Skewed sex ratios can have negative implications for population growth or persistence if not congruous for a species system. A skewed tertiary sex ratio (2.3 males per female) has been detected in the breeding population of a grassland shorebird experiencing population declines, the mountain plover (Charadrius montanus). To evaluate the ontogeny of the observed male skew this study examined the early life stages, from laying to fledging, of mountain plover young during their breeding season from 2010 2012 in eastern Colorado. The life stages between laying and fledging that allows for differentiation between production and survival of males and females. Early stages encompass the primary (eggs produced) ratio which allows for evaluation of applied sex allocation theory, the secondary sex ratio (successfully hatched chicks) which determines if a sex specific mortality is occurring pre-hatching, and the chick stage which determines if a sex specific mortality is occurring post-hatching. Mountain plovers are a sexually monomorphic species at all stages therefore DNA samples were used to determine the sex of individuals. The primary sex ratio was 1.01 (± 0.01) males per females. The secondary sex ratio consisted of 1.1 (± 0.02) males per female. Neither the primary nor secondary sex ratio was able to account for the magnitude of the skew observed later in this species adult population. Radio telemetry was used to evaluate the next stage of life, survival of male and female chicks from hatching until fledging. Using a multi-state mark recapture analysis, the top model for predicting chick survival rates estimates differed between males (0.55 ± 0.13) and females (0.47 ± 0.15). The estimated survival difference between the sexes during the chick stage can drive a population with equal survival rates at all other life stages to a ~2.1 :1 adult sex ratio. Results from this study suggest survival difference between males and females at the chick stage is possibly contributing to a male skewed population.

Small populations are at increased risk of extinction due to their vulnerability to stochastic events. The population of fisher (<italic>Pekania pennanti</italic>, formerly <italic>Martes pennanti</italic>) in the southern Sierra Nevada Mountains of California is small and completely genetically isolated. My dissertation research investigates the timing and cause of this population's isolation, the degree of genetic subdivision within the population, the landscape features shaping gene flow, and the detection of population declines. I detected a 90% decline in effective population size and dated the time of decline to over a thousand years ago. Analyzing historical and contemporary genetic samples, I also found a recent bottleneck signal in the northern portion of the southern Sierra Nevada, indicating the southernmost tip of these mountains may have acted as a refugium for fisher in the late 19th century. I conclude that this population became isolated pre-European settlement, and that portions of the southern Sierra Nevada subsequently experienced another more recent bottleneck post-European settlement. I found that the southern Sierra Nevada fisher population is not highly genetically subdivided as previously thought. This population follows a pattern of isolation by distance with additional structuring that corresponds to geographic features and management boundaries. It can be characterized as having areas that are resistant to gene flow but without major barriers. I show that both sex-biased dispersal and spatial landscape heterogeneity can affect the determination of what landscape features structure gene flow, and that the landscape features influencing gene flow are different for each sex and within different geographic regions. Using a spatially-based simulation approach, I investigated the power of the Sierra Nevada fisher monitoring program to detect population trend, and illustrate the relationship between occupancy and abundance in this population. I show that a simulated 43% decline in abundance over an 8-year period only resulted in a 23% decline in occupancy. I also found that increasing the effective sampling area, implementing biennial instead of annual sampling, and increasing the type I error rate all increase statistical power to detect trend. Overall this research provides a better understanding of the historical and contemporary connectivity of this population and our ability to monitor population trends over time that will contribute to the conservation of fisher populations in the future.

Transient dynamics describe short-term responses to unstable conditions in population models. Although the theoretical potential of these short-term effects to change interpretation of model behavior has been demonstrated, it is unclear whether transient analyses will be relevant or useful in management applications. This dissertation explores the role of transient dynamics in plant populations based on long-term demographic data. Based on a survey of modeling results for plant populations in the literature, I found that theoretical indices of transient behavior greatly overemphasized the role of transient responses for the populations for which data were available. Transient indices were indicative of the variation in distance from asymptotic conditions that the models experienced; however, empirical data on long-term environmental variability was substantially closer to asymptotic conditions than theoretical measures. However, transient responses do play an important role in the variability that populations experience. Across nine perennial plant species, transient responses contributed more on average to variability in annual population growth rates than variation in vital rates alone. I also found evidence that transient responses may at times have a buffering effect on the variation that populations experience, by pushing the population in the opposite direction as demographic variation. These results demonstrate the importance of viewing transient dynamics and demographic variation as interrelated processes, with implications for both understanding population dynamics and in management applications. Finally, I explored the role of transient dynamics to assess the non-target impacts of herbicide use on population dynamics of Balsamorhiza sagittata, a native perennial forb in Montana grasslands. Using long-term monitoring data, I found that stage-specific effects of herbicide on Balsamroot demography, combined with episodic recruitment, lead to highly variable population demographic structures during the 10 year study period. My analyses suggest that timing herbicide use based on current population stage structures and mitigating changes to stage structure after spraying could help to minimize long-term impacts of herbicide use on long-lived perennial forbs like Balsamroot. More generally, my analysis demonstrated how information on current population status and specific timescales can be used to better inform management.

