Mountain Scholar :: Browsing by Author "Hobbs, N. Thompson, committee member"

Browsing by Author "Hobbs, N. Thompson, committee member"

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Open Access
An alternate state approach to range management in the sagebrush steppe
(Colorado State University. Libraries, 2011) Kachergis, Emily, author; Fernandez-Gimenez, Maria Edith, advisor; Rocca, Monique Elisabeth, 1974-, advisor; Hobbs, N. Thompson, committee member; Knapp, Alan K., 1956-, committee member
Describing and predicting sudden shifts between alternate states in ecosystems is a frontier in ecology with important implications for natural resource management and human well-being. The range profession has recently adopted an approach to land management decision-making based on alternate state theory. The Natural Resource Conservation Service and partners are creating state and transition models (STMs), conceptual models that describe shifts in ecosystems, for many types of land throughout the US. Motivated by this national STM-building effort, this dissertation has two practical objectives: 1) to create data-driven STMs that describe sagebrush steppe ecosystem response to management, and 2) to develop guidelines for STM creation. A third objective grew out of the need to create theoretically accurate STMs: to determine whether spatial and temporal patterns of vegetation in northwest Colorado sagebrush steppe are consistent with predictions of alternate state theory. The first chapter introduces this work with a review of alternate state theory and how it is applied in constructing STMs. I conducted an observational study of sagebrush steppe response to management practices and ecological disturbances on two soil types in the lower Elkhead watershed. The second chapter examines plant species composition as an indicator of alternate states, a test of the current approach to building STMs. The third chapter investigates whether areas with different structure also differ in function, as predicted by alternate state theory. The fourth chapter compares trait-based group composition to species composition as an indicator of alternate states. From these chapters, I conclude that there are large, management-relevant differences in species composition within environmentally similar areas and that many of these differences are related to site history, as would be expected if these represent alternate states. The Indicators of Rangeland Health show that some states defined by species composition are associated with unique processes that may serve as positive feedback mechanisms which maintain alternate states. Relationships between species composition, processes and environmental gradients suggest that environmental variation may make some transitions between states more likely and should be acknowledged in STMs. Multiple-trait based group composition identifies many of the same potential states and transitions as species composition, but is also sensitive to some different management practices. The Indicators of Rangeland Health and plant traits are simple additions to current STM-building methods that can improve and expedite STM creation. In the final chapter, I describe long-term sagebrush steppe dynamics based on 50 years of monitoring data from the upper Elkhead watershed and evaluate evidence for alternate states. Gradual changes in composition after spraying and the steady increase of a non-native grass suggest that this high-elevation sagebrush steppe ecosystem does not experience sudden shifts between alternate states. I conclude that the alternate state approach to range management shows promise for describing management-relevant ecosystem dynamics and organizing current knowledge. Given the equivocal evidence supporting predictions of alternate state theory for Elkhead watershed sagebrush steppe, further research should determine which aspects of alternate state theory must be confirmed to create useful STMs. In addition, long-term monitoring, modeling, and experiments are needed to validate and update models as we learn more about the sagebrush steppe.
Open Access
An eco-epidemiological approach to management of tuberculosis in free-ranging and captive wildlife
(Colorado State University. Libraries, 2018) Rosen, Laura Elizabeth, author; Olea-Popelka, Francisco J., advisor; Miller, Michele A., committee member; Huyvaert, Kathryn P., committee member; Hobbs, N. Thompson, committee member
Tuberculosis (TB) is a disease of global importance affecting millions of humans, livestock, and wildlife. Control and eventual eradication of TB depends on dedicated management actions for all species. Accurately diagnosing TB can be challenging in wildlife species, for which validated tests may be unavailable or of limited sensitivity or specificity. Managing TB in wildlife poses additional difficulties, requiring considerable time and resources to implement at an appropriately broad scale. Each unique ecosystem where TB occurs requires management interventions designed to meet the area's conservation, ecological, social, and financial needs. In this dissertation, I explored the diagnosis and management of tuberculosis in wildlife in three different settings: free-ranging European badgers (Meles meles) in Ireland, working African elephants (Loxodonta africana) in Zimbabwe, and captive African and Asian elephants (Elephas maximus) in North America. Badgers are a reservoir of bovine TB in Ireland, while captive elephants around the world are at risk of TB from their human handlers. Badgers have historically been managed by culling, but there is a current transitioning to vaccination as the primary management tool. In contrast, captive elephants in high-resource settings are typically treated for TB upon diagnosis, although this option may be limited in low-income countries. The first objective of this research was to assess the impact of environmental factors in management of TB over three different studies. I explored how biotic and abiotic factors influence trapping success of badgers being managed for bovine TB in Ireland. In a second study of badgers, I estimated density of a population undergoing vaccination in relation to environmental variables and prior management history. Underlying badger density is an important driver in the TB disease dynamics between cattle and badgers, and can be used in predictions about and assessment of outcomes under vaccination. Finally, I examined potential risk factors for TB seropositive status in working African elephants in Zimbabwe, and identified unique potential exposures from the environment. The second objective of this dissertation was to study the performance of diagnostic tests in a novel setting and interpret the results in the context of exposures within the ecosystem. This study employed two serological tests, STAT-PAK and DPP, for the first time in working African elephants in a range country. I interpreted the results suggestive of exposure to mycobacteria in some elephants based on possible interactions with the complex community of humans, livestock, wildlife, and mycobacteria. The third objective of this dissertation was to develop recommendations for TB management programs based on surveys, capture data, and consideration of individual, population, and community factors. The results from our badger trapping study in Ireland formed the basis of suggested conditions under which vaccine delivery can be increased, because captures are most likely. We used mark-recapture data to estimate badger density in a vaccination area, which adds an important dimension to the Irish TB management program that includes badgers and cattle. Population density is an important factor in pathogen transmission and estimating density using these methods may be a priority for other wildlife populations being managed for TB. Our study of TB treatment in elephants provided a compilation of empirical data for elephant managers and veterinarians to inform clinical decision making. It also underscores the need for improved diagnostics to more confidently identify when animals are no longer infectious. For working African elephants, we documented other wildlife species with host potential on and around facilities, and considered these as possible sources for mycobacterial transmission. Our management guidelines for TB prevention specifically include measures to reduce direct and indirect contact with potential host species. Management of TB across humans and animal species remains a challenging prospect. A One Health approach that incorporates data and techniques across disciplines to build a complete picture of disease control is ideal for TB in wildlife. I drew from ecology and epidemiology to implement a holistic approach to diagnosing and managing TB in species of conservation concern, provide insight into the challenges of diagnosing and managing TB in free-ranging and captive wildlife, describe the benefits of a transdisciplinary approach, and expose areas in need of further research.
