The "Den Mother" marten habitat quality models were created to provide insight into American marten habitat selection behavior and to promote the recovery of the Newfoundland marten (Martes americana atrata) population. Although these objectives are typical of most wildlife habitat modeling projects, the marten's idiosyncratic habitat ecology and apparently intractable conflicts associated with timber harvesting motivated a unique, process-oriented approach to appraising landscapes. The Den Mother models used optimal decision-making principles to synthesize critical resources (den sites and foraging opportunities) and constraints (adverse thermal situations and exposure to predations) into a single hierarchical framework. The resulting spatially explicit, combinatorial optimization models depend on a complex array of interacting assumptions. However, in mechanistic models, explicit assumptions provide the means by which insights are gained. For example, manipulating prey population parameters provided a clear demonstration of how resource conditions confound the relationship between landscape configuration and marten fitness, thereby challenging conventional definitions of habitat based on vegetation alone. Likewise, the models' sensitivity to spatial circumstances argued against the concept of an "optimal landscape," a traditional objective for wildlife habitat analyses. Although the model analyses did not refute the conventional wisdom that marten are strongly associated with (and may depend on) large contiguous blocks of senescing and defoliated forests, they did suggest that the marten is an opening-sensitive, rather than coresensitive, species. The models also suggested new avenues for research addressing marten den site selection, predator avoidance behavior, foraging efficiency, and space use strategies, as well as new techniques for assessing the trade-offs that govern marten habitat selection behavior. Finally, the models also suggested new guidelines for promoting marten recovery in an adaptive management context, including recommendations for placing artificial resting structures; creating favorable landscape mosaics; managing ephemeral resources such as transition old-growth forests, defoliation, and coarse woody debris; and developing alternative, competing management scenarios that address both forest and prey conditions simultaneously.

The goal of this research was to determine the relative quality of near shore marine areas by investigating their influence on Haemulidae community structure, distribution pattern, condition, and growth. Habitat was defined at the small spatial scale of individual habitat types such as seagrass beds, mangroves and coral reefs, and at the broader spatial scale of the interconnection of these individual habitat types within a mosaic (IHM). Ten spatial, biotic and abiotic parameters (percentage coverage of sand, mangroves, hard substrate, and seagrass, turbidity, pH, salinity, temperature, average depth, and predator density) were investigated. These environmental characteristics acted as proxies for the quality of IHMs. The major findings of the research were: (1) IHMs and discrete habitat types in tropical marine systems are not always equal in quality. Further, the highest quality IHMs/discrete habitat types have the critical resources whether spatial, abiotic or biotic, at the optimum levels needed by organisms to carry out their critical life functions; (2) IHMs of the highest quality contain all the discrete habitat types needed by organisms to carry out their life processes in a spatial arrangement that maximizes energy savings; (3) IHMs can be of high quality in the absence of one habitat type, if this habitat type is replaced by another that can take on its ecological role; and (4) the percentage cover of hard substratum and seagrass, temperature, and predator density have a big impact on Haemulidae distribution pattern, community structure, condition and growth. In addition, this research highlighted some of many characteristics of benthic habitats such as type and configuration that should be included in the design of Marine Protected Areas for the effective management of fisheries resources. Effective Marine Protected Areas should have (1) large overall area with benthic habitat types of high quality; (2) spatial configurations with short distances (corridors) between habitat types; (3) spatial arrangements that place all individual habitat types in connection with all other habitat types so that energy expenditure in moving among habitat types is reduced; (4) habitats with high structural complexity; and (5) the inclusion of all the habitat types needed by focal organisms to carry out their life processes, or surrogate habitat types that can take on the role of ones that are absent.

