<p> Effective conservation of migratory species is hindered by a lack of knowledge of population links between breeding, wintering and stopover habitats. The Pacific-slope flycatcher (<i>Empidonax difficilis</i>) is one of the many Neotropical migratory songbirds whose populations are steadily declining throughout western North America. This research contributed to the assessment of connectivity in this species by inferring relative breeding origins and habitat selection of juvenile birds that migrate along the Pacific Flyway to the South San Francisco Bay Area in the fall. Feather data collected from July 20 to October 12, 2014 were analyzed for three stable isotopes (&delta;²H, &delta;¹³C, &delta;¹⁵N). Findings revealed that populations migrated sequentially from western regions throughout expected breeding latitudes, with early season migrants most likely coming from the more southern, warmer, and dryer regions of northern California, Oregon, and southern Washington while late season migrants had probable origins in the more northern, cooler, and wetter regions of northern Washington and southwestern British Columbia. This study provided new information on the annual cycle and migratory timing of Pacific-slope flycatchers, and lays the foundation for future assessments of migratory connectivity of this species.</p><p>

For purposes of conservation, we require methods to predict where species occur currently, and where they are likely to move in the future. Species distribution models can be useful tools, by predicting where species are in areas that cannot be surveyed but where management decisions must occur. However, they are rarely tested using independent field surveys to determine their accuracy. These models are also generally developed over broad spatial scales; in contrast, distributions must often be predicted over local to regional scales for conservation purposes. Using butterfly surveys along transects in eastern Ontario, we tested whether independent regional observations of butterflies could be predicted from distribution models developed on Canada-wide species ranges. We also developed a set of regional models using Maximum entropy software to compare with the independent field surveys. Our results show that regional field occurrences are not accurately predicted by the national models, which explain between 0 and 31% (median 4.2%) of the deviance in species presence/absence. Even when species distribution models developed using regional variables have high apparent accuracy (AUC values exceed 0.8), they do not appear to accurately predict occurrence at local spatial extents, explaining between 0 and 46% (median 3.4%) of the deviance in species presence/absence. Species distribution models' inaccuracy in predicting species' presence within their ranges indicates that field-based observations remain indispensable when making conservation decisions. Misusing models can be costly if they lead to errors in predicting the presence of species of concern or their habitat and can result in poor management decisions if used improperly.

Growth plays a key role in regulating ecological and population dynamics. Life history characteristics such as age at maturity, fecundity and age and size at migration are tightly linked to growth rate. In addition, size can often determine survival and individual breeding success. To fully understand the process of growth it is important to understand the mechanisms that drive growth rates. In Atlantic salmon, growth is critical in determining life history pathways. Models to estimate growth could be useful in the broader context of predicting population dynamics. In this dissertation I investigate the growth process in juvenile Atlantic salmon (Salmo salar). I first used basic modeling approaches and data on individually tagged salmon to investigate the assumptions of different growth metrics. I demonstrate the size-dependency in certain growth metrics when assumptions are violated. Next, I assessed the efficacy of linear mixed effects models in modeling length-weight relationships from longitudinal data. I show that combining a random effects approach with third order polynomials can be an effective way to model length-weight relationships with mark-recapture data. I extend this hierarchical modeling approach to develop a Bayesian growth model. With limited assumptions, I derive a relatively simple discrete time model from von Bertalanffy growth that includes a nonparametric seasonal growth function. The linear dynamics of this model allow for efficient estimation of parameters in a Bayesian framework. Finally, I investigated the role of life history in driving compensatory growth patterns in immature Atlantic salmon. This analysis demonstrates the importance of considering life history as a mechanism in compensatory growth. Information provided in this dissertation will help provide ecologists with statistical tools to estimate growth rates, estimate length-weight relationships, and forecast growth from mark-recapture data. In addition, comparisons of seasonal growth within and among life history groups and within and among tributaries should make a valuable contribution to the important literature on growth in Atlantic salmon.