Invasion is associated with unexpected increases in aboveground net primary productivity and altered ecosystem function, including increased nitrogen availability and cycling. These shifts are well documented, however many previous studies have been observational, focused on a single plant species, or have not examined belowground microbial communities. I combined field and experimental techniques to examine changes in productivity and ecosystem function, and the abundance of ammonia- oxidizing bacteria (AOB) for the exotic invaders Bromus tectorum, Centaurea stoebe, Euphorbia esula, and Potentilla recta. To quantify effects of these invasive species on N cycling and AOB abundance we compared soil from invaded and native communities in the field and in an experimental garden. AOB are bacteria responsible for a rate-limiting step in nitrification. We found that invasion was associated with increased abundance of AOB across all species of invader. For other variables, the magnitude of response to invasion varied by species, but we found in general invasion was associated with increased aboveground net primary productivity and soil nitrogen cycling. In addition results from the experimental garden suggest some species of invader may drive increases observed in the field. Finally we report on a novel relationship between aboveground net primary productivity and soil NO3-N indicating that invaders may drive ecosystem processes in ways different from native communities.

As wild species face anthropogenic stressors, they will either adapt, shift their geographic range, or decline, perhaps towards extinction. The relative scope of these responses has not been well studied, especially for climate change where geographic range shifts and population declines have been widely discussed but the potential for adaptation mostly ignored. Adaptation to anthropogenic stressors can occur through phenotypic plasticity and/or evolution. My thesis first establishes, based on field studies of wild snowshoe hares, a novel and high-profile stressor directly linked to climate change. The stressor arises from a decrease in snow duration due to climate change, which causes seasonal coat color molt of individual hares to become mismatched with their background. The immediate adaptive solution to this form of camouflage mismatch is phenotypic plasticity, either in phenology of seasonal color molts or in behaviors that reduce mismatch or its consequences. Based on nearly 200 snowshoe hares across a wide range of snow conditions and two study sites in Montana, USA that differed in elevation and climate, I found minimal plasticity in response to mismatch between coat color and background. I found that molt phenology varied between study sites, likely due to differences in photoperiod and climate, but was largely fixed within study sites where seasonal changes in phenology were limited across years of very different snow duration. Hares exhibited some plasticity in the rate of the spring molt in response to immediate snow conditions but temperature or snow cover were not strong modifiers of the white-to-brown molt phenology. I also found no evidence that individual hares modify their behavior in response to color mismatch. Hiding and fleeing behaviors and immediate microsite preference of hares were more affected by variables related to season, site, and concealment, than by color mismatch. Although hares do not appear to be responding to camouflage mismatch with behavioral plasticity, adaptation could also occur through evolutionary changes facilitated by natural selection. We found that the raw material for natural selection to act on does exist in our populations in the form of individual variation in coat color phenology and consequently in color mismatch. We also found high fitness costs of coat color mismatch, with hares suffering 3 to 7% lower weekly survival rates when mismatched against their background. Coupling these fitness costs to local estimates of increased seasonal color mismatch as snow duration decreases in the future, we predict that annual hare survival will decline up to 12% by mid- and 24% by late century. Such changes in survival are sufficient to cause increasing hare populations to decline strongly towards extinction, with annual population geometric growth rate decreasing by 11% (24%) by mid (late) century. We conclude that plasticity in molt phenology and behaviors in snowshoe hares is insufficient for adaptation to camouflage mismatch, and that potential adaptive responses to future climate change will have to be facilitated by natural selection. These results form the basis for future work to evaluate whether evolution by natural selection can operate fast enough to prevent decline of this species.

