Efforts to reintroduce and maintain populations of pronghorn (Antilocapra americana) to the California Central Valley, specifically the Carrizo Plain National Monument (CPNM) and the Mojave Desert (Antelope Valley) portion of Tejon Ranch, have largely been unsuccessful due to dwindling numbers of translocated animals. The objective of this study was to improve upon previous models for the CPNM using aerial survey data and then apply the model to the Tejon Ranch. Aerial survey data collected from 2000-2010 on the CPNM was used to establish “use” and “non-use” areas in the model. Model variables included vegetation type (forest, shrub, grassland, semi-desert scrub, crops, and bare areas), slope, and road density. Vegetation and road density variables were treated categorically and slope as a continuous variable. Kernel density estimation (KDE) was used to estimate utilization distributions and home ranges (Fieberg 2007). An 80% isopleth was used to define “used” and “unused” habitat areas within the study site. Binary logistic regression was used to detect correlations between habitat variables and habitat use by pronghorn. Results of the regression analysis indicated overall significance with a p-value of < 0.0001 (testing that all slopes = 0). Each habitat variable comparison was made after adjusting for the other variables (e.g., slope effects were evaluated after adjusting for road density and vegetation type) and was found to be significant. Each variable coefficient was then included in a predictive equation and entered into GIS to generate a map to predict where pronghorn would likely be observed. Similar layers were created for the Tejon Ranch and the predictive equation was run with the CPNM statistical analysis. Limited conclusions about habitat suitability on the CPNM or the Tejon Ranch can be made based on the habitat data available for this model. While slope, road density, and vegetation type are all significant habitat variables influencing pronghorn habitat use, further study is needed to understand the mechanisms driving these relationships. With additional data expansion of the current habitat suitability model would help to further define pronghorn habitat use, specifically the creation of a focused model of a particular season, life history period, or individual animal use to identify more detailed habitat use patterns.

The red-headed woodpecker is a primary cavity excavator found throughout the Eastern Deciduous Forest and parts of the Great Plains. Although widespread, the red-headed woodpecker is generally considered uncommon, with patchily distributed populations. Over the past 50 years, this species has experienced precipitous, range-wide declines. The red-headed woodpecker uses a variety of cover types to meet resource needs across the annual cycle, ranging from oak savannas and wetlands, to mature beech forests and urban parks. Given their apparent adaptability to such a wide range of habitats, causes of declines are perplexing. To understand and stem declines, recent studies have focused on quantifying this species’ habitat requirements. Most of these studies have focused on a single cover type, often open forests, during the breeding season. However, effective management requires comprehensive knowledge of red-headed woodpecker habitat needs in a variety of cover types across the annual cycle. My thesis seeks to address this knowledge gap. I studied red-headed woodpecker habitat selection during both the breeding and non-breeding seasons at Fort A.P. Hill (FAPH) in Caroline County, Virginia. FAPH contains a variety of cover types that red-headed woodpeckers are known to use for breeding and overwintering, including: wetlands, open forests and closed forests. In Chapter 1, I investigated winter roost-site selection of red-headed woodpeckers in a burned forest stand. My study was the first to quantify winter habitat selection for this species. My aim was to identify variables driving winter roost-site selection at two relevant spatial scales, and estimate their parameter weights using logistic regression. I found that red-headed woodpeckers preferred habitat around the roost tree that contained a higher basal area of snags and mast-producing trees. They differentially selected roost trees based on taxon and decay state. My results indicate that managers should adopt practices that promote snag generation and retention, and mature oak recruitment. In chapter 2, I focused on red-headed woodpecker breeding season habitat requirements, as many other studies have done. However, unlike other studies that investigated habitat selection within a single cover type, I found and characterized nest-sites in three distinct cover types (wetlands, closed forests, open forests). I used a comparative approach to identify cover-type specific nest-habitat thresholds at the landscape, patch and tree scales using boosted regression trees (BRT). Although models at the landscape scale inadequately discriminated between nest and available sites, models at the patch and tree scales achieved excellent discrimination ability. I found that red-headed woodpeckers are consistent in their preference for a number of habitat features at the patch (high medium/large snag density, open canopy) and tree (large diameter tree with less bark) scales, irrespective of cover type context. However, I also found cover-type specific habitat preferences at the patch scale, indicating red-headed woodpeckers are flexible in their selection of features surrounding the nest and responsive to the broader habitat context. My findings suggest that there are a number of habitat features that facilitate breeding for red-headed woodpeckers generally, and management that promotes these features will be effective in a variety of habitat contexts. They also indicate that management can be tailored to provide the most suitable habitat for each of these three commonly used cover types. Together, Chapters 1 and Chapter 2 expand our knowledge of this declining keystone species’ habitat needs across the full annual cycle. But there is still much to know. The choices of habitat selection have consequences. Determining the conditions under which habitat features function to either help or harm populations is a necessary next step. While not a part of this thesis, I am currently investigating the factors that drive nest success among cover types, linking breeding-site selection to population dynamics. I also have behavioral data that will help reveal the mechanisms that either facilitate or constrain the exploitation of food resources across cover types. Finally, the red-headed woodpecker is a facultative migrant that often shifts habitat associations to take advantage of seasonally available resources. Data from my point count surveys—conducted over two successive winter and summer seasons—allow for development of dynamic occupancy models. Modeling shifts in occupancy across seasons will show the habitat factors underlying seasonal shifts. Site-specific differences in colonization, extinction and frequency of occupancy, within seasons but across years, will further our understanding of what constitutes habitat quality for this species, in both the breeding and non-breeding seasons.

