Ecology is the scientific study of processes that determine the distribution and abundance of organisms in space and time. Animal movement plays a crucial role in determining the fates of individuals, populations, communities, and ecosystems. Hence, understanding how and why animals change their spatial location through time is fundamental to ecological research. Animal movement patterns reflect behavioral, physiological and physical interactions between individuals and their environment. Coupling movement and environmental data may thus provide a rich source of information regarding many aspects of animal ecology. In my PhD thesis, I develop and demonstrate different approaches to understanding and predicting animal movement patterns in relation to their environment. In the first chapter, I merge two fundamental ecological models, the functional response and random walk, to formally derive diffusion rates of consumers as function of their handling time and the abundance, distribution and mobility of their resources. This mechanistic null model provides a simple behavior-free explanation to commonly observed negative associations between movement rates and resource abundance, often attributed to area-restricted search behavior. In the second chapter, I use positional data of woodland caribou in Ontario to calculate random walk-based movement expectations for each individual during each month. I then statistically link these expectations to ecologically significant environmental conditions. I show that landscape correlates of forage abundance and habitat permeability explain much of the observed variation in caribou movement characteristics and that residual variability may be attributed to spatial population structure. In the third chapter, I develop a novel state-space approach, enabling simultaneous consideration of resource preference, cognitive capacities and movement limitations, within a simulation model of animal movement across heterogeneous landscapes. The model is designed to enable direct parameterization based on empirical movement and landscape data. This approach allows one to both theoretically explore the consequences of different cognitive abilities and to predict animal space-use patterns across novel or altered landscapes. Overall, my thesis contributes to the rapidly developing field of movement ecology by formulating mechanistically defendable linkages between animal movement and landscape characteristics.

An important theme of wildlife ecology is understanding how animals move through their landscapes and inferring the strategies of resource acquisition. Eastern wild turkeys (Meleagris gallapavo silvestris) are a model species for evaluating the responses of movements and habitat selection to spatiotemporal variability of resources. I hypothesized that scales of area-restricted search (ARS) would change with variation in the landscape. I identified the ARS locations of high first passage time values using segmentation algorithms and hidden Markov models, and evaluated spatial variations in habitat selection for foraging-like activities of wild turkeys using Dirichlet multinomial models. The ARS scale for daily movement paths did not change over time substantially. Wild turkeys placed home ranges in heterogeneous landscapes to maximize forage availability. However, continuous-time Markov chain models demonstrated that habitat selection varied between individuals indicating that fine-scale selection may depend on the local resource availability and status of individuals.

Many well-studied elasmobranch populations have recently exhibited significant decline. The limited data related to fisheries and sightings for many unstudied or poorly understood populations indicate that these are also suffering. Directed fisheries and more cryptic threats such as entanglement and vessel strike represent significant risk to mobulid rays, arguably one of the most vulnerable elasmobranch groups. Very little information currently exists describing the basic ecology of manta rays or quantifying anthropogenic threats and impacts; however, recent efforts have drastically improved the body of knowledge available for these species, including oceanographic influences on movement, seasonal migration, and mating behaviors. Nevertheless, Red Sea mantas remain completely enigmatic. In this thesis, Chapter 1 details results from tagging 18 reef manta rays Manta alfredi in the eastern Red Sea using satellite and acoustic tag technology and demonstrates that mantas occupy areas with high human traffic. The combined satellite and acoustic techniques define both regional movements and ‘hotspots’ of habitat use where there is significant potential for manta-human interaction. I also present opportunistic sighting data that corroborate anthropogenic impacts on this population. Chapter 2 explores the vertical component of the nine satellite tags that were deployed on Manta alfredi as described in the previous chapter. Seven tags returned adequate data for analysis. Three of the seven were physically recovered yielding full archival datasets of depth, temperature, and light levels every 10-15 seconds for over 2.6 5 million cumulative data points. Mantas frequented the upper 10 m during the day and occupied deeper water through nocturnal periods. Individuals also exhibited deep diving behavior as deep as 432 m, extending the known depth range of the species. An investigation of 76 high-resolution deep dives suggests gliding is a significant behavioral component of these dives and may provide an efficient mechanism for travel compared to continuous horizontal swimming. This study is the first to employ satellite telemetry techniques on Manta alfredi and is the only study directed at mobulids in the Red Sea. A holistic understanding of these behaviors is essential for developing and implementing appropriate management techniques, and this work is particularly timely in light of recent international trade regulation as mantas were listed on Appendix II of the Convention on International Trade in Endangered Species.