Open Access
Bacterial coldwater disease investigations
(Colorado State University. Libraries, 2021) Avila, Brian Walter, author; Winkelman, Dana L., advisor; Huyvaert, Kathryn P., committee member; Fetherman, Eric R., committee member; Hobbs, N. Thompson, committee member
To view the abstract, please see the full text of the document.
Open Access
Barriers to establishment and growth of cottonwoods in Yellowstone National Park's northern range
(Colorado State University. Libraries, 2012) Rose, Joshua Robert, author; Cooper, David J., advisor; Hobbs, N. Thompson, committee member; Hufbauer, Ruth A., committee member
Riparian ecosystems play a vital role in water storage, sediment retention, nutrient and contaminant removal, and wildlife habitat in western North American landscapes. Cottonwood (Populus spp.) trees form the principle riparian forest type in the semi-arid western United States and therefore understanding their abundance and processes affecting establishment and survival are critical. Within Yellowstone National Park (YNP) herbivory by ungulates shapes ecosystem structure and function of riparian forests. However, our understanding of the interactions between herbivores and cottonwoods is largely from studies of domestic livestock grazing and may not reflect free ranging herds of wild ungulates. In this study I quantify the influence of stream hydrologic regime and herbivory on cottonwood establishment and growth along three rivers in Yellowstone's northern range. My research addresses three questions: 1) What is the current distribution and composition of cottonwood communities? 2) What is the relative influence of ungulates and hydrologic regime on cottonwood establishment? 3) Does herbivory by ungulates limit cottonwood height? Approximately 500,000 of the 1.9 million cottonwoods in Yellowstone established between 1996 and 1998, the years immediately following wolf (Canis lupus) reintroduction to YNP. Recruitment was driven by the largest sequence of peak stream flows in the 20 th century. The flows caused large scale channel changes, and provided suitable habitat for cottonwood seedling establishment and survival. The Lamar River cottonwood forest appears to regenerate following infrequent to rare large peak flow events as occur on many streams in western North America. However, Soda Butte Creek and the Gardner River cottonwoods exhibited nearly annual recruitment similar to other low-order montane streams. For the three rivers studied, over 92% of cottonwoods occur along the Lamar River. After the 1997 flood, establishment has been nearly continuous on the Lamar River with the resulting cottonwood biomass exceeding herbivore demand. However, even with their relatively low consumption rates bison are able to remove a significant proportion of total cottonwood production in the study areas and limit plant height and forage available to wintering elk. In the absence of human perturbation of bison populations, either in pre-history or today, bison and other ungulates shape their environment. Future investigation of how these species shape the structure of their environment will serve to inform management decisions and educate park visitors on habitat dynamics in a multi-herbivore system.
Open Access
Behavioral response of mule deer to natural gas development in the Piceance Basin
(Colorado State University. Libraries, 2015) Northrup, Joseph M., author; Wittemyer, George, advisor; Anderson, Charles R., Jr., committee member; Hobbs, N. Thompson, committee member; Hooten, Mevin B., committee member
To view the abstract, please see the full text of the document.
Open Access
Causes and management of exotic riparian plant invasion in Canyon de Chelly National Monument, Arizona
(Colorado State University. Libraries, 2009) Reynolds, Lindsay Vail, author; Cooper, David J. (David Jonathan), 1952-, advisor; Stohlgren, Thomas J., committee member; Wohl, Ellen E., 1962-, committee member; Hobbs, N. Thompson, committee member; Brown, Cynthia Stokes, committee member
The ecological, economic and social impacts of invasive plant species on native plant communities have stimulated broad concern among researchers, land managers and the general public. Riparian areas are of particular concern because they are critical to regional biodiversity despite covering a small percentage of the landscape. Controlling harmful invasive plants is an important challenge for land managers and understanding how to effectively remove exotic species is essential to managing native ecosystems such as riparian areas. In the southwestern United States (U.S.), the most dominant riparian plant invaders are the woody species tamarisk (Tamarix ramosissima Ledebour, T. chinensis Loureiro, and their hybrids) and Russian olive (Elaeagnus angustifolia L.). Tamarisk and Russian olive have invaded riparian habitats throughout Canyon de Chelly National Monument in northeastern Arizona. The goals of my research were to: 1) describe the history and mechanisms of exotic plant invasion into Canyon de Chelly, 2) understand the niche space requirements of tamarisk, Russian olive and native cottonwood in terms of light and water and determine if tamarisk and cottonwood are facilitating the invasion of Russian olive, and 3) describe response of the riparian ecosystem to exotic plant removal and determine the effectiveness of two different removal strategies. My results from analyzing the history of invasion showed that although plantings and river regulation by dams probably played a role in tamarisk and Russian olive invasion into Canyon de Chelly, these species required hydroclimatic drivers and stream bed adjustments for wide-spread establishment. Controlled experiments and field surveys in my second research study demonstrated that Russian olive is exploiting empty niches along wide gradients of water and light availability in southwestern riparian ecosystems. However, Russian olive invasion does appear to be limited by seed dispersal. Finally, I found that both cut-stump and whole plant removals similarly reduced exotic species cover and increased native species cover after two years. Both removal methods also reduced aerial seed rain inputs of tamarisk seeds, cut-stump removals increased available nitrogen near dead Russian olive boles within two years of removal, and both treatments seem to have no effect on ground water levels. This research helps guide the management of riparian plant communities in Canyon de Chelly, across the southwestern U.S., and informs our understanding of exotic plant invasions.