Animal populations are limited by their environment and interactions with one another, the latter proportional to density. How density-dependent mechanisms regulate populations is poorly understood, particularly for migratory animals. Winter, or non-breeding, mechanisms remain particularly poorly understood for almost all migratory bird species. This dissertation tested the hypothesis that American Redstarts (Setophaga ruticilla) are regulated both within and between habitats in the winter by two mechanisms, a crowding effect and a buffer effect. As population size increases, crowding increases competition for space and resources and more individuals are relegated to lower quality habitats and forced into a transient behavioral strategy, which buffers high quality habitats from negative feedback of density. My study was carried out in Jamaica, where redstarts occupy diverse habitats. I found that population size varied among habitats, but accounting for both territorial and transient individuals was critical for accurate assessment of this variation. Ecological conditions drive differences in habitat suitability and redstart density at multiple spatial scales. Regionally, redstart survival, density, and numbers of transient individuals distinguish inland from coastal populations, consistent with differences in ecological conditions (e.g. rainfall). Locally, timing of spring departure, as well as age and sex structure distinguish neighboring habitats, consistent with increased competition for food. When population size increased over the years of this study, changes in local density were similar among habitats, and thus not the result of a buffer effect. However, increasing densities decreased food availability, which corresponded with negative feedback on departure timing and territorial behavior, i.e. more transients, in poorer habitats. This supported a crowding effect on spatial behavior (territoriality) and late-winter condition of individuals relegated to low suitability habitats. High quality inland habitats appear to buffer individuals from the effects of changing population abundance, as well as ecological conditions, evidence of a regional buffer effect. / acase@tulane.edu

Driving into Yellowstone National Park for the first time is a moving experience. Gazing over the sweeping landscapes, seeing a geyser erupt 80 feet into the air, and having your first ‘wildlife encounter’, whether that be a 2 ton bull bison aggressively wallowing on his dirt mound, snorting and kicking up dust, or watching a pack of 6 wolves move through a valley off in the distance, pausing to howl in search of their companions. Yellowstone staff wishes to manage our park in a way that preserves these remarkable experiences. In order to effectively manage this dynamic ecosystem, it is critical to thoroughly understand how different animal and plant species interact with each other and their environment. Wolves were reintroduced to Yellowstone in 1995-1997 and park researchers and managers are still trying to understand how their presence impacts the ecosystem. In Yellowstone, wolves primarily prey on elk; however, predation on bison has started to increase in recent years. We still know little about how wolves hunt bison and what impacts wolves have had on how bison use their environment. The objective of this study was to better understand the behavioral and ecological interactions of wolves and bison, the most dangerous prey for wolves in North America. Since reintroduction, researchers have collected data on how wolves hunt both elk and bison. I used these data to understand 1) the conditions that allow wolves to capture their most dangerous prey, bison, 2) whether wolves have started preying on bison more often as the bison population increased, and 3) whether wolf reintroduction has limited bison use of Yellowstone’s most extreme high-elevation winter range. Finally, I collaborated with ecologists in Scandinavia to determine how wolf predation was affected by a competitor, the brown bear. My study adds to the current body of work addressing the effects of wolf reintroduction in Yellowstone. This research is unique because it focuses on wolf bison interactions, about which little is known in this system. This research also sheds light on the behavioral relationships at play in a special type of predator-prey interaction: predators that hunt dangerous prey