The annual hydrological cycle of floodplains supports fishes that are uniquely adapted to optimize resources throughout the year. Such adaptations to changing environments include air-breathing for seasonally hypoxic waters and directed movements to best utilize habitats as they become available. This study examined the environmental, temporal and body-size influences on air-breathing behavior and movement ecology of Arapaima sp., one of the most economically and ecologically significant species in the Amazon. Acoustic (n=15) and radio (n=12) telemetry was used to study the influences on air-breathing and movement ecology of arapaima in the Central Amazon. Generalized additive mixed models showed that temperature was the most influential predictor of air-breathing intervals, followed by body size. The shortest breathing intervals were associated with consecutive "aggressive" breaths while the longest breathing intervals had consecutive "calm" breaths. Generalized linear mixed models showed that flood stage was the most important predictor of residency time, directional movement, and rate of movement. Fish moved faster in the flood and dry stages than the rising and falling stages, and spent longer in one place in the rising and falling stages than the flood and dry stages. Findings of this study may be used to inform management decisions for arapaima conservation, such as protected habitat and population counts, with applications to fishes across river-floodplain ecosystems globally. / Master of Science

Cognition shapes how we perceive and react to our environment. Throughout my Master of Science, I have studied two major fields of animal cognition. My thesis first reports on the cognitive aspects of animal navigation in home ranging and seasonal migration, then I explore the development of group expertise through extensive experience with collective decision-making. The key contributions of the first manuscript (Chapter 2) are a condensed yet detailed summary of the behaviours involved in individual and collective animal movement, followed by research ideas to fill the gaps of the current literature. The key contribution of the second manuscript (Chapter 3) is developing an experiment to study group expertise, a topic that currently lacks controlled experiments, via testing the effect of experience on collective decision-making. This thesis expands the existing knowledge on animal movement and collective decision-making. / Thesis / Master of Science (MSc) / Cognition is the process of attaining, processing, and using information. Perception, learning, and memory are the main cognitive processes that are responsible for how we understand the world around us. In my thesis, I first review the cognitive processes involved in short-distance and long-distance animal movements. Secondly, I examine how a specific type of cognition, collective decision-making, improves with experience. Together, I reflect on various pillars of animal cognition, discuss my contributions to the field, and suggest further research ideas.