Open Access
Disentangling drivers of colonization success in laboratory and natural systems
(Colorado State University. Libraries, 2017) Vahsen, Megan, author; Hufbauer, Ruth, advisor; Brown, Cynthia, committee member; Hobbs, N. Thompson, committee member
Understanding why colonizing populations successfully establish is important for predicting dynamics of invasive species. Propagule pressure, or the number of individuals in a founding group, is considered the most consistent predictor of establishment success, however, there remains considerable variance around predictions that demography alone cannot explain. The identity of individuals within a founding group (e.g. level of pre-adaptation to the recipient environment, diversity) as well as how individuals are introduced (e.g. frequency and timing of discrete introduction events) can influence establishment. The relative importance of these factors is unclear, and could vary across species and environmental contexts. To address these inconsistencies, we conducted two experiments: one with Tribolium castaneum (red flour beetle) populations maintained in controlled laboratory conditions, and one with Bromus tectorum (cheatgrass) founding populations introduced to a natural environment. For the Tribolium experiment, we varied the level of prior adaptation, diversity, and introduction frequency and timing for groups of eggs colonizing in a novel environment across three levels of propagule pressure (n = 15, 30, 60). Founding groups that were larger and more adapted to the novel environment survived the founding event better than smaller and less adapted groups. Further, we found that a high frequency of smaller introductions reduced initial survival. After a generation of mating, establishment success was driven predominantly by adaptation to the novel environment and diversity of founders. In the second experiment, we introduced groups of B. tectorum seeds at a constant propagule pressure (n = 32) to a common garden in Colorado, varying in source diversity (1, 2, 4, 8, or 16 source populations) and source region (Colorado = pre-adapted or Nevada = unadapted). We evaluated establishment success by deriving the number of seeds produced by each founding group after one generation of growth and reproduction using a hierarchical Bayesian model. We found that increasing source diversity increased the number of seeds produced per founding group, but source region did not influence establishment success. Results from these experiments particularly speak to the context-dependency of the importance of pre-adaptation and diversity in predicting establishment success. This suggests that propagule pressure alone is not enough to explain why founding populations establish.
Open Access
Evaluating habitat suitability and connectivity for the endangered northernmost population of jaguars (Panthera onca)
(Colorado State University. Libraries, 2020) Landau, Vincent A., author; Noon, Barry R., advisor; Theobald, David M., advisor; Hobbs, N. Thompson, committee member
Understanding the distribution of wildlife habitat as well as landscape connectivity for threatened or endangered wildlife populations provides valuable information for conservation planning efforts. The northernmost population of jaguars (Panthera onca) is threatened with extinction, and has been extirpated from much of its historic range in the United States due to habitat loss/fragmentation, hunting, and poaching. Recent efforts by the United States government to expand U.S.-Mexico border infrastructure threaten to further fragment jaguar habitat in the borderlands. Models of habitat for jaguars in the United States have been developed, but they can be improved by using a finer analytical resolution, appropriately accommodating uncertainty by using a statistical framework, and using more appropriate data. Existing connectivity models have also been at coarse resolution, been broad in scope, and have not explicitly considered to effects of U.S.-Mexico border infrastructure. The Draft Recovery Plan for the jaguar was released by the United States Fish and Wildlife Service in 2017 and identified a need for additional research on jaguar habitat use and to identify key habitat and movement corridors in the U.S.-Mexico borderlands. To address these research needs, the goal of my thesis research was to provide updated and improved models of habitat and landscape connectivity for the northern population of jaguars in Sonora and Chihuahua, Mexico and Arizona and New Mexico, United States. For Chapter one, I developed a novel statistical model and applied it to predict and explain habitat selection by the northern population of jaguars. The study area for this chapter encompassed the Madrean Sky Islands (a complex of small mountain ranges in southeastern Arizona, southwestern New Mexico, and northwestern Mexico) and surrounding areas. Like many imperiled species and populations, data on jaguars are sparse, which limits our ability to gain insight into their ecology. To maximize inference, I developed a novel integrated Bayesian model that makes use of both presence-only and detection/non-detection data to model habitat selection. Results show that terrain ruggedness (+) and distance to riparian vegetation (-) are key predictors of habitat selection. There is a mean predicted 25,463 km2 of jaguar habitat in the study area. A mean predicted 40.6% of this habitat lies in the United states, suggesting that habitat in the U.S. could play an important role in the long term persistence of the northern jaguar population if jaguars are able to recolonize the region. In Chapter two, I turn focus to evaluating landscape connectivity, particularly in the context of U.S.-Mexico border infrastructure. I modeled landscape connectivity using Circuitscape, where the resistance surface was derived from the habitat suitability model from Chapter one in combination with human land use intensity and data on functional movement barriers (roads and border infrastructure). I evaluated the impacts of present-day border infrastructure as well as a likely future border scenario by running models for three different border infrastructure scenarios: 1) A scenario with no border infrastructure in place, 2) the present day border infrastructure scenario, and 3) a possible future scenario in which present day vehicle barriers are converted to pedestrian fencing. The resulting connectivity maps revealed that existing border infrastructure has far reaching consequences for habitat connectivity in the borderlands, and border wall expansion threatens to further isolate jaguar habitat in the United States from the breeding population in Mexico.