Bacterial source tracking (BST) methods often involve the use of phenotypic or genotypic fingerprinting techniques to compare indicator bacteria such as Escherichia coli isolated from unknown sources against a library of fingerprints from indicator bacteria found in the feces of various known source animals. The predictive capability of a library is based in part on how well the library isolates reflect the true population diversity of indicator bacteria that can potentially impact a water body. The purpose of this study was to compare the behavior of E. coli population structures in the feces of humans, beef cattle and horses across different parameters. Ribotyping and antibiotic resistance analysis were used to "fingerprint", or subtype E. coli isolates. Significantly greater diversity was observed in the E. coli population of horses compared to the human or beef cattle sampled. Subtype sharing between individuals from all host categories was infrequent, therefore the majority of E. coli subtypes were sampled from a single individual. The dominant E. coli populations of nine individuals (three per host source category) were monitored over time, which demonstrated that E. coli subtypes within a host individual vary on a monthly time frame, and an increase in the frequency of subtype sharing was noted between individuals within the same source group over time. The E. coli population of a single human that had just finished antibiotic treatment was studied on a daily basis for one month. The loss of an E. coli subtype with high antibiotic resistance was observed over time, however there was a single dominant E. coli subtype that was present at every sampling event during the entire month. Geographic distinctiveness of E. coli populations was investigated by sampling four herds located in different geographical regions. We observed that E. coli populations are not geographically distinct, but are somewhat individual-specific, as most E. coli isolates had a subtype that was found in a single individual. This study defines factors that should be considered when constructing a successful BST library, and suggests that E. coli may not be the appropriate indicator organism for BST.

Biological management of populations plays an indispensable role in all areas of population biology. In deciding between possible management options, one of the most important pieces of information required by population managers is the likely population status under possible management actions. Population dynamic models are the basic tool used in deriving this information. These models elucidate the complex processes underlying the population dynamics, and address the possible consequences/merits of management actions. These models are needed to guide the population towards desired/chosen management goals, and therefore allow managers to make informed decisions between alternative management actions. The reliability that can be placed on inferences drawn from a model about the fate of a population is undoubtedly dependent on how realistically the model represents the dynamic process of the population. The realistic representation of population characteristics in models has proved to be somewhat of a thorn in the side of population biologists. This thesis focuses in particular on ways to represent environmental stochasticity and density dependence in population models. Various approaches that are used in building environmental stochasticity into population models are reviewed. The most common approach represents the environmental variation by changes to demographic parameters that are assumed to follow a simple statistical distribution. For this purpose, a distribution is often selected on the basis of expert opinion, previous practice, and convenience. This thesis assesses the effect of this subjective choice of distribution on the model predictions, and develops some objective criteria for that selection based on ecological and statistical acceptability. The more commonly used distributions are compared as to their suitability, and some recommendations are made. Density dependence is usually represented in population models by specifying one or more of the vital rates as a function of population density. For a number of reasons, a population-specific function cannot usually be selected based on data. The thesis develops some ecologically-motivated criteria for identifying possible function(s) that could be used for a given population by matching functional properties to population characteristics when they are known. It also identifies a series of properties that should be present in a general function which could be suitable for modelling a population when relevant population characteristics are unknown. The suitability of functions that are commonly chosen for such purposes is assessed on this basis. I also evaluate the effect of the choice of a function on the resulting population trajectories. The case where the density dependence of one demographic rate is influenced by the density dependence of another is considered in some detail, as in some situations it can be modelled with little information in a relatively function-insensitive way. The findings of this research will help in embedding characteristics of animal populations into population dynamics models more realistically. Even though the findings are presented in the context of slow-growing long-lived animal populations, they are more generally applicable in all areas of biological management.