Declining populations of plant and animal species is a major concern threatening global biodiversity. If we want to conserve threatened species, we must understand the requirements of the species. Recent data suggests Golden Eagle populations in the Western United States are declining. Future threats from expanded energy development, habitat loss and climate change are also a concern. Apparent declines and perceived threats have caused management agencies to classify the Golden Eagle as a species of concern requiring the creation of conservation plans. Yet, an effective conservation plan is dependent on information that is currently lacking. To address this lack of available information, I studied a population of breeding Golden Eagles in south-central Montana which has increased in the last 50 years. I was interested in determining which factors were responsible for the increase in the population and changes in measures of breeding performance. I used information from the current phase to identify which environmental factors are important for the eagles now and assessed whether the identified factors were responsible for the documented changes since the 1960s. I found that Golden Eagles in the current phase were selecting areas for nesting territories based on prey habitat and terrain ruggedness. Within their territories, Golden Eagles selected areas conducive to uplift dependent on proximity to prey habitat, on a western aspect and closer to their nest. My results related to measures of breeding performance were unclear. I found prey habitat was likely not limiting the probability of territories being occupied between phases but instead, anthropogenic disturbance was likely limiting the historic population. My results suggest management plans should focus current protection on areas with prey habitat in close proximity to topography eagles can use to exploit uplift. To better understand the current population trends, I suggest expanding monitoring efforts to areas without a large degree of habitat loss in the last 50 years and to unprotected areas. Golden Eagle populations in these locations may be more indicative of the current status of the population range-wide.

The woodland caribou (Rangifer tarandus caribou) population in Newfoundland has been declining since the mid-1990s, and will likely continue to decline into the foreseeable future. This decrease in numbers has been accompanied by a large drop in recruitment. Predation is the primary cause of caribou calf mortality in Newfoundland, and since 2003, >80% of radio-collared calves died within the first 6 months of life. Two Newfoundland herds also have shifted their calving grounds over the past 15 to 20 years. Our objective was to investigate why these shifts have occurred. We analyzed female telemetry locations spanning 29 years, to delineate early-use (1980s and 1990s) and late-use (2003 and 2010) calving grounds, and to compare use and availability within and across these early- and late-use areas. We used a resource selection framework and evaluated shifts with respect to land-use, landcover, and NDVI over time. We found that females were not avoiding human disturbance or responding to climatic changes, but instead were changing selection choices. Models indicated that caribou were selecting for post-burn vegetation and more cover in late-use calving grounds. These results will likely help direct future research and management decisions to boost calving success in Newfoundland.

Identification of population structure and connectivity is important for understanding and managing animal populations, in part, because they can influence spread of disease. Respiratory disease is one of the most important factors affecting populations of bighorn sheep and transmission of disease is believed to occur via direct contact. Therefore, risk of disease spread is related to the level of connectivity in bighorn sheep populations. We investigated population subdivision and connectivity of bighorn sheep across central Idaho at behavioral (fine) and genetic (broad) scales. We assessed fine-scale connectivity within a bighorn sheep population using radio telemetry data from 56 individuals from 2007-2013. We defined social groups of bighorn sheep using cluster analysis and estimated connectivity between these groups using a multi-state mark-recapture model. We evaluated the effects of sex, age, and season on the probability that an individual from one social group would transition into the area of another social group. We found that social groups of bighorn sheep along the lower Salmon River were well connected. While males were the primary source of connectivity between social groups, ewes also transitioned into other social groups but to a lesser degree. Rams had a 3 times higher probability of moving during the winter associated with the rut than during the summer. We employed genetic techniques to assess broad-scale connectivity across a metapopulation of bighorn sheep in Idaho using nuclear and mitochondrial DNA from 410 and 206 individuals, respectively. We defined subpopulations of bighorn sheep using a Bayesian clustering program and examined connectivity between these subpopulations using measures of genetic differentiation. We also looked at the contribution of males and females to connectivity. We found evidence for 4 subpopulations of bighorn sheep where 3 of those subpopulations were well connected. We observed some connectivity due to females but population connectivity was largely the result of male movements and dispersal. If contact is sufficient for disease transmission, then males are the most likely vector of disease spread given an outbreak at each scale.