Open Access
Interaction among societal and biological drivers of policy at the wildlife-agricultural interface
(Colorado State University. Libraries, 2017) Miller, Ryan S., author; Webb, Colleen T., advisor; Hobbs, N. Thompson, committee member; Antolin, Michael F., committee member; Opp, Susan M., committee member
This dissertation research on wildlife policy and biology focuses on understanding the mechanisms that drive development of wildlife-agricultural policy and also on understanding the underlying ecological drivers of pathogen transmission and population growth for an invasive species. This research uses a combination of meta-analyses, mathematical models, and Bayesian statistics to examine the drivers of emerging wildlife policy, transient population dynamics, and ecological determinants of pathogen prevalence, using wild pigs (Sus scrofa) as a study system. Chapter One investigates cross-species disease transmission between wildlife, domestic animals and humans, which is an increasing threat to public and veterinary health. The risk to agricultural and human health was investigated by evaluating the status of 84 pathogens; the host species most at risk for transmission; and the co-occurrence of wild pigs, agriculture and humans. This was accomplished with a combination of meta-analysis and network analysis approaches. Thirty-four economically important swine pathogens (bacterial, viral, and parasitic) that cause clinical disease in livestock, poultry, wildlife, and humans were identified with the potential for transmission. Chapter Two investigates the conflicts between wildlife and agriculture and characterizes the processes that drive emergence of policy at the wildlife-agricultural interface. Using data describing congressional policy activity related to wild pigs, generalized linear models were used to relate the frequency of policy activity to the frequency of negative newspaper articles and amount of the U.S. agricultural industry potentially impacted by wild swine over a 30-year period. A strong linkage between wild pig policy activity and predictors representing news media, specifically negativity of media, geographic distribution of media, and amount of agriculture potentially impacted were identified as important. Results suggest that agriculture and media coverage may act as determinants for wildlife-agricultural policy development. Chapter Three investigates the ecological drivers of pathogen prevalence, specifically the role of species diversity. To accomplish this, a hierarchical Bayesian model that accounted for imperfect detection probability was used to investigate the influence of species diversity on the infection probability in wild pigs for pathogens with broad and narrow host ranges. Consistent with the species-diversity dilution hypothesis, prevalence of a single-host pathogen, pseudorabies virus, was negatively influenced by increasing richness of non-competent hosts. Contrary to the species-diversity amplification hypothesis, a multi-host pathogen, swine brucellosis, did not increase in prevalence as competent hosts increased in richness. Accounting for imperfect detection was important and indicated that processes other than diagnostic test error alone may be important for determining pathogen prevalence. Environmental gradients associated with changes in pathogen prevalence were linked to host species survival, specifically the severity of temperature and precipitation during the coldest period of the year. This together with species diversity may limit the ability of single-host pathogens to invade populations experiencing stressful conditions. Chapter Four investigates environmental drivers of short-term population dynamics for invasive and native populations. Short-term transient population dynamics are common in vertebrates, particularly invasive vertebrates, and by their nature are directly influenced by the interaction of population structure and vital rates. Using a novel methodological framework, we found consistent differences in the way vital rates and age structure in invasive and native wild pig populations contribute to transient dynamics suggesting that invasive and native populations are influenced by differing mechanisms. These dynamics appear to be linked with environmental conditions that regulate demography. Vital rates with the largest influence on population growth had the greatest variability across populations, contrary to the demographic buffering hypothesis. In native populations, vital rates contributed most to population growth. Invasive populations demonstrated a trade-off in the contribution of vital rates and age structure that may have unexpected consequences for invasive species management.