Worldwide, many wildlife populations are in decline or facing extinctions due to overhunting, habitat loss and fragmentation, infrastructure development, resource extraction, and climate change. These threats are particularly detrimental to Madagascar's most iconic wildlife - lemurs (Primates: Lemuridae) – which have been declared Earth's most threatened mammal group, with 103 of 107 species currently threatened with extinction. Due to the numerous anthropogenic pressures facing lemurs, concerted efforts have been made to design and implement effective conservation management plans as well as to maintain captive populations. My dissertation focused on understanding the behavior and physiology of two critically endangered lemur species: the golden crowned sifaka (Propithecus tattersalli) and the Coquerel's sifaka (P. coquereli). To gain a better understanding of free-living golden-crowned sifaka habitat requirements, I combined behavior data with Dynamic Brownian Bridge Movement Models and Resource Selection Functions to examine the influence of abiotic, biotic, and anthropogenic factors on movement and foraging patterns. I found that movement rates and core area use were greater in the rainy season than in the dry season. My findings also indicated that roads and human villages influenced the locations where sifakas choose to forage, demonstrating the need to strategically place infrastructure to limit wildlife disturbance (Chapter 2). Second, having explored potential stressors in wild sifaka, I wanted to explore relationships between physiological stress and captive care in sifakas. Specifically, I investigated relationships between captive sifaka fecal glucocorticoid metabolite levels and captive husbandry conditions. I found that age and contraceptive use, but not enclosure type, season, or sex, influenced glucocorticoid excretion (Chapter 3). These results highlight the importance of assessing the physiological impacts of captive husbandry conditions to ensure that the best animal welfare practices can be maintained. Third, to combat challenges in studying animal behavior using observational approaches, I designed and constructed low-cost, open-source proximity loggers to remotely examine fine-scale movement and social behaviors in wild and captive sifakas. I found a relationship between radio signal strength and distance between tracking devices (R2 = 0.8812), demonstrating that proximity sensors can effectively collect data on close range group-level behavior (Chapter 4). These modular devices can be used on an array of wildlife species to explore social interactions that require high resolution spatial data. Taken together, these results illustrate the opportunity of connecting behavioral, ecological, physiological, and technological approaches to gain critical insight into the multidimensional nature of wildlife conservation. Lastly, I discussed future steps that can be taken to extend the framework established by my dissertation research to address the complex dynamics shaping conservation in Madagascar (Chapter 5). / Doctor of Philosophy / Worldwide, many wildlife populations are at risk of extinction due to hunting, habitat loss, infrastructure development, and climate change. These threats are particularly detrimental to lemurs – a diverse group of primates found only on the island of Madagascar. Due to the numerous pressures facing lemurs, efforts have been made to design and implement effective conservation management plans and maintain captive populations. My dissertation focused on understanding the behavior and physiology of two critically endangered lemur species: the golden crowned sifaka (Propithecus tattersalli) and the Coquerel's sifaka (P. coquereli). To better understand wild golden-crowned sifaka habitat needs, I followed six groups of sifakas in humid, moderate, and dry forests to examine the influence of season, forest type, and human development on their movement patterns and feeding locations. I found that sifakas moved more and used more space in the rainy season than in the dry season. Several sifaka groups also avoided feeding near roads and human villages, demonstrating the need to strategically place infrastructure to limit negative effects on wildlife (Chapter 2). Second, having explored potential stressors in wild sifaka, I wanted to explore relationships between physiological stress and captive care in sifakas. Specifically, I analyzed sifaka fecal samples to investigate relationships between captive sifaka husbandry conditions and physiological stress (i.e., glucocorticoid levels). I found that age and birth control use, but not enclosure type, season, or sex, influenced glucocorticoid levels (Chapter 3). These results highlight the importance of assessing the physiological impacts of captive husbandry conditions to ensure that the best animal welfare practices can be maintained. Third, to combat challenges in studying animal behavior using observational approaches, I designed and constructed low-cost, open-source tracking devices to remotely study fine-scale movement and social behaviors in wild and captive sifakas. I found that the distance between tracking devices can be determined by using proximity sensing radio chips. This demonstrated that proximity sensors can effectively collect data on close range group-level behavior (Chapter 4). These modular devices can be used on an array of wildlife species to explore social interactions that require high resolution spatial data. Taken together, these results illustrate the benefits of using behavioral, physiological, and technological approaches to gain insight into the multidimensional nature of wildlife conservation. Lastly, I discussed future steps that can be taken to extend the framework established by my dissertation research to address the complex dynamics shaping conservation in Madagascar (Chapter 5).

Doctor of Philosophy / Department of Biology / Jack F. Cully, Jr. / Dispersal remains one of the most important, yet least understood, life history traits. As the vehicle of gene flow among populations, dispersal can both relieve inbreeding depression and prevent local adaptation. Regionally, dispersal can stabilize or destabilize metapopulations, given its critical roles in disease transmission among populations as well as recolonization following local extinction events. Furthermore, in light of climate change and increasing habitat loss and fragmentation, the ability to navigate through unfamiliar, unsuitable habitat between populations is essential to the long-term survival of a species across its range. In my dissertation, I present a multi-scale investigation of factors affecting gene flow and disease transmission among populations of a keystone species and an agricultural pest of the North American prairie: the black-tailed prairie dog (Cynomys ludovicianus). Black-tailed prairie dogs are social, ground-dwelling squirrels that live in spatially isolated populations called colonies. First, we conducted a landscape genetic analysis of black-tailed prairie dogs throughout a large portion of their current range. Our estimates of gene flow indicate that the genetic neighborhood size of both male and female prairie dogs reaches 40-60 km within short-grass prairie, whereas colonies within mixed-grass prairie are more isolated. At a broad scale, we observed isolation-by-distance among colonies and great influence of grassland productivity on genetic connectivity; however, neither distance nor landscape characteristics greatly explained observed genetic differentiation among colonies separated by < 50 km. Last, we investigated whether landscape features could predict disease transmission patterns of sylvatic plague among colonies in short-grass prairie and found evidence that pastures act as corridors for plague transmission. Our results indicate that black-tailed prairie dogs are more resilient to habitat loss and fragmentation than other obligate grassland species and likely capable of transmitting sylvatic plague over long distances. Taken together, these studies illustrate how a multi-scale approach can reveal complexities of dispersal dynamics that would otherwise remain undetected.