Annual reproductive variation is the central focus of many ecological studies. Variation in reproductive success is an important vital rate to study because it can lead to inferences about population health, extinction risk, human disturbance and habitat quality. The identification of the causes of reproductive variability can help guide conservation and management efforts of a species. In Glacier National Park, Montana I studied causes of annual reproductive variation and behavioral responses to human disturbance in a breeding population of harlequin ducks (Histrionicus histrionicus). Harlequins are rare sea ducks with a Holarctic distribution and winter along rocky coast lines of North America. Females reach reproductive maturity at age 3. At this time they bond with a male that they will breed with for life. Recent band re-sighting has revealed that these ducks can live up to at least 21 years. In spring pairs migrate inland to the females natal montane stream to breed. My study focused on the breeding season from April September on Upper McDonald Creek, Glacier National Park, Montana. My objective was to study 3 potential indirect and direct sources of reproductive variation in Harlequin ducks on this breeding stream; 1) stream flow effects on annual reproductive success, 2) human presence and effects on stream patch occupancy and resource selection, and 3) carry-over effects of physiological measures of body condition, baseline corticosterone levels (primary stress hormone in birds), and integrated measures of corticosterone deposition in feathers. For my first objective I identified 4 different parameters of stream flow that accounted for 32% of the annual variation in reproductive success. I conclude that these parameters will be very sensitive to climate change, making reproduction challenging for harlequins into the future. For my second objective I found greater probability of occupancy of ducks in high human use sites and in stream patches closer to roads. I also found greater occupancy in pool habitat; surprisingly, this pool habitat also had a greater distribution close to road. I conclude from this analysis that there were no strong negative effects of human disturbance on harlequin duck occupy and resource selection, but recommend that harlequin habitat near to human use areas be monitored closely. For my third objective I found that concentrations of corticosterone deposited in feathers grown just prior to reproduction predict reproductive success for that year. I did not find any predictive value of body condition or baseline corticosterone levels. The carry-over effects that I documented in the feathers grown during the prenuptial molt indicate that is an import period that reflects reproductive decision (may be 2 month separation from feather growth to egg lay). These 3 lines of inquiry identified important sources of annual reproductive variation and will help guide management and conservation efforts. I recommend further study to better understand important resources that harlequins select for on the breeding stream and intensive study of harlequin wintering habitat, especially prenuptial molt areas.

The Kittlitzs murrelet (Brachyramphus brevirostris) is a small alcid endemic to Alaska and eastern Russia. Due to its pelagic lifestyle, researchers lack information regarding environmental conditions experienced by Kittlitzs murrelets throughout the year and how these conditions impact their physiology and vital rates. Further, unlike most seabirds, the Kittlitzs murrelet is a dispersed nester; therefore, data are limited for this species even within the breeding season. The goal of this research was to evaluate and improve the monitoring methods for the Kittlitzs murrelet throughout the year. I approached this goal from 2 different perspectives. First, I worked to clarify abundance and trend estimates that have been questioned due to uncertainty in species identification. Second, I used physiological measures to examine the relationships between stress, parental investment, breeding propensity, and environmental conditions experienced by Kittlitzs murrelets throughout the year. To address uncertainties in species identification, I conducted a field experiment to quantify misidentification and non-identification rates of Brachyramphus murrelets during abundance surveys and evaluate the impacts of covariates on each. I found that misidentification of species was rare and did not bias abundance estimates. Additionally, non-identification was common beyond observation distances of 140 m, though this depended on observer experience, murrelet behavior, and sea conditions. To understand the environmental conditions experienced by Kittlitzs murrelets throughout the year, I measured corticosterone (avian stress hormone) and prolactin (parental expression hormone) and evaluated their relationships with breeding propensity and ocean productivity metrics. Higher levels of stress during the pre-and post-breeding seasons reflected lower rates of breeding propensity in the following season. Additionally, higher stress was associated with lower sea surface temperatures during the pre-breeding season, and earlier capture dates, longer time-spans between capture and processing, and lower body mass during the late-breeding season. Prolactin positively reflected CORT during the early breeding season and sex during the late breeding season. These results emphasize the need for continued research to understand the mechanisms linking the stress physiology, foraging ecology, and breeding ecology of the Kittlitzs murrelet and other species that depend on similar resources.