Two-thirds of United States stream length is in either fair or poor biological condition. However, we do not yet have reliable, quantitative tools to diagnose site-specific causes of biological impairment. One way to diagnose causes of impairment is to compare the environmental tolerances or preferences of the taxa expected at a site to those of the observed community. Stream ecologists have derived tolerance values (TVs) from field data for use in causal analysis, but inconsistencies across studies cast doubt on the accuracy of these TVs. Published TVs may not agree with one another for several reasons, including: differences in the methods used to estimate TVs, confounding among environmental variables, effects of environmental interactions on taxon abundance, and bias from incomplete sampling of a taxon’s niche space. My objectives were to determine if and how these four potential problems affect TVs and to determine if TVs can be used reliably in causal assessments. I collected macroinvertebrate, substrate, temperature, conductivity, and velocity data from 45 streams in the western U.S. Analyses of data from this field study suggest that incomplete sampling can profoundly influence TVs, whereas interactions may have little effect. Significant spatial correlations between environmental variables suggest that confounding may also affect the derivation of TVs, but the magnitude of this effect is unclear. Also, though each method used to estimate TVs has limitations, TVs derived from different methods appear to reveal the same environmental signal, and there may be little reason to prefer one method over another in a causal analysis. Over last few decades, researchers have begun to add biological traits, including estimates of preference and tolerance, to the suite of metrics used in bioassessments. As descriptors of important biological traits, TVs should help water quality managers reliably diagnose and combat the causes of biological stream impairment.

Black-naped Oriole (Oriolus chinensis), Oriolidae, Passeriformes, is a member of old world songbirds. It has a wide distribution all over the eastern Asia, and is divided into 18 to 20 subspecies by differences in breeding sites, residents or migrants, morphological characters and songs. The populations breeding in Taiwan are classified as subspecies Oriolus chinensis diffusus. Black-naped Orioles inhabit in wooded habitats with a preference for tall secondary forests and disturbed wooded habitats and the staple foods of Black-naped Orioles are fruits, larvae, pupae and imagines of insects. This study was intented to understand the habitat preference and to explore the fundamental ecological data of Black-naped Oriole in Taiwan. Breeding seasons of Black-naped Oriole started from March and ended in July, and reached its peak from April to June. Most of the birds had two broods each year. Females built nests and incubated for 17-21 days alone, and males shared feeding and protecting juveniles after hatching. The birds of Pingtung population often built their nests on tall Albizia falcate and those of Fenglin population on Pachira macrocarpa. The breeding success was 23.3% in Pingtung and 18.2% in Fenglin. The breeding failure were due to human disturbance, climate, and poaching. The materials used for nest were bark, grass, leaves, and some artificial materials. Black-naped Orioles prefer to build nests at the same tree but on different branches. The nests were often closed to nests of Dicrurus macrocercus. Cooperative defenses between these two birds were observed.

The waters off the west coast of Scotland have one of the highest densities of harbour porpoise (Phocoena phocoena) in Europe. Harbour porpoise are listed under Annex II of the EU Habitats Directive, requiring the designation of Special Areas of Conservation (SACs) for the species’ protection and conservation. The main aim of this thesis is to identify habitat preferences for harbour porpoise, and key regions that embody these preferences, which could therefore be suitable as SACs; and to determine how harbour porpoise use these regions over time and space. Designed visual and acoustic line-transect surveys were conducted between 2003 and 2008. Generalised Estimating Equations (GEEs) were used to determine relationships between the relative density of harbour porpoise and temporally and spatially variable oceanographic covariates. Predictive models showed that depth, slope, distance to land and spring tidal range were all important in explaining porpoise distribution. There were also significant temporal variations in habitat use. However, whilst some variation was observed among years and months, consistent preferences for water depths between 50 and 150 m and highly sloped regions were observed across the temporal models. Predicted surfaces revealed a consistent inshore distribution for the species throughout the west coast of Scotland. Regional models revealed similar habitat preferences to the full-extent models, and indicated that the Small Isles and Sound of Jura were the most consistently important regions for harbour porpoise, and that these regions could be suitable as SACs. The impacts of seal scarers on distribution and habitat use were also investigated, and there were indications that these devices have the potential to displace harbour porpoise. These results should be considered in the assessment of sites for SAC designation, and in implementing appropriate conservation measures for harbour porpoise.