Open Access
Molecular ecology and hierarchical models elucidate chronic wasting disease dynamics
(Colorado State University. Libraries, 2018) Galloway, Nathan L., author; Antolin, Michael F., advisor; Hobbs, N. Thompson, committee member; Miller, Michael W., committee member; Huyvaert, Kathryn P., committee member
Prions present a unique evolutionary scenario because a single gene codes for both a disease agent and a functionally constrained native protein. The prion precursor gene, Prnp, codes for the prion precursor protein, PrP, which is constitutively expressed as a native isoform within all mammals. Upon misfolding to the disease isoform, known as prions, the same protein causes fatal neurodegenerative diseases known as transmissible spongiform encephalopathies. We review the literature and available data for the genetics of Prnp in order to examine its molecular evolutionaryhistory, and the likely force of natural selection acting on it, by analyzing genetic diversity both within and between species within Class Mammalia. We accessed Prnp nucleotide sequences of a large number of mammalian species from GenBank. We undertook three distinct analyses of these molecular data to characterize the force of selection acting on Prnp through comparisons of gene sequences and allele frequencies within and between species. Our analyses include: 1.) comparisons of genetic and amino acid polymorphisms across protein domains within Prnp, 2.) a within and between species comparison of nucleotide diversity within Prnp to characterize natural selection acting on the gene, and 3.) observed frequencies of genetic and amino acid polymorphisms from natural populations of animals. We show that amino acid substitutions reported to correlate with prion disease risk within species do not aggregate within particular protein structural domains, but rather are disparately located throughout. Branch model estimates using Phylogenetic Analysis by Maximum Likelihood across mammals show that Prnp undergoes strong purifying selection at the broad scale, that purifying selection is stronger between species than it is within species but no evidence that species orally susceptible to prion disease experience unique positive selection. We do show, however, that amino acid substitutions occur at higher frequencies than synonymous substitutions within Prnp, in direct conflict with the expectations for purifying selection. This evidence suggests that Prnp is experiencing balancing selection in opposition to the purifying selection observed at the large scale; this unique selective pressure may be due to the presence of prion disease. Ecological processes such as reproduction, habitat use, and disease epizootiology contribute to the growth or decline of wildlife populations, but many of these processes go directly unobserved. We set out to describe gene flow and disease transmission to better understand the ecological role of chronic wasting disease (CWD) in a northern Colorado population of mule deer (Odocoileus hemionus). CWD, a fatal prion disease, has been affecting this population for many decades. It has not caused extirpation of the deer, but may play an important limiting role in population growth and resilience. We employed genetic methods to analyze neutral genetic markers, which provide information about gene flow. Further, we examined allelic variation in the functional prion precursor gene, Prnp, which codes for the disease-causative prion of CWD and has alternative alleles with one (225F) that confers some resistance to prion disease within individual deer. The study in northern Colorado included sampling across four winter ranges. Genetic analysis identified four genetic lineages of deer, but lineages were distributed throughout the study area and did not correspond with winter ranges used annually with high fidelity by groups of females. Further, we show that males drive gene flow across genetic lineages. In contrast, CWD prevalence was spatially segregated: CWD-positive female deer were located in two of the winter ranges and absent from the others. This suggests that neither breeding sites nor natal dispersal are the primary means of disease spread in females across the winter ranges. Furthermore, we found, as previously reported, that an individual deer's Prnp genotype predicts the likelihood of a positive disease test. Even so, the frequency of the Prnp 225F allele was similar across winter ranges, and was notably higher than that reported in neighboring populations a decade earlier. Thus, it appears that gene flow spreads the favored allele across the study area despite different selective regimes in winter ranges. Our work shows the benefit of using population genetics to gain insight into ecological processes that go directly unobserved, such as the epizootiology of chronic wasting disease. Chronic wasting disease is a fatal neurodegenerative prion disease that infects members of the deer family in North America and Scandinavia. We conducted a five-year mark recapture study of a northern Colorado population of mule deer (Odocoileus hemionus) with endemic disease, including 217 females. All study animals were also genotyped at the prion precursor gene, Prnp, which has alternative alleles in many species to express amino acid differences that alter prion disease dynamics. Mark-recapture analysis revealed decreased disease incidence for individuals expressing genotypes with at least one copy of the minor allele, including heterozygotes, Prnp 225SF (expressing both a serine and phenylalanine at amino acid position 225) , and rare homozygotes, 225FF.We found no evidence for an evolutionary trade-off of decreased survival of CWD-negative deer for this group but emphasize the difficulty in estimating dynamic rates for the rare homozygotes alone. We employed estimates of annual disease risk and survival from this study as well as recruitment estimates from the literature, to forecast the expected future minor allele frequency in the population under the observed disease risk. This forecast revealed a clear expected evolutionary increase in the Prnp minor allele (225F) frequency given our model and field data.
Open Access
Parameter inference and model selection for differential equation models
(Colorado State University. Libraries, 2015) Sun, Libo, author; Hoeting, Jennifer A., advisor; Lee, Chihoon, advisor; Zhou, Wen, committee member; Hobbs, N. Thompson, committee member
Firstly, we consider the problem of estimating parameters of stochastic differential equations with discrete-time observations that are either completely or partially observed. The transition density between two observations is generally unknown. We propose an importance sampling approach with an auxiliary parameter when the transition density is unknown. We embed the auxiliary importance sampler in a penalized maximum likelihood framework which produces more accurate and computationally efficient parameter estimates. Simulation studies in three different models illustrate promising improvements of the new penalized simulated maximum likelihood method. The new procedure is designed for the challenging case when some state variables are unobserved and moreover, observed states are sparse over time, which commonly arises in ecological studies. We apply this new approach to two epidemics of chronic wasting disease in mule deer. Next, we consider the problem of selecting deterministic or stochastic models for a biological, ecological, or environmental dynamical process. In most cases, one prefers either deterministic or stochastic models as candidate models based on experience or subjective judgment. Due to the complex or intractable likelihood in most dynamical models, likelihood-based approaches for model selection are not suitable. We use approximate Bayesian computation for parameter estimation and model selection to gain further understanding of the dynamics of two epidemics of chronic wasting disease in mule deer. The main novel contribution of this work is that under a hierarchical model framework we compare three types of dynamical models: ordinary differential equation, continuous time Markov chain, and stochastic differential equation models. To our knowledge model selection between these types of models has not appeared previously. The practice of incorporating dynamical models into data models is becoming more common, the proposed approach may be useful in a variety of applications. Lastly, we consider estimation of parameters in nonlinear ordinary differential equation models with measurement error where closed-form solutions are not available. We propose a new numerical algorithm, the data driven adaptive mesh method, which is a combination of the Euler and 4th order Runge-Kutta methods with different step sizes based on the observation time points. Our results show that both the accuracy in parameter estimation and computational cost of the new algorithm improve over the most widely used numerical algorithm, the 4th Runge-Kutta method. Moreover, the generalized profiling procedure proposed by Ramsay et al. (2007) doesn't have good performance for sparse data in time as compared to the new approach. We illustrate our approach with both simulation studies and ecological data on intestinal microbiota.
