 2004-March 2006. Interior-marsh habitats contained fewer but larger crabs than bay habitat. Crabs contributing greatest to biomass were smallest (11-30 mm carapace-width) in bay habitat, larger (31-80 mm) along interior-marsh pond edges, and largest (41-130 mm) in interior-marsh open water. Model selection revealed crab density was most influenced by micro-site characteristics (habitat, water column structure type and structural complexity). Overall, shallow bay provided important nursery habitat for young blue crabs and interior marsh ponds were important for dispersing juvenile and adult crabs.

About 1,600,000 ha of desert mule deer range in Mexico are currently altered with vegetation clear-cutting and establishment of buffelgrass pastures. Consequently, the availability of resources as cover and forage from scrub vegetation has been reduced for mule deer. No previous research has been conducted to investigate how desert mule deer respond to those alterations. Therefore, the purpose of this research was to examine movements of mule deer, evaluate their home range sizes and determine habitat use, and analyze their diets in areas of central and western Sonora, Mexico. The approach involved the use of radiotelemetry techniques and GIS programs to calculate home range sizes, examine selection of vegetation associations, and identify the specific components of habitat that distinguished the characteristics of selected sites by desert mule deer. I used the microhistological technique to determine botanical components of desert mule deer diets, and compare diets of desert mule deer and cattle in habitat with buffelgrass pastures. Diet analyses included spatial and temporal comparisons of diversity and similarity indices. Sizes of home ranges were larger in the more arid environments of western Sonora (27.3 km2) than in central Sonora (14.5 km2). Desert mule deer used altered habitat differently than use areas without buffelgrass, however, there was no difference in the size of home ranges of mule deer from inside buffelgrass areas and the size of home ranges of deer in native scrub vegetation. Thermal cover, ground cover, and percent of gravel in the ground were the variables that distinguished locations selected by desert mule deer. Desert mule deer selected xeroriparian vegetation and sites closer to water sources. Water sources may have influenced mule deer to stay in buffelgrass areas despite the lack of cover and forage from shrubs and trees. For diets of mule deer, I identified 96 plant species, 69 of which have not previously been reported as forage for this herbivore. Desert mule deer and cattle shared 45 forage species from central Sonora. However, biological overlap of diets occurred only for spring. Results from these studies provide information to understand ecological relationships of desert mule deer on altered habitats.

This dissertation has been prepared in manuscript format and contains four individual papers. Each paper/chapter is formatted for the journal to which it has been, or will be, submitted. In the first manuscript, "From Whaling to Tagging: The evolution of knowledge regarding humpback whales in their North Atlantic breeding grounds", I describe the evolution of humpback whale research from the days of Yankee whaling to the most recent satellite telemetry project in the West Indies breeding grounds. The humpback whales that over-winter in the West Indies are part of one of the most heavily studied whale populations in the world; projects conducted in this area have served as models for humpback whale research world-wide. This manuscript will be submitted for publication in Mammal Review in 2014. In my second manuscript, "Local and migratory movements of humpback whales satellite tracked in the North Atlantic Ocean", I report the results of a satellite telemetry project that was conducted in the winters of 2008 through 2012 in the breeding areas of Silver Bank (Dominican Republic) and Guadeloupe (French West Indies). The results from this project add a level of detail to the current knowledge about North Atlantic humpback whale habitat use, migration, and population structure that could not be obtained without current satellite tagging technology. This paper has been reviewed and accepted for publication by the Canadian Journal of Zoology and will be published by November, 2013 ii In my third manuscript, "Individual variation in movements of humpback whales satellite tracked in the eastern Aleutian Islands and Bering Sea", I report the results from a satellite telemetry project conducted off Dutch Harbor, (Alaska, USA) in the summers of 2007 through 2011. Satellite telemetry from this project showed the fine-scale use of foraging habitat in a North Pacific feeding ground. Additionally, a long-distance, within-season travel event was recorded in 2010, prompting speculation about the humpback population structure throughout the Bering Sea. This manuscript has been reviewed and accepted for publication by Endangered Species Research and will be published by November, 2013. In the fourth manuscript, "Assessing implantable satellite tag extrusion using light sensors", I report the results of a novel approach for remotely quantifying tag rejection; the use of tag-mounted light sensors to indicate extrusion rate. The data for this paper were collected during a 2011 follow-up study aimed at assessing the behavioral and physiological responses of Gulf of Maine humpback whales to current tagging methods. Tag diagnostic technology like this, while still being developed, could significantly improve future telemetry work by updating tag design and placement methods to increase overall project efficiency. This paper has been accepted as a poster presentation at the 20th Biennial Conference on the Biology of Marine Mammals (December 2013, Dunedin New Zealand). It will be updated with the results from the 2013 Gulf of Maine tagging field season and submitted to a peer reviewed journal in 2014.