Abstract. The objectives of this thesis are to evaluate (1) the influence of slope aspect on boreal plant responses to clear-cutting and (2) the effects of post-harvest extraction of bioenergy (logging residues or slash) on plant composition, richness and performance in clear-cuts. Such insight is essential for understanding changes in species composition and richness in response to clear-cutting and application of intensified harvesting systems. The focus is on productive and managed spruce dominated forests and focal organisms are mosses, liverworts (i.e. bryophytes) and vascular plants. Space-for-time substitution studies were performed in south- and north-facing slopes located in 10 forests and 10 adjacent clear-cut stands in central Sweden. Differences between forests and clear-cuts were interpreted as effects of clear-cutting. The results show that the response of all three focal groups differed between aspects. More species were lost in south-facing slopes and clear-cutting reduced species richness of liverworts as well as of bryophytes and vascular plants associated with sheltered habitats. By contrast, clear-cutting caused no reduction in any group and more species were added in north-facing slopes. As a result north-facing clear-cuts generally had higher species richness than their forest counterparts. The disparate patterns in species’ response between aspects were most likely caused by initial microclimatic differences and a greater microclimatic change in south-facing slopes, in response to clear-cutting. A paired comparative study of conventionally harvested (i.e. slash left) and slash-harvested clear-cut stands was performed 5-10 years after clear-cutting in south-central Sweden. Both the species composition and the richness of mosses and liverworts were affected by slash harvest, whereas the composition of vascular plants was not. Slash harvest also reduced richness of mosses and liverworts associated with forests and organic substrates (e.g. dead wood and litter). Species richness of vascular plants and bryophytes associated with inorganic substrates (i.e. mineral soil) was unchanged. Differences between conventionally harvested stands and slash-harvested stands were most likely a result of reduced cover of organic material reducing substrate availability and shelter in the latter. Increased mechanical disturbance in slash-harvested stands that destroys remnant forest vegetation and favours pioneers may also play a role. A bryophyte transplant experiment was performed in seven clear-cuts in central Sweden and monitored over one vegetation period. The results show that logging residues (or slash) and forest edges may shelter ground-dwelling bryophytes by buffering the clear-cut microclimate. In conclusion, both slope aspect and extraction of forest bioenergy affect plant survival in clear-cut boreal forests. As surviving plant populations facilitate re-colonisation, north-facing slopes and conventionally harvested clear-cuts (i.e. slash left) may potentially recover faster than south-facing slopes and slash-harvested clear-cuts.

Conservation frequently requires immediate responses to prevent further declines of imperilled populations, often in the absence of detailed information. Consequently, population distribution patterns are often used to guide conservation decisions. However, distribution patterns may be misleading if threats have restricted species to low quality habitat. This issue means it is not always apparent where management efforts should be concentrated for maximum conservation gain. My aim was to improve the effectiveness of threatened species conservation by investigating this issue in whio (blue duck - Hymenolaimus malacorhynchos), a New Zealand riverine duck that has undergone serious declines. I used population and spatial modelling to answer three questions: (1) what are the threats to whio, (2) how can these threats be managed, and (3) managing which whio habitats will give the greatest conservation gain? A spatial analysis of contemporary whio habitat using boosted regression trees revealed whio are only secure in 1 % of their historical range, with predation likely causing significantly greater range contraction (83 %) than habitat modification (29 %). In that analysis, I identified 39,000 km of occupiable whio habitat, providing extensive opportunities to expand their contemporary range through management. Intensive monitoring identified stoats (Mustela erminea) as the primary cause of whio population declines, with stoat predation severely reducing whio nest survival (10 % and 54 % in the absence and presence of stoat control, respectively). Population viability analyses indicated whio populations in the absence of stoat control were at high risk of extinction (λ = 0.74) but large-scale, low-intensity predator control was useful for short-term whio conservation. However, whio populations with stoat control still had a declining population growth rate (λ = 0.95) and further intervention may be required to prevent whio extinctions. Such management needs to target high quality habitat to ensure the greatest conservation value. Analyses of habitat quality revealed whio fitness was highest in warm, low gradient rivers, although fitness gradients differed between North and South Islands. Comparisons of fitness relationships with spatial model predictions showed that South Island whio occurred more frequently in poorer habitat, indicating they may occupy a relict distribution. Limited resources for conservation mean identifying effective management techniques is critical for species persistence. My modelling approach enabled the effectiveness of whio management to be assessed and areas of high quality habitat where such management should provide the greatest benefit to be identified. These tools are directly applicable to the conservation management of many threatened species by quickly informing managers in situations where distributions may not follow habitat quality.