Open Access
Parasites and immunogenetic diversity in prairie dogs
(Colorado State University. Libraries, 2018) Harp, Elizabeth M., author; Antolin, Michael F., advisor; Ballweber, Lora R., committee member; Hobbs, N. Thompson, committee member; McGrew, Ashley K., committee member
Prairie dogs (Cynomys spp.) are an important component of North American grassland communities. Prairie dogs have been characterized as ecosystem engineers and keystone species because their extensive burrow systems alter ecosystem dynamics and provide homes for a variety of species. Prairie dog populations have declined dramatically over the past century as a result of eradication programs, habitat loss, and introduced plague. This research explores factors related to host-parasite ecology and immunogenetics of prairie dogs. The second chapter is a systematic review of parasites recorded from all five prairie dog species. The third chapter characterizes genetic diversity and investigates selection at the hyperdiverse MHC DRB locus in black-tailed prairie dogs. The fourth chapter uses multimodel inference to investigate host and environmental factors affecting flea aggregation on black-tailed prairie dogs. I found host-parasite records documenting at least 104 parasites species from prairie dogs. Over 2/3 of parasite species were ectoparasites, primarily fleas. Most endoparasites were protozoa. Bacteria and viruses are essentially undescribed from prairie dogs. Potentially related to the diversity of parasites they are exposed to, the DRB gene in black-tailed prairie dogs was characterized by high levels of diversity. I also found considerable evidence for contemporary directional selection and historical balancing selection acting on the DRB gene in black-tailed prairie dogs. However, I found only weak evidence for a relationship between DRB genotype and flea parasitism in black-tailed prairie dogs. Primary drivers of flea aggregation on black-tailed prairie dogs, identified by multimodel inference of generalized linear models, were host sex and month of capture. Males were more heavily parasitized than females, and flea loads are greatest in September and lowest in June.
Open Access
Reproductive ecology and population viability of alpine-endemic ptarmigan populations in Colorado
(Colorado State University. Libraries, 2017) Wann, Gregory T., author; Aldridge, Cameron L., advisor; Ghalambor, Cameron K., committee member; Hobbs, N. Thompson, committee member; Noon, Barry R., committee member
To view the abstract, please see the full text of the document.
Open Access
Spatial ecology and conservation of tigers and their prey in the Central Terai Landscape, India
(Colorado State University. Libraries, 2016) Chanchani, Pranav, author; Noon, Barry, advisor; Bailey, Larissa, committee member; Crooks, Kevin, committee member; Hobbs, N. Thompson, committee member
Remnant populations of the world’s ~3800 wild tigers (Panthera tigris) are generally small (< 20 adult individuals), subject to high rates of poaching, and confined to fragmented habitats with high levels of human disturbance. The species persistence requires an in-depth understanding of the suite of exogenous and endogenous factors that drive spatial heterogeneity in its occurrence and abundance. We intensively sampled tiger habitats in the populous 4500 km2 Central Terai Landscape along the India-Nepal border and investigated the following questions: (a) what is the relative influence of protection designation (protected area or multiple use forests), prey availability, patch connectivity, human presence and habitat quality on landscape and local-scale tiger occurrence; (b) how do these and other factors drive spatial heterogeneity in tiger density at broad and fine spatial scales; and (c) what are the relationships between landscape fragmentation, adult sex ratios, and inter-specific interactions? We found that tiger occupancy and abundance were similar or higher in multiple use forests with high human use, than in several protected areas. Further, the distribution and abundance of prey and key habitats such as tall grasslands, –rather than protection designation, were the best predictors of spatial heterogeneity in tiger occupancy and density. The co-occurrence of tigers and humans in areas with high human use may be facilitated by refugia habitats such as tall grasslands and temporal partitioning of use. Habitat connectivity promoted high occupancy only when all habitats connected by corridors were effectively protected. Finally, we documented exacerbated potential for inter- and intra-sex competition and reduced population fitness in small, isolated tiger populations with male-biased adult sex ratios. Overall, our study reveals that the establishment of protected areas alone may be an inadequate strategy to secure the future of wild tigers. We identified key ecological and anthropogenic factors that cumulatively enable the species persistence in populous human dominated landscapes.
Open Access
Statistical models for dependent trajectories with application to animal movement
(Colorado State University. Libraries, 2017) Scharf, Henry R., author; Hooten, Mevin B., advisor; Cooley, Daniel S., committee member; Fosdick, Bailey K., committee member; Hobbs, N. Thompson, committee member
In this dissertation, I present novel methodology to study the way animals interact with each other and the landscape they inhabit. I propose two statistical models for dependent trajectories in which depedencies among paths arise from pairwise relationships defined using latent dynamic networks. The first model for dependent trajectories is formulated in a discrete-time framework. The model allows researchers to make inference on a latent social network that describes pairwise connections among actors in the population, as well as parameters that govern the type of behavior induced by the social network. The second model for dependent trajectories is formulated in a continuous-time framework and is motivated primarily by reducing uncertainty in interpolations of the continuous trajectories by leveraging positive dependence among individuals. Both models are used in applications to killer whales. In addition to the two models for multiple trajectories, I introduce a new model for the movement of an individual showing a preference for areas in a landscape near a complex-shaped, dynamic feature. To facilitate estimation, I propose an approximation technique that exploits of locally linear structure in the feature of interest. I demonstrate the model for the movement of an individual responding to a dynamic feature, as well as the approximation technique, in an application to polar bears for which the changing boundary of Arctic sea ice represents the relevant dynamic feature.