Natal dispersal is at the nexus of ecology, ethology, population genetics, and evolution. While abundant research exists on emigration and associated proximate and ultimate causes, less is known about exploration, settlement, and factors that influence settlement decisions. Further, the role of individual behavioral phenotypes in the domains of wildlife ecology and conservation, which include natal dispersal, is a recent and expanding area of inquiry. Understanding the relationships among individual phenotype, environmental conditions, and natal dispersal is increasingly important as landscapes become altered by disturbance, fragmentation, and climate change. I investigated natal dispersal in endangered Mt. Graham red squirrels (Tamiasciurus hudsonicus grahamensis), an isolated, peripheral subspecies of North American red squirrel persisting at the southern edge of the species' range. We tested hypotheses about the importance of proximate and ultimate drivers of emigration, dispersal distance, and settlement, and estimated perceived landscape connectivity within a mosaic of forest damage in the Pinaleño Mountains, Arizona. Compared to other red squirrel populations in North America, natal dispersal in Mt. Graham red squirrels is sex-biased and non-philopatric with mean dispersal distance over 8 times that observed in non-peripheral populations. Resources, indicated by mother's body mass in spring (a reflection of her intrinsic quality and territory quality) and individual body condition, contribute to individual behavioral tendencies for movement and exploration. Individuals with behavioral tendencies for movement and exploration dispersed the farthest, and for both males and females the longest observed dispersal distances and proportion of individuals dispersing occurred in a year of lowest food availability. Our research highlights the important role individual behavioral syndromes may play in observed heterogeneity in life history strategies with populations. Following emigration from the natal area, we provide evidence that individual dispersers rely upon forest structural cues similar to their natal area to select locations for settlement; the first test of natal habitat preference induction in a single vegetation community type. We used circuit theory to evaluate landscape connectivity and identify areas important for long-distance dispersal movements. Because single connectivity models may not adequately represent functional connectivity for an entire population, we summarized landscape connectivity across varying levels of landscape resistance to identify areas that promote movement and long-distance dispersal for individuals with different perceptions of landscape resistance. We show that composite connectivity models are a useful method to identify forest areas important for the promotion of long-distance movements as well as areas that constrain movement.

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.

Anthropogenic influences and climate change are warming rivers in New Brunswick and threatening the cold water habitats of native salmonids. When ambient river temperatures in summer exceed the tolerance level of Atlantic salmon and brook trout, individuals behaviourally thermoregulate by seeking out cold water refugia. These critical thermal habitats are often created by tributaries and concentrated groundwater discharge. Thermal infrared imagery was used to map cold water anomalies along a 53 km reach of the Cains River on 23 July 2008. Although efficient and useful for mapping surface temperature of a continuous stream reach, the fish did not use all identified thermal anomalies as refugia. Overall, 100 % of observed large brook trout >35 cm in length were found in 30 % of the TIR-mapped cold water anomalies. Ninety eight percent of observed small brook trout 8 – 30 cm in length were found in 80 % of the mapped cold water anomalies and their densities within anomalies were significantly higher than densities outside of anomalies. Fifty nine percent of observed salmon parr were found in 65 % of the mapped anomalies; however, they were dispersed within study sites and their densities were not significantly different within anomalies compared to outside of the anomalies. No brook trout were observed at the seven noncold water study sites that were investigated. Preference curves for various habitat variables including velocity, temperature, depth, substrate, and deep water availability near cold water anomalies were developed based on field investigations during high temperature events (ambient river temperature >21 oC). Combined with thermal imagery, managers can use the physical descriptions of thermal refugia developed here as a tool to help conserve and restore critical thermal refugia for Atlantic salmon and brook trout on the Cains River, and potentially similar river systems.

The thick shelled river mussel (Unio crassus) has a fragmented distribution in southern Sweden. It is a threatened and protected species. In both the Swedish red list and the IUCN Red List of Threatened Species Unio crassus is classified as Endangered (EN). Causes for this classification are for instance differentiated bottom substrate and deterioration in water quality. In this study, habitat preferences of Unio crassus were investigated to assist in future restoration work. The environmental parameters that were used to characterize the habitat in sites with or without Unio crassus were water depth, bottom substrate, water velocity, slope, and shading. In this thesis I focused in bottom substrate and water velocity. Sites with Unio crassus had finer bottom substrate and lower water velocity than sites without (t>2.54, p<0.05, t-test). Most of the sites with Unio crassus had a bottom substrate with a size <4 mm and a water velocity around 0.3-0.5 m/s. These two variables were correlated with each other. When the water velocity was higher, the bottom substrate was coarser. These results are in line with other studies, showing that if the bottom substrate is either too coarse or too fine, it could impact Unio crassus. Too coarse bottom substrate probably results in difficulty in burrowing and too fine most likely results in interfering with respiration and feeding. Earlier studies indicate that the water velocity can have a greater impact on unionids than bottom substrate. Because of the correlation between bottom substrate and water velocity it is not easy to disentangle the importance of each factor.