Many factors affect the productivity of songbirds. Which vegetation types the birds inhabit, nest-site characteristics, and adult behavior at the nest may affect predation and parasitism frequencies, fecundity, and nest survival and fledgling survival. All of these metrics determine reproductive success of individuals and may influence population persistence, especially for threatened and endangered species. My research investigated factors that affected these metrics for endangered black-capped vireos (Vireo atricapilla). Shrubland is considered high quality vireo habitat, with woodland vegetation types considered marginal. I located and monitored nests, conducted nest behavior observations, recorded behavior and predation at nests using video cameras, and resighted fledglings in shrubland, oak-juniper woodland, and deciduous woodland during the 2008–2010 breeding seasons. I monitored 302 black-capped vireo nests in 259 territories and resighted 350 fledglings with unique color combinations. Apparent nest success, nest survival, success of first nest attempts, parasitism and predation frequency, and fecundity did not differ statistically among vegetation types. Parasitism frequency was nearly twice as high in shrubland (22 percent) than in either woodland (12 percent in each) and varied by year. Nest-site characteristics differed among vegetation types, but nest survival was affected only by nest height and year; nests placed higher from the ground and nest attempts in 2008 and 2009 had lower survival. Fledgling survival was not affected by vegetation type or proximity of the nest to oak-juniper woodland. Nest behavior was not affected by vegetation characteristics, though nest attentiveness during incubation increased as average cover from 0 to 2 m increased. Females spent 80 percent more time on nests during incubation and 250 percent more time on nests during the nestling stage than males, but visitation was similar for each sex. Overall, the probability of nest success improved as male participation increased. My results emphasize the importance of male participation in determining the outcome of nests for species exhibiting bi-parental care. Furthermore, woodland habitats previously considered marginal may be good quality habitat in areas with large populations of black-capped vireos. Recognizing woodlands as non-typical, yet still suitable, habitat will allow managers to incorporate these vegetation types into management plans and recommendations for landowner conservation incentive programs.

Today traditionally managed wooded hay meadows only exist in small fractions of their former distributions. Because of the fragmentation and degeneration of hay meadows and the fact that pollinating insect diversity and abundance also are declining, pollination services in these habitats requires attention. To examine the pollination services in traditionally managed hay meadows I collected Ranunculus acris (Buttercup) in 20 meadows of varying quality on Gotland and evaluated the mean seed set and mean number of produced seeds per plant. I also collected Filipendula vulgaris (Dropwort) in 18 meadows and evaluated the mean seed set to be able to compare the pollination success of the insect pollinated R. acris with the wind pollinated F. vulgaris. A range of habitat variables were collected in the meadows and in older surveys to examine their relative impact on seed set. I found significantly higher seed set for R. acris in the meadows with higher habitat quality, than in meadows with lower quality. In contrast seed set in F. vulgaris was not related to habitat quality. The population density also seemed to play an important role in fertilization rate for R. acris, through increased seed set in high density areas, while plant height was positively correlated with number of produced seeds. For F. vulgaris seed set was positively correlated with moss cover, and number of seeds per plant was positively correlated with population density. These results suggest that reproductive success among insect pollinated plants are more sensitive to habitat degeneration than among wind pollinated plants. The status of pollination services in traditionally managed wooded hay meadows should be evaluated further.