Open Access
The ecological legacy of the mountain pine beetle in the southern Rockies: forest change and disturbance interactions
(Colorado State University. Libraries, 2014) Perovich, Carlyn, author; Sibold, Jason, advisor; Hobbs, N. Thompson, committee member; Jacobi, William R., committee member
Mountain pine beetle (Dendroctonus ponderosae; MPB) outbreaks are naturally occurring ecological disturbances in western North America, but the last two decades have seen eruptions of unprecedented severity and extent. These outbreaks have created novel conditions in lodgepole pine forests that have historically had disturbance regimes dominated by large, stand-replacing fires. Previous research has found that MPB outbreaks increase relative abundance of non-host species. I use the lodgepole pine forest on the west side of Rocky Mountain National Park to examine mechanisms in this predicted forest change and the ecological legacy of the mountain pine beetle outbreak, particularly in terms of its implications for future disturbances. The recent mountain pine beetle outbreak increased spatial heterogeneity of species composition as a result of spatial variability in mechanisms of post-outbreak forest composition. Post-outbreak variances of up to 5 times greater and patch sizes up to 7 times smaller than pre-outbreak conditions. The increase in species heterogeneity will inhibit future landscape-level bark beetle outbreaks, though projected increases in Engelmann spruce and subalpine fir may make post-MPB forests more susceptible to other disturbances, including drought and fire. The MPB outbreak has increased landscape asynchrony, which will increase resiliency to future disturbances. However, this heterogeneity is a result of more spruce and fir on the landscape, species which are less adapted to projected future climate conditions.
Open Access
The effects of bark beetle-fire disturbance interactions on post-disturbance forest regeneration
(Colorado State University. Libraries, 2015) Fleming, Jean L., author; Sibold, Jason, advisor; Baron, Jill, committee member; Hobbs, N. Thompson, committee member
Disturbances in forested ecosystems create ecological legacies that can affect future disturbances and these disturbance interactions influence post-disturbance establishment. In addition, disturbances can become compounded and cause drastic ecosystem changes including decreased post-disturbance establishment, regeneration of unexpected species assemblages, or shifts to alternative stable states. I studied the post-disturbance establishment of five tree species following two interacting disturbances, a bark beetle outbreak and a high-severity fire. The goal of my research was to identify the factors that influence post-disturbance seedling establishment, and to determine how bark beetle-fire interactions affect forest regeneration. I evaluated seedling establishment at 98 study sites across the Cow Creek fire in Rocky Mountain National Park. Two bark beetle species, mountain pine beetle (Dendroctonus ponderosae) and spruce beetle (Dendroctonus rufipennis), caused epidemic scale tree mortality in the five years before the fire. I created a Bayesian mixture model for each tree species to assess the independent variables that influenced the abundance of the species' establishment. The variables that influenced mean seedling abundance were different for each species. Forest age, distance to a seed source following the fire, and disturbance interactions affected the seedling abundance for most of the species. The presence of recent bark beetle activity had a measurable affect on post-disturbance establishment for three species. P. contorta and P. tremuloides mean abundance increased by a factor of 3.1 and 1.4, respectively, in areas with mountain pine beetle disturbance. The mean abundance of P. engelmannii seedlings was 3.8 times greater in areas where spruce beetle had caused tree mortality before the fire. This increase in seedling abundance in areas with bark beetle presence was independent of the other studied factors, including fire severity and elevation. The increased seeding abundance I recorded following bark beetle and fire disturbance suggests that interacting disturbances can increase the likelihood that forests will recover to their original species assemblages. The results of this study should be utilized to inform future forest management and to avoid unnecessary management action.
Open Access
The interactive effects of climate and disturbance on tree species distributions
(Colorado State University. Libraries, 2015) Renwick, Katherine M., author; Rocca, Monique E., advisor; Hobbs, N. Thompson, committee member; Sibold, Jason, committee member; Stohlgren, Thomas J., committee member
Climate change is expected to alter species distributions as ranges shift to track favorable temperature and precipitation regimes. Range shifts are already being observed across a wide range of taxa, but many species are not keeping pace with the rate of recent climate warming. This is particularly true for tree species, which often experience significant migration lags due to a variety of non-climatic factors that can hinder range expansion or delay range retreats. Because many other species depend on trees for food or habitat, migration lags in tree species may have cascading impacts on a wide range of taxa that would otherwise face few barriers to migration. The importance of understanding how climate change will affect tree species distributions prompted several related research questions: 1) What factors contribute to the observed lags in tree species distributions? 2) Can biotic disturbances accelerate climate-driven shifts at the range margins of trees species? 3) How important is climate in determining landscape-scale vegetation patterns? My dissertation research addresses these questions using an integrated approach that draws on exiting literature, field sampling, and statistical models to inform our understanding of potential climate change impacts on tree species distributions. Observations of contemporary tree species migrations occurring throughout the world suggest that migration lags are pervasive and can be caused by a wide variety of abiotic factors and biotic processes. Tree migrations are likely to occur episodically when migration constrains are overcome, resulting in temporal variability in the migration rate. Physical disturbances such as fire can reduce competition and initiate periods of rapid change, but the effects of biological disturbances such as insect outbreaks are more nuanced. A case study examining the impacts of climate change and mountain pine beetle (Dendroctonus ponderosae) disturbance at lodgepole pine (Pinus contorta) range margins suggests that while biological disturbances may accelerate a range retreat by killing mature trees, they do not initiate range expansion for the target species. The impact of non-climatic constraints on current tree species distributions was also evident at the landscape scale, and climatic variables alone proved insufficient to explain patterns of co-occurrence among tree species. Together, these findings suggest that Rocky Mountain tree species will not uniformly shift upward in elevation as the climate continues to warm. Range shifts will likely be episodic and idiosyncratic, and forecasts based solely on climate data may over-estimate the rate and under-estimate the landscape-scale heterogeneity of potential distribution changes.