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Master of Science / Biology / Alice Boyle / Dispersal is a behavior common to virtually all taxa with important consequences for gene flow, demography, and conservation. Mobile animals such as birds frequently engage in breeding dispersal, but the factors shaping this behavior are not well understood. In mid-continental grasslands, preliminary evidence suggested that Grasshopper Sparrows (Ammodramus savannarum) engaged in breeding dispersal within a single breeding season. This intriguing pattern shaped my research questions: (1) what are the patterns of within-season breeding dispersal in Grasshopper Sparrows? (2) why do some individual sparrows disperse, and others do not? and (3) what shapes settlement decisions following dispersal? I tested hypotheses based on spatial and temporal variation in nest predation, nest parasitism, and food availability. I studied Grasshopper Sparrows at 18 experimentally-managed watersheds with different fire and grazing regimes at Konza Prairie Biological Station during 2013-2015. To describe patterns, I combined re-sighting of 779 marked individuals, territory mapping, and radio-telemetry to quantify territory densities, turnover, and dispersal distances. To determine if nest predation or nest parasitism affected dispersal, I monitored the fate of 223 nests. I estimated food intake rates using plasma metabolites, and prey availability using sweep sampling. Densities of territorial Grasshopper Sparrows varied seasonally in management-specific ways. Turnover was remarkably high, with over half of territorial males being replaced each month. Over a third of males changed territories within-season, dispersing 0.1-9 km between breeding attempts. Dispersal decisions were related to past nest predation, but not nest parasitism. Dispersal likely yields fitness benefits, as sparrows that dispersed increased their chances of nest survival by 23% relative to site-faithful individuals. However, food availability did not affect settlement decisions. My study provides the first evidence of within-season breeding dispersal in Grasshopper Sparrows, and represents one of few tests of alternative hypotheses explaining dispersal decisions of songbirds. My results are consistent with a growing literature on the role of predation shaping dispersal, but suggest, somewhat surprisingly, that food is not important in post-dispersal habitat selection. High dispersal capacity coupled with adaptability to temporal and spatial change may be typical of grassland songbirds, implying that demographic studies and management decisions must consider their mobility for conservation.

For young animals, surviving the first year of nutritional independence requires rapid development of effective foraging behaviour before the onset of terminal starvation. Grey seal (Halichoerus grypus) pups are abandoned on the natal colony after a brief (15-21 days) suckling period and must learn to dive and forage without parental instruction. Regional and sex-specific differences in diet and foraging behaviour have been described for adults and juveniles, but the early-life behaviour of pups during the critical first months at sea remains poorly understood. This thesis investigates sources of intrinsic and extrinsic variation in the development of foraging behaviour and resource selection in grey seal pups. The studies presented here feature tracking and dive data collected from 52 recently-weaned pups, tagged at six different breeding colonies in two geographically-distinct regions of the United Kingdom (UK). Original aspects of this thesis include: (Chapter I) a comprehensive review of analytical methods for inferring foraging behaviour from tracking and dive data in pinnipeds; (Chapter II) description and comparison of regional and sex differences in movements and diving characteristics of recently-weaned pups during their first trips at sea; (Chapter III) implementation of a novel generalized hidden Markov modelling (HMM) technique to investigate the development of foraging movement patterns whilst accounting for sources of intrinsic (age, sex) and extrinsic (regional) variation; and (Chapter IV) the first analysis of grey seal pup foraging habitat preference, incorporating behavioural inferences from HMMs and investigating changes in preference through time.