Conservation frequently requires immediate responses to prevent further declines of imperilled populations, often in the absence of detailed information. Consequently, population distribution patterns are often used to guide conservation decisions. However, distribution patterns may be misleading if threats have restricted species to low quality habitat. This issue means it is not always apparent where management efforts should be concentrated for maximum conservation gain. My aim was to improve the effectiveness of threatened species conservation by investigating this issue in whio (blue duck - Hymenolaimus malacorhynchos), a New Zealand riverine duck that has undergone serious declines. I used population and spatial modelling to answer three questions: (1) what are the threats to whio, (2) how can these threats be managed, and (3) managing which whio habitats will give the greatest conservation gain? A spatial analysis of contemporary whio habitat using boosted regression trees revealed whio are only secure in 1 % of their historical range, with predation likely causing significantly greater range contraction (83 %) than habitat modification (29 %). In that analysis, I identified 39,000 km of occupiable whio habitat, providing extensive opportunities to expand their contemporary range through management. Intensive monitoring identified stoats (Mustela erminea) as the primary cause of whio population declines, with stoat predation severely reducing whio nest survival (10 % and 54 % in the absence and presence of stoat control, respectively). Population viability analyses indicated whio populations in the absence of stoat control were at high risk of extinction (λ = 0.74) but large-scale, low-intensity predator control was useful for short-term whio conservation. However, whio populations with stoat control still had a declining population growth rate (λ = 0.95) and further intervention may be required to prevent whio extinctions. Such management needs to target high quality habitat to ensure the greatest conservation value. Analyses of habitat quality revealed whio fitness was highest in warm, low gradient rivers, although fitness gradients differed between North and South Islands. Comparisons of fitness relationships with spatial model predictions showed that South Island whio occurred more frequently in poorer habitat, indicating they may occupy a relict distribution. Limited resources for conservation mean identifying effective management techniques is critical for species persistence. My modelling approach enabled the effectiveness of whio management to be assessed and areas of high quality habitat where such management should provide the greatest benefit to be identified. These tools are directly applicable to the conservation management of many threatened species by quickly informing managers in situations where distributions may not follow habitat quality.

Fifty-seven Trumpeter swans (Cygnus buccinator) were translocated to the Bear River Migratory Bird Refuge and the Bear River Club Company in northern Utah. The purpose of this effort was to encourage dispersal of the Rocky Mountain population of Trumpeter swans during the winter, and to reestablish a migratory route to southern wintering grounds. I assessed the success of the translocation by evaluating 13 translocation criteria proposed in the literature. In this study I addressed two of these criteria in detail by evaluating habitat quality at the translocation sites and by analyzing potential competitive interactions with Tundra swans (Cygnus columbianus). Habitat quality was determined by analyzing the spatial distribution of sago pondweed (Potamogeton pectinatus) tubers in wetland sediments before the fall and after the spring migration of Tundra swans. Sixty-four transects were established within the study sites with 10 sediment cores per transect. Geostatistical procedures were employed to account for autocorrelation between samples. Tuber biomass was not randomly distributed within the studied wetlands. In fact, discrete areas of high values appeared to exist before and after swan foraging . It is not likely that sago pondweed tubers are limiting swan abundance in this system. Thus, the habitat quality of the study sites is sufficient for Trumpeter swan translocation. Potential competitive interactions with Tundra swans were evaluated by examining differences in resource utilization patterns of the two species. I measured body size differences, dietary overlap, resource availability, and the efficiency of extracting available resources. Trumpeter swans appear to benefit from a larger body size and a longer neck because they are more efficient in extracting tubers from the sediment, and are able to exploit tubers to a greater sediment depth than Tundra swans. However, Trumpeter swans incur higher traveling costs due to the larger body size. The trade-off between higher foraging efficiency of Trumpeter swans and higher traveling efficiency of Tundra swans may be a potential mechanism for coexistence. Lack of support by governmental and non-governmental agencies did not allow for more than one year of translocation. Even though the Trumpeter swan translocation in 1996 was successful, I concluded that the Utah translocation program failed because the translocation did not meet translocation goals.