Open Access
The response of a Rocky Mountain forest system to a shifting disturbance regime
(Colorado State University. Libraries, 2019) Carlson, Amanda R., author; Sibold, Jason S., advisor; Assal, Timothy J., committee member; Hobbs, N. Thompson, committee member; Rocca, Monique E., committee member
Climate change is likely to drive widespread forest declines and transitions as temperatures shift beyond historic ranges of variability. Warming temperatures and shifting precipitation patterns may lead to increasing disturbances from wildfire, insect outbreaks, drought, and extreme weather events, which may greatly accelerate rates of ecosystem change. However, the role of disturbance in shaping forest response to climate change is not well understood. Better understanding the impacts of changing disturbance patterns on forest decline and recovery will allow us to better predict how forest ecosystems may adapt to a warming world. Severe wildfires and bark beetle outbreaks are currently affecting large areas of forest throughout western North America, and increasing disturbance size and severity will have uncertain impacts on forest persistence. The goal of my dissertation was to investigate the factors shaping disturbance response in a region of the San Juan Mountains, Colorado, which has undergone impacts from a high-severity spruce beetle outbreak and wildfire in the last 15 years. I conducted three separate studies in the burn area of the West Fork Complex wildfire, which burned in 2013, and in surrounding beetle-affected spruce-fir forests. The goals of each study were to 1) assess whether the severity of spruce beetle outbreaks occurring before wildfire resulted in compounded disturbance interactions affecting vegetation recovery, 2) determine how the severity of each disturbance type influenced fine-scale below-canopy temperature patterns across the landscape, and 3) assess how conifer seedling regeneration densities were influenced by effects of disturbance severity on seed dispersal, temperature, and vegetation structure. I found that disturbances influenced seedling regeneration and ecosystem resilience through several mechanisms. First, pre-fire beetle outbreak severity was negatively correlated with post-fire vegetation cover, indicating that the combined disturbances were inhibiting regeneration beyond what may have been expected with fire alone. Second, disturbances had significant effects on below-canopy temperatures, with burned areas ~0.5 °C warmer than unburned forest areas and differences in overnight minimum temperatures resulting from loss of live canopy in unburned, beetle-killed forests. Third, the large fire size and high severity resulted in very little spruce seed dispersal or conifer regeneration in most of the burned area, while spruce regeneration in unburned forest was negatively correlated with increasing overstory mortality from the spruce beetle. My results indicate that disturbance is playing an important role in determining the future trajectory of the forest in my study area. The West Fork Complex fire has caused a severe ecosystem transformation, has increased landscape exposure to warming temperatures, and is preventing forest re-establishment as a result of a lack of seed sources. The spruce beetle outbreak has not resulted in such a severe transformation, but is possibly leading to reduced forest resilience by reducing spruce seedling re-establishment and by altering fuel structures to make forests more prone to high soil burn severity if fire follows within ~10 years. Warming of below-canopy microclimates is not exacerbated by spruce beetle outbreak, and is rather partially offset by cooling of overnight temperatures. These findings provide insights into how forest responses to climate change may be shaped by disturbance processes, which are occurring with increasing severity and frequency worldwide.
Open Access
The role of wildfire and topography in shaping aspen regeneration after the Hayman Fire, CO, USA
(Colorado State University. Libraries, 2019) Porter, Arianna A. B., author; Sibold, Jason, advisor; Hobbs, N. Thompson, committee member; Assal, Timothy, committee member
Unusually rapid and widespread mortality in Quaking aspen (Populus tremuloides) has been documented throughout the 21st century primarily as a result of warm, dry weather conditions. Although aspen are not drought-adapted, aspen are well adapted to wildfire. Increases in wildfire severity and extent as a result of climate change may provide opportunities for aspen regeneration, especially at mid- and high-elevation sites. Aspen's sensitivity to drought suggests that regeneration following fire might be constrained to cooler and wetter topographic locations on the landscape which reduce drought stress on vegetation. While aspen mortality is demonstrated to occur at low elevation sites, aspen establishment and persistence is known to occur at high elevation sites due to cooler, wetter conditions. Low- and high-elevation aspen persistence is well-understood; however, patterns of aspen regeneration and persistence at mid-elevation sites is still relatively unexplored. We use the 2002 Hayman fire (Colorado, USA) to explore whether high-severity wildfire has provided opportunities for aspen regeneration at mid-elevations in which aspen was not observed before the fire. If regeneration has occurred, we ask if regeneration is contingent on topographic conditions. Cool, wet microclimates created by fine-scale topography at mid-elevations may allow for increased aspen regeneration, however this is unexplored in the Hayman landscape. Our findings demonstrate that the Hayman fire provided opportunities for aspen regeneration at mid-elevation sites in which aspen were not observed before the fire and that the density of regeneration is contingent on topography. Specifically, aspen regeneration is most dense at mid-elevations on steep slopes. Ecosystem management may focus on threats to aspen health and vigor (i.e. ungulate herbivory) on steep slopes at mid-elevations rather than at low-elevation sites.