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The goals of captive breeding programs for endangered species include preserving genetic diversity and avoiding inbreeding. Typically this is accomplished by minimizing population mean kinship; however, this approach becomes less effective when errors in the pedigree exist and may result in inbreeding depression, or reduced survival. Here, both pedigree- and DNA-based methods were used to assess inbreeding depression in the critically endangered Attwater’s prairie-chicken (Tympanuchus cupido attwateri). Less variation in the pedigree-based inbreeding coefficients and parental relatedness values were observed compared to DNA-based measures suggesting that errors exist in the pedigree. Further, chicks identified with high parental DNA-based relatedness exhibited decreased survival at both 14- and 50-days post-hatch. A similar pattern was observed in later life stages (> 50 days post-hatch) with birds released to the wild; however, the pattern varied depending on the time post-release. While DNA-based inbreeding coefficient was positively correlated with mortality to one month post-release, an opposite pattern was observed at nine months suggesting purging of deleterious alleles. I also investigated whether immunocompetence, or the ability to produce a normal immune response, was correlated with survival; however, no significant correlation was observed suggesting that inbreeding was a more important factor influencing survival. Pairing individuals for breeding by minimizing DNA-based parental relatedness values resulted in a significant increase in chick survival. This study highlights the importance of using DNA-based methods to avoid inbreeding depression when errors exist in the pedigree.

Payments for ecosystem services (PES), or conservation incentives, are an increasingly popular approach to encouraging natural resources conservation on private lands. The goal of PES approaches is to motivate conservation by private landowners that would not otherwise take place by providing an economic incentive. To achieve this goal, incentive programs must be available to landowners who can provide the desired services; supportive policy structures must be in place; landowners must be willing to participate as sellers of ecosystem services; and the program itself must have an institutional structure that effectively regulates the production, sale, and maintenance of targeted ecosystem services. This dissertation uses a combination of case study and comparative research methods to develop new knowledge and tools for assessing each of these necessary conditions for success. The potential development of an incentive program to conserve habitat for endangered jaguars in southern Arizona and southwestern New Mexico is used as a case study to understand the attitudes of ranchers toward participation in PES programs and related policies and regulations. Results show that ranchers have strong intrinsic conservation motivations unrelated to economic incentives, coupled with significant concerns about the impacts of government regulations that could accompany participation in a PES program. Comparative research of the institutional structures of existing PES programs is carried out using the Institutional Analysis and Development framework. Focusing on water quality trading, one of the most common types of PES program, a classification system for PES program institutional arrangements is developed and the utility of the classification system for analyzing institutional diversity is demonstrated. Together, the case study and comparative research provide a means of linking empirical assessment of PES governance models with the preferences of targeted participants, increasing the likelihood of successful conservation outcomes.

In the management of threatened and endangered species, informed population estimates are essential to gage whether or not recovery goals are being met. In the case of Pacific salmonids, this evaluation often involves sampling a small subset of the population and scaling up to estimate larger distinct populations segments. This is made complicated by the fact that fish populations are not evenly distributed along riverscapes but respond to physical and biological stream properties at varying spatial extents. We used rapid assessment survey methods and the River Styles classification to explore fish-habitat relationships at a continuous network scale. Semi-continuous surveys were conducted across nine streams in the upper Middle Fork John Day River watershed and increased the number of sites surveyed eight-fold over other monitoring methods within the watershed. Using this increased sample size and continuous habitat metrics we improved watershed-wide steelhead (Oncorhynchus mykiss) abundance models. We first validated the distinctions among River Styles through a classification analysis using physical metrics measured at the rapid assessment sites. Overall classification accuracy, using a combination of reach and landscape scale metrics, was 88.3% and suggested that River Style classification was identifying variations in physical morphology within the watershed that was quantifiable at the reach scale. Leveraging the continuous River Styles classification of physical habitat and a continuous model of primary production improved the prediction of steelhead abundance across the network. Using random forest regressions, a model that included only habitat metrics resulted in R2 = 0.34, while using the continuous variables improved the model accuracy greatly to R2 = 0.65. Random forest allowed for further investigation into the predictor variables through the analysis of the partial dependence plots and identified a gross primary production threshold, below which production might be limiting steelhead populations. This method also identified the rarest River Style surveyed within the watershed, Confined-Valley Step Cascade, as the morphology that had the largest marginal effect on steelhead. The inherent physical properties and boundary conditions unique to each River Style has the potential to inform fish-habitat relationships across riverscapes and improve abundance estimates on a continuous spatial scale.

Cavity-nesting communities are structured by the creation of and competition for cavities as nest-sites. Viewing these communities as interconnected webs can help identify species interactions that influence community structure. This study examines cavity-nesting bird community interactions within the fire-maintained longleaf pine (Pinus palustris) ecosystem at Eglin Air Force Base, Florida. In chapter 1, I provide a background review of the ecology of my study system. In chapter 2, I use nest webs to depict the flow of cavity-creation and use at Eglin. I identified 2 webs into which most species could be placed. One web contained 6 species associated with pines. The second web contained 5 species associated with hardwoods. Red-cockaded woodpeckers (Picoides borealis) and northern flickers (Colaptes auratus) created most cavities used by other species within this community. In chapter 3, I describe snag densities and nest-site selection of the cavity-nesting bird community at Eglin. Large, mature pine snags were abundant, exceeding other reported densities for southern pine forests. Pine snags were heavily-used, despite the abundance of available red-cockaded woodpecker cavities in living pine. Hardwood snags accounted for 10% of nests found, and were used by 12 of 14 species. Diameters of nest-trees and available snags were below the range of optimal nest-snag diameters reported in other studies, indicating the need for site-specific snag management guidelines. In chapter 4, I combine a study of basic ecological principles with endangered species management to examine interactions within the cavity-nesting bird community at Eglin. I used a nest web to identify a potential indirect interaction between the red-cockaded woodpecker and large secondary cavity-nesters, mediated by the northern flicker. I used structural equation modeling to test a path model of this interaction. By experimentally manipulating cavity availability, I blocked links described in the model, confirming cavity creation and enlargement as mechanisms that influence this indirect relationship. I demonstrated that a red-cockaded woodpecker cavity-management technique could disrupt this indirect relationship by affecting northern flicker behavior, and provided an empirical example of how, in interactive ecological communities, single-species management can have indirect effects on non-target species. / Ph. D.