Urbanization, as it transforms natural biotic systems into human-dominated landscapes, is recognized as one of the greatest threats to biodiversity throughout the world. Furthermore, urban dwellers are becoming increasingly disconnected with the natural world. Here I investigate whether residential landscape designs that mimic the natural environment can provide habitat for native birds. First I uncover some of the patterns of bird distribution in residential yards by incorporating habitat features, urbanization measurements and socioeconomic factors with bird monitoring data into a multivariate analysis. The results indicate that native birds associate with neighborhoods with native plants and shrubs, neighborhoods closer to desert tracts, and higher income neighborhoods. Very few bird species associate with low income and predominantly Hispanic neighborhoods. Additional analyses based on social survey data demonstrate that residents notice the varying levels of bird variety in their neighborhood. Second, I address whether perceived habitat quality differs between residential landscape designs by testing foraging decisions at artificial food patches. Birds foraging in yards landscaped with native plants consume fewer resources than birds foraging in exotic landscaped yards. This suggests that alternative food sources are more available in the native landscaped yards, indicating better quality habitat. Third, I investigate the relationship between native bird diversity and neighborhoods with a Homeowner Association (HOA). Neighborhoods with an HOA have higher native bird diversity, perhaps due to an active and enforceable landscape maintenance plan. I suggest an HOA adapt features from the Sustainable Sites Initiative to further improve habitat conditions for native birds and other wildlife. Results from the Dissertation support the implementation of native landscaping in residential yards to help reverse the loss of urban biodiversity. Consequentially, these landscapes will provide positive opportunities for urban dwellers to reconnect with the natural world.

Indonesia has one of the highest diversities of plants and animals in the world and nine of the eleven felid species present in Southeast Asia are found in Indonesia. Yet, Indonesia now leads the world in the number of threatened and endangered mammal and bird species, with new species constantly added to the list. The biggest factor driving the disappearance of wildlife in Indonesia is large-scale habitat loss and degradation. The country is losing its forests at the fastest rate of any nation in the world. In Sumatra alone, nearly 3.1 million hectares of forest were lost in the past decade, and lowland forests have all but disappeared. In the face of continued habitat loss and fragmentation, and a continually increasing human population, it is becoming increasingly apparent that we have to gain some knowledge of these species on Sumatra in order to create effective conservation initiatives, else we risk losing them for good. The present project was initiated to gain such information on small felids in Sumatra. There were three elements to our study: camera trapping, live trapping, and an analysis of human-felid conflict. The camera trapping portion of our study allowed the examination of the distribution, habitat preferences, and activity patterns of small felids on Sumatra. This is the first such information on these species from anywhere in their range and is invaluable to managers as they prioritize habitats for conservation. Our study was the first to attempt live trapping and collaring of small felid species in Sumatra, and one of a very few which had been conducted in the tropical forests of Asia. We were able to capture and collar the first golden cat ever collared in Indonesia, and only the third in the world. The information gained from tracking her movement once again provides invaluable information on the ecology of this species in Sumatra. Finally, we conducted surveys of human-small felid conflict around BBSNP. Prior to our study, human conflict with small felids was not thought to be a major factor in their conservation in Southeast Asia because it was rarely reported to governmental officials. Our study is the first in Southeast Asia to characterize this conflict and its effect on the conservation of small felids in Sumatra. We also assessed the efficacy of simple education and mitigation techniques in reducing conflict, creating a successful model that can be replicated throughout the species range. Overall, this study provides valuable knowledge on the Sunda clouded leopard, the Asiatic golden cat, the marbled cat, and the leopard cat, generating information which may be used for their more effective conservation in Sumatra.