Spatial heterogeneity of the environment, as measured by floral diversity, composition and structure, is known to influence the distribution and diversity of invertebrates. Heterogeneity brought about by anthropogenic disturbance may be a threat to invertebrate diversity. This thesis investigates the impacts of vegetation heterogeneity at a range of scales on the diversity of invertebrate populations in modified high-altitude indigenous grasslands on the Rock and Pillar Range, Central Otago. Invertebrates were sampled in and on the edges of snow tussock fragments to assess whether species richness increased systematically with fragment area. Invertebrate composition was poorly related to fragment area, plant composition and environmental variables. Taxon richness, abundance and/or diversity for three invertebrate groups increased as fragment area decreased, perhaps reflecting an influx of species from the surrounding matrix. For snow tussock leaf invertebrates in autumn, richness and abundance were at least two times lower in tussocks exposed to the wind than those in the centre of fragments, suggesting selection of habitat may be based on microclimatic characteristics. Invertebrates were sampled from the bases of tussocks after they were clipped to simulate three levels of vertebrate grazing. Invertebrate community composition differed between sites and sampling dates but was unaffected by clipping treatment. At the higher altitude site invertebrate abundance was 1.45 times greater and Shannon-Wiener diversity (H�) 1.22 times lower than at the lower altitude site. The latter sampling date had higher abundance (2.12 times) and taxon richness (1.14 times) than the earlier date. Pitfall-trapped invertebrates in cushionfield, herbfield and snow tussock differed in community composition and often by taxon richness, abundance and diversity. Across habitats, plant composition, plant diversity and some environmental variables were correlated with invertebrate variables, but could not be separated from vegetation type. The invertebrates collected in the course of the study are listed. Four Phyla, eight Classes, 24 orders and over 300 taxa were recorded. Almost all taxa are endemic and many have limited distributions and/or are undescribed. A species list is provided with collection altitude, method and habitat type. Invertebrate assemblages from sites differing in altitude, vegetation type and level of habitat modification on the Rock and Pillar Range are compared. Sites differed in species composition and rank orders of abundance and richness. At lower elevations, invertebrate richness was at least 25% less, and standardised trap abundance at least 44% less, than that at the highest elevation. Richness and abundance of exotic invertebrates decreased with increasing altitude. This thesis highlights several points concerning the study of grassland invertebrates and heterogeneity on the Rock and Pillar Range. First, there are differences in invertebrate assemblages at a range of scales. Conserving invertebrate diversity will therefore require altitudinal sequences and different habitat types, including disturbed areas. At high elevations, tussock habitat may be disproportionately important due to its relative rarity. Second, the effects of disturbance on invertebrates were only visible at large spatial scales. Third, there is a paucity of research on New Zealand invertebrates, especially in regard to terrestrial disturbance, which has resulted in a shortfall of biological, distributional, taxonomic and ecological knowledge.

Understanding complex population dynamics is critical for both basic and applied ecology. Analysis of genetic data has been promoted as a way to reconstruct recent non-equilibrium processes that influence the apportioning of genetic diversity among populations of organisms. In a structured-deme context, where individual populations exist as geographically distinct units, island biogeography theory and metapopulation genetics predict that the demographic processes of extinction, colonization, and migration will affect the magnitude and rate of genetic divergence between demes. New methods have been developed to attempt to detect the influence of non-equilibrium dynamics in structured populations. I challenged two of these methods: decomposed pairwise regression and allele frequency analyses, using simulations of genetic data from structured demes. I found that these methods suffer from a high type II error rate, or failure to reject the null hypothesis of mutation-migration-drift equilibrium for demes experiencing historical demographic events. In addition, island biogeography and metapopulation ecology predict that at equilibrium, some species in a patch will be recent colonists, as equilibrium indicates a balance between colonization of the patch and extinction from the patch. Recent colonists are unlikely to have reached population mutation-migration-drift equilibrium; hence a paradox exists between population and community level equilibrium. I used nuclear and mitochondrial genetic data from populations of two species of reptiles from the Turks and Caicos Islands, British West Indies to test for patterns of equilibrium vs. non-equilibrium. I found unexpected shallow genetic divergence in the Turks Island boa (Epicrates chrysogaster), indicating that this species likely existed as a panmictic population prior to the inundation of the Turks and Caicos Banks during the last glaciation. As the initial methods I tested using simulations proved unreliable, I used methods from phylogeography, landscape genetics, and island biogeography to detect significant non-equilibrium dynamics in the Turks and Caicos curly-tailed lizard (Leiocephalus psammodromus), finding evidence for high levels of biased gene flow. I propose that studies of genetic diversity on island archipelagos use tools from all three of these methods to evaluate empirical data in the context of equilibrium and the null hypotheses offered by island biogeography and population genetics theory. I frame the results both in the context of conservation and an understanding of equilibrium and non-equilibrium dynamics.