The thick shelled river mussel (Unio crassus) has a fragmented distribution in southern Sweden. It is a threatened and protected species. In both the Swedish red list and the IUCN Red List of Threatened Species Unio crassus is classified as Endangered (EN). Causes for this classification are for instance differentiated bottom substrate and deterioration in water quality. In this study, habitat preferences of Unio crassus were investigated to assist in future restoration work. The environmental parameters that were used to characterize the habitat in sites with or without Unio crassus were water depth, bottom substrate, water velocity, slope, and shading. In this thesis I focused in bottom substrate and water velocity. Sites with Unio crassus had finer bottom substrate and lower water velocity than sites without (t>2.54, p<0.05, t-test). Most of the sites with Unio crassus had a bottom substrate with a size <4 mm and a water velocity around 0.3-0.5 m/s. These two variables were correlated with each other. When the water velocity was higher, the bottom substrate was coarser. These results are in line with other studies, showing that if the bottom substrate is either too coarse or too fine, it could impact Unio crassus. Too coarse bottom substrate probably results in difficulty in burrowing and too fine most likely results in interfering with respiration and feeding. Earlier studies indicate that the water velocity can have a greater impact on unionids than bottom substrate. Because of the correlation between bottom substrate and water velocity it is not easy to disentangle the importance of each factor.

Speciation is an important process that is responsible for the generation of biodiversity on Earth. The importance of gene flow during speciation is hotly debated; however, it can be investigated by studying the process of intraspecific population differentiation. Here, I investigate the mechanisms that influence population differentiation and gene flow in brown (Sula leucogaster) and red-footed boobies (S. sula). These species are congeneric, broadly sympatric, and ecologically similar; however, they differ in their marine habitat preference (inshore vs. pelagic). I hypothesized that: (i) gene flow is restricted by major physical barriers in both species, and (ii) gene flow in the absence of physical barriers is more prevalent in red-footed boobies due to their pelagic marine habitat preference. First, I characterized the structure and function of the booby mitochondrial genome. Using extensive DNA sequencing and phylogenetic methods, I found that boobies have tandemly duplicated mitochondrial control regions that evolve in concert. I suggest that concerted evolution of duplicated control region may be common in seabirds. To quantify matrilineal population genetic structure and gene flow, I sequenced one control region in 513 brown and red-footed boobies. Both species exhibited strong population genetic structure that was attributable to continental barriers to gene flow such as the Isthmus of Panama. In the absence of physical barriers, gene flow was more prevalent in red-footed boobies. I also used microsatellite and nuclear intron loci to perform multilocus phylogeographic analyses of brown and red-footed boobies. Individuals of both species could be grouped into four genetic populations that corresponded to oceanographic regions. In red-footed boobies, gene flow following secondary contact of previously isolated lineages was common, perhaps due to a pelagic habitat preference. In brown boobies, major genetic populations apparently diverged in the absence of gene flow. Despite this, Isla San Benedicto in the Eastern Pacific is a site of secondary contact between brown booby lineages that diverged approximately one million years ago, and hybrids are apparently fertile. These findings suggest that gene flow following secondary contact may be an important, but overlooked, component of speciation. / Thesis (Ph.D, Biology) -- Queen's University, 2012-04-28 17:28:53.302

Anthropogenic influences and climate change are warming rivers in New Brunswick and threatening the cold water habitats of native salmonids. When ambient river temperatures in summer exceed the tolerance level of Atlantic salmon and brook trout, individuals behaviourally thermoregulate by seeking out cold water refugia. These critical thermal habitats are often created by tributaries and concentrated groundwater discharge. Thermal infrared imagery was used to map cold water anomalies along a 53 km reach of the Cains River on 23 July 2008. Although efficient and useful for mapping surface temperature of a continuous stream reach, the fish did not use all identified thermal anomalies as refugia. Overall, 100 % of observed large brook trout >35 cm in length were found in 30 % of the TIR-mapped cold water anomalies. Ninety eight percent of observed small brook trout 8 – 30 cm in length were found in 80 % of the mapped cold water anomalies and their densities within anomalies were significantly higher than densities outside of anomalies. Fifty nine percent of observed salmon parr were found in 65 % of the mapped anomalies; however, they were dispersed within study sites and their densities were not significantly different within anomalies compared to outside of the anomalies. No brook trout were observed at the seven noncold water study sites that were investigated. Preference curves for various habitat variables including velocity, temperature, depth, substrate, and deep water availability near cold water anomalies were developed based on field investigations during high temperature events (ambient river temperature >21 oC). Combined with thermal imagery, managers can use the physical descriptions of thermal refugia developed here as a tool to help conserve and restore critical thermal refugia for Atlantic salmon and brook trout on the Cains River, and potentially similar river systems.