It is increasingly apparent that climate change and its associated impacts are a major threat to the rich biodiversity of the Cape floristic region. As the knowledge of the associations between biological traits and climate change impacts strengthens it has become clear that the assessment of climate change vulnerability is a key consideration in the management of biodiversity. This study is the first attempt to use a trait-based approach at the scale of a single national park, focusing on the climate change vulnerability of reptile and amphibian species found in Table Mountain National Park (including historically present species). The park and its immediate surrounding areas are home to a rich diversity of herpetofauna including the Critically Endangered Table Mountain ghost frog (Heleophryne rosei), Rose's mountain toadlet (Capensibufo rosei) and micro frog (Microbatrachella capensis), and the Endangered western leopard toad (Sclerophrys pantherina). Amphibian and reptile-specific assessment frameworks of biological and ecological traits were designed to identify the species most sensitive and least able to adapt to climate change pressures. Using a combination of a literature review and expert consultation, 18 species of amphibian and 41 species of reptile were assessed. The assessment highlighted that, in the worst-case scenario, 85% of the park's reptile species and 67% of the park's amphibian species are predicted to be highly vulnerable to climate change. The southern adder (Bitis armata), Cape long-tailed seps (Tetradactylus tetradactylus), Table Mountain ghost frog (Heleophryne rosei) and the Lightfoot's moss frog (Arthroleptella lightfooti) were identified as being the species most vulnerable to climate change within their respective taxa. All three of the Critically Endangered amphibian species were identified as having both high sensitivity and low adaptive capacity to climate change. Among the focal reptile species, climate change vulnerability was independent of current IUCN Red List status, highlighting that species currently not identified to be under threat by other anthropogenic pressures could imminently become threatened by climate change. Spatiallyexplicit presentation of the assessment output will help prioritise the management of areas within Table Mountain National Park that contain a high diversity of climate-vulnerable species. By reducing the threats from other human-associated impacts to these species, and by identifying when direct intervention is appropriate, the park's management can give these species the best opportunity of persistence in an uncertain climate future.

Native freshwater fish are in decline worldwide due to human impacts including impoundment, changes to water quality, over-abstraction, climate change and the introduction of non-native species. South Africa's Cape Fold Ecoregion (CFE) harbours exceptionally high freshwater fish endemism, yet the majority of these species are threatened with extinction. The Clanwilliam sandfish (Labeo seeberi), an endangered cyprinid, has declined across its range in the CFE and currently exists in only a handful of tributaries of the Doring River in severely fragmented populations. The last remaining recruiting sandfish population occurs in the Oorlogskloof River, making this tributary one of critical conservation value. In this study, I analysed a six-year dataset comprising fish survey data from 38 sites along 25 km of the Oorlogskloof River to characterise spatio-temporal variation in sandfish abundance and size structure and evaluate the relative influence of different environmental factors on sandfish population trends. The environmental factors considered included other fish in the system, especially three non-native fishes (banded tilapia Tilapia sparrmanii, smallmouth bass Micropterus dolomieu and bluegill sunfish Lepomis macrochirus), temperature, precipitation, habitat characteristics and a range of physicochemical factors. The results show that sandfish have experienced a 93% decline in the sampled stretch of the Oorlogskloof River since 2013 and that the ongoing drought may be preventing recovery. They also suggest that banded tilapia do not adversely affect the Oorlogskloof River sandfish population, while predation of juveniles by smallmouth bass and/or bluegill sunfish apparently reduces the abundance of sandfish, especially of juveniles, where these non-native fish are present. Future studies should attempt to isolate the relative impacts of the different invasive fish species and examine habitat requirements of different sandfish life stages. Management of the river's sandfish population should focus on precautionary actions such as continued monitoring and landowner engagement, as well as clearing dams of non-native species high in the catchment, to prevent the further upstream invasion of smallmouth bass and bluegill sunfish. Proactive measures, such as eradicating smallmouth bass and bluegill sunfish from the Oorlogskloof River, are also necessary to restore connectivity of suitable sandfish habitat in the Doring River system.

Arid zones, such as the Kalahari in southern Africa, are experiencing an increase in the number of hot days, as well as in the intensity of heat waves. Research is being conducted to try and understand how increasing temperatures will impact bird communities and population persistence in these areas. Understanding the mechanisms through which birds are vulnerable to climate change is key to answering these questions. This study investigated how changes in air temperature affect arid-zone birds' response to predators. The flight initiation distances (FID), i.e. the distance from a predator when the prey initiates escape, of eight bird species in the Kalahari were measured over a range of air temperatures during October and November 2015. The results from this study show a negative relationship between air temperature and FID. This relationship was weak across the full range of temperatures observed during the study period (11.9 ⁰C - 40.4 ⁰C), with a large amount of variability in FID not explained by air temperature. However, high air temperatures (> 35 ⁰C) were important in explaining some of the variation in FID. Starting distance, time of day, bird species, plant species, bird location (on the ground / in the canopy / at the top of the tree / in a dead tree), bird exposure (whether the bird was in the sun or in the shade) and bird activity (whether mobile / stationary) were consistently found to explain some of the variation in FID in this dataset. The relationships between the behavioural variables (plant species, bird location, bird exposure and bird activity) and air temperature were investigated and revealed a potential mechanism through which air temperature may also indirectly be affecting FID. The reduction in FID at high air temperatures, and thus the potentially increased risk of predation, may have negative consequences for these species in the Kalahari in light of rising air temperatures associated with climate change