Because of increasing frequency of bear sightings, vehicle collisions, and nuisance incidents in coastal South Carolina, the South Carolina Department of Natural Resources is developing a comprehensive black bear management plan. However, no reliable estimates of population abundance or density are available. I used genotypes of black bears determined from hair samples collected in Lewis Ocean Bay and Carvers Bay to estimate population abundance and density. I obtained hair samples from snares during 8 weekly sampling periods in 2008 and 2009. I used Huggins closed population models to estimate abundance and spatially explicit capture- recapture models to estimate density. Based on model averaging, black bear abundance was 30 (SE = 9.3) on Carvers Bay and 42 (SE = 5.4) on Lewis Ocean Bay. Model-averaged density was 0.037 bears/km2 (SE = 0.003) for Carvers Bay. For Lewis Ocean Bay, population densities were much higher: 0.307 bears/km2 (SE = 0.025). I extrapolated the density estimates to the upper coastal region of South Carolina, using logistic regression to weight density based on similarity of the regional landscape with the 2 study areas. Predicted bear densities were low throughout the coastal region but several areas centered on more productive habitats (e.g., Carolina Bays, pocosin) and public lands (e.g., Francis Marion National Forest, Lewis Ocean Bay) had high densities. I also sampled an area in North Carolina and assessed genetic structure among the 3 areas. Based on heterozygosity, genetic distance, and genetic assignment, I found no evidence of historic or recent barriers to gene exchange among the 3 sampled populations. However, demographic connectivity may be a concern for areas such as Lewis Ocean Bay, which is surrounded by highways and development. If the goal is to maintain current black bear densities in those areas, maintaining connectivity with other habitat areas and mitigating impacts of highways would be important. The regional map of potential black bear density may be useful to identify areas that should be surveyed for occupancy or where additional studies may be conducted (e.g., Francis Marion National Forest).

In 1992, the Louisiana black bear (Ursus americanus luteolus) was granted threatened status under the Endangered Species Act primarily because of extensive habitat loss and fragmentation. Currently, the Louisiana black bear is restricted to 3 relatively small, disjunct breeding subpopulations located in the Tensas River Basin of northeast Louisiana, the upper Atchafalaya River Basin (ARB) of south-central Louisiana, and coastal Louisiana. The 1995 Recovery Plan mandates research to determine the viability of the remaining subpopulations. I conducted a capture-mark-recapture study during 2007–2009 to estimate population parameters for the ARB bear subpopulation by collecting hair samples (n = 2,977) from 115 barbed-wire hair traps during 8 1-week periods each summer. DNA was extracted from those hair samples and microsatellite genotypes were used to identify individuals. I analyzed encounter histories using the Huggins full heterogeneity estimator in a robust design framework in Program MARK. I compared candidate models incorporating heterogeneity, behavior, and time effects on capture using information-theoretic methods. I directly estimated apparent survival, temporary emigration, probability of capture and recapture, and probability of belonging to 1 of 2 mixtures; population abundance was a derived parameter. Apparent survival was 0.91 (SE = 0.06) and did not vary by gender or year. There was some evidence of temporary emigration for males only (0.10, 95% CI = 0.001–0.900). I modeled capture probabilities with a 2-mixture distribution for both male and females. Overall mean weekly capture probability was 0.12 (SE = 0.03) and 0.25 (SE = 0.04) for males and females, respectively. Recapture rates indicated a positive behavioral response to capture. Model-averaged mean annual abundance was 56 (SE = 4.5, 95% CI = 49–68). I calculated population density using spatially-explicit maximum-likelihood methods; model-averaged density was 0.15 bears/km2 (SE = 0.03). My results updated previous abundance estimates for the ARB bear subpopulation and will be used in a population viability analysis to determine if recovery criteria for the Louisiana black bear have been met.