As habitat loss and fragmentation are major causes of decline in animal species, studying habitat requirements in these species is a key component of their recovery. I investigated the relationship between landscape composition and habitat use of Blanding’s turtles, Emydoidea blandingii, a freshwater turtle threatened by habitat loss and road mortality on most of its Canadian range. In 2010, I conducted a radio-telemetry survey of 44 Blanding’s turtles in southern Québec, Canada, and modelled their home range size from land cover proportions measured at many spatial scales. I also used data from a visual survey conducted in 2008 and 2009 to model wetland occupancy of the species at the landscape scale. Home range size of the Blanding’s turtle was significantly correlated to landscape composition, and the proportions of agriculture, open water and anthropogenic lands had the strongest relationships with home range size. However, those relationships were weak and the models were unable to predict home range size accurately. At the landscape scale, land cover and road density poorly predicted probability of occurrence, and Blanding’s turtles occupied wetlands in both disturbed and natural sites. Management of the species should focus on protecting sites of occurrence with high wetland density, low road density, and sufficient suitable habitat to cover their seasonal movement patterns.

Canada is the second highest producer of hydroelectric energy in the world. Nearly 50 of the hydroelectric reservoirs in the country have a capacity larger than 1 billion m3. Despite the great number and extent of hydropower developments in Canada and around the world, relatively little is known about how dams and their operations influence terrestrial and semi-aquatic wildlife. Reservoirs at northern latitudes are characterized by large fluctuations in water level, which create modified shorelines called drawdown zones. To evaluate the impact of these disturbances on amphibians and reptiles, I conducted visual encounter surveys at two sites in the drawdown zone of Kinbasket Reservoir, near Valemount, B.C. From April to August of 2010 and 2011, I documented the habitat use, reproductive phenology, and body condition of two amphibian species (Anaxyrus boreas and Rana luteiventris) as well as the growth, movements, diet, and distribution of one species of garter snake (Thamnophis sirtalis). At two sites in the drawdown zone, A. boreas and R. luteiventris were present for the duration of the summer and utilized several ponds for reproduction. The presence and abundance of Rana luteiventris eggs were generally associated with ponds that had higher mean temperatures, higher mean pH, and the presence of fish. In 2010, there was sufficient time for amphibian breeding and metamorphosis to occur before the reservoir inundated the drawdown zone, but low precipitation levels in that year led to desiccation of many breeding ponds. In 2011, high rainfall and snowmelt led to early inundation of breeding ponds, and thousands of tadpoles were presumably swept into the reservoir. Gravid Thamnophis sirtalis were found at just one of two sites in the drawdown zone, but both sites were frequented by foraging individuals of this species. Anaxyrus boreas appears to be the primary prey of T. sirtalis in the drawdown zone. An improved understanding of how the amphibians and reptiles at Kinbasket Reservoir have persisted in this highly disturbed environment may be vital to their conservation — the activation of a new generating unit at Mica Dam in 2014 will alter the pattern and timing of reservoir inundation for the first time since it was constructed 40 years previously. / Graduate