Despite their importance to regional biodiversity, temporary wetlands and their invertebrate communities are generally understudied and under-conserved. Resurrection ecology is used to study the communities present in the dry phase of temporary wetlands to gain a better understanding of the functioning and health of these systems. The hatching success of invertebrate propagules in dried soil sediments, collected from temporary wetlands in Cape Sand Fynbos regions of Cape Town, were investigated in 2016. Soil samples were collected from conserved and urban sites (during May and June 2016) using a standard soil auger method and complemented with monthly aquatic phase sampling using standard sweep net methods (during September and October 2016). The effects of fire were tested, on hatching success by staging vegetation fires over the collected soil samples for five temporary wetland areas in the same region. Mann-Whitney U tests were used to test differences in abundances between treatments, whereas for comparison of taxon richness, Shannon diversity and Pielou's evenness linear mixed effect models (LMER) were used. Non-metric multidimensional scaling (nMDS) plots were used to graphically visualize the community composition between the different treatments, with 'adonis' analysis used to test their statistical significance. Results found a total of 18 invertebrate taxa hatched, while a total of 27 taxa were identified from the wet phase. Results from hatching assays showed no significant differences in diversity patterns of invertebrates between conserved and urban areas in the dry phase. However, wetlands that were in the conserved area supported higher invertebrate diversity during the wet phase, although not significant (lmer, Z = -1.75, p = 0.08). These results suggest that human activity (alien vegetation, littering and polluting) in the area did not impact the ability of invertebrate propagules to emerge, but did slightly affect the natural aquatic phase. Fire had a significantly negative impact on invertebrate diversity measures (lmer, p < 0.001) and community composition (adonis, F = 24.494, p = 0.001) during hatching assays. Management of unpredicted and uncontrolled fire in urban areas is essential to ensure future protection of critical biodiversity areas created by these temporary wetlands. More research should focus on the impact of increasing fire frequency and intensity on these systems to understand the management challenges in a changing climate.

Includes bibliographical references. / Fire is a ubiquitous ecosystem process with important implications for savanna ecology and conservation. In this study we aimed to explore the short-term and long-term effects of recent fire history on bird communities in the greater Serengeti savanna ecosystem in Tanzania. The study investigated the influence of immediate fire event history ( < one year), cumulative fire regime history (over 14 years), and fire seasonality on bird assemblages. We predicted that the occurrence of recent fire events and cumulative fire regime history would influence bird communities, particularly through its impact on vegetation structure. We mapped fire activity from remote sensing data (2000-2013) and extracted mean rainfall and nitrogen estimates from interpolated maps. We conducted field sampling of bird community composition and vegetation structure at 207 sample sites distributed across the western Serengeti ecosystem. We tested the structuring effect and regression trends of recent fire event occurrence, cumulative fires regimes, rainfall, and nitrogen on bird community structure and vegetation, and tested the response of birds to vegetation. Despite a high degree of variation in bird communities and vegetation structure, our results suggested that fire regimes do indeed impact bird communities with important conservation implications. We detected the strongest changes in bird community structure, diversity, and density in response to the immediate impact of a fire event and post-fire regeneration processes, and weaker effects to cumulative fire regime history. Short fire season burning (Feb-April) appears to have significant influence on birds and vegetation structure, and these preliminary findings warrant further investigation. While our findings do not have alarming conservation implications, the effects of seasonality and frequency of fires are not negligible. We recommend against extensive burning practices over short periods to allow continuity in the landscape. We recommend greater forethought among conservation managers, bearing in mind both short-term and longterm habitat changes caused by burning and the consequent bird assemblages impacted. We advise focused research on species and functional groups of conservation interest.