The movement of individuals is foundational to many ecological processes. For example, the movement of an organism from one place to another alters population density at both sites and has potential for affecting the genetic dynamics within the new population. Individual movement events may be in synchrony with overall trends in populations, e.g. spawning migrations, or may be atypical (asynchronous). This latter movement type can affect population and metapopulation dynamics, depending on its prevalence within a population. Nevertheless, given the complexity of interactions, the causative factors of movement are understood vaguely, much less for aquatic organisms. Drivers of movement are extrinsic (e.g. habitat quality, predation or habitat heterogeneity) and intrinsic (e.g. sex, size, or behavioral tendencies). Interactions among these drivers provide crucial insight into the patterns of movement observed within populations. Habitat is here shown to affect observed movement patterns of populations of southern leatherside chub (Lepidomeda aliciae). Streams with higher-quality habitat were inhabited by populations exhibiting lower overall movement compared to lower-quality streams. However, observations of individual long distance movement relative to the norm within the population suggest that movement may also be behaviorally based. In further tests, it is shown that, indeed, behavioral tendencies of individuals can be measured and are predictive of annual movement by individuals. Other drivers, habitat availability and quality, were also found to influence movement on a yearly basis. Movement patterns are also affected by the presence or absence of predators. A tropical livebearer (Brachyrhaphis rhabdophora) has a higher percentage of individuals classified as generally moving when predators are absent from the environment compared to predator sites. Predation environment also significantly affects individual body shape with predator sites possessing caudal peduncles with greater surface area, an adaptation likely promoting burst speed for greater escape abilities. Classification of individuals as generally moving or generally not moving was also significantly related to variation of body shape of these fish. However, biological significance is ambiguous given the absence of obvious morphology trends explained by this factor. It is critical to understand these drivers to better understand the dynamic interface between ecology and evolution.

The southwestern willow flycatcher (Empidonax traillii extimus) is a federally-endangered neotropical migrant that breeds in the southwestern United States. The population of southwestern willow flycatchers on the South Fork Kern River in California was once thought to be one of the largest E. t. extimus populations. It declined from 38 pairs in 1997 to 12 pairs in 2000. My goals were to examine E. t. extimus habitat selection on the South Fork Kern River, to determine how habitat characteristics and food availability affect E. t. extimus demographics, and to make inferences about possible reasons for the decline. My first objective was to determine southwestern willow flycatcher habitat selection on the Kern on two spatial scales: territory and nest site. Southwestern willow flycathers selected habitat characteristics that appeared to be related to food availability, foraging ecology, or nest cover. Territories within the riparian forest were closer to water and the edge of forest and had fewer cottonwoods than unused areas. Nest sites had denser and more uniform canopy cover and a denser understory than randomly selected sites within territories. My second objective was to determine a relationship between measures of fitness (reproductive success and occupancy frequency) and territory categories (occupied 2 years, occupied 1 year, abandoned). Also, I examined the relationship between indirect measures of fitness, habitat characteristics and food availability, and territory categories. Compared to other territories, territories occupied more frequently had higher reproductive success, higher insect abundance indices, greater habitat heterogeneity, denser understories, and more stems 30-50 cm dbh. All of the habitat characteristics important in habitat selection and habitat quality on the South Fork Kern River were similar to other recent studies on E. t. extimus habitat selection and reproductive success. On the Kern, both suitable and optimal habitat appear to be limited and this limitation appears to be contributing to the population decline. Habitat quality may affect E. t. extimus demographics, particularly when the number of high quality territories in a population is limited as in site-dependent population regulation. Since the amount of suitable habitat is likely to continue to decline across the range of southwestern willow flycatchers, managers should consider manipulating habitat for high quality E. t. extimus habitat to aid conservation of this endangered species. / Master of Science