Browsing by Author "Webb, Colleen T., committee member"

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Open Access
Black bear ecology and human-bear interactions in an urban system
(Colorado State University. Libraries, 2012) Baruch-Mordo, Sharon, author; Wilson, Kenneth R., advisor; Breck, Stewart W., advisor; Webb, Colleen T., committee member; Crooks, Kevin R., committee member
To view the abstract, please see the full text of the document.
Open Access
Complex evolution of mitochondrial genomes: lessons from salamanders
(Colorado State University. Libraries, 2014) Chong, Rebecca A., author; Mueller, Rachel L., advisor; Webb, Colleen T., committee member; Funk, W. Chris, committee member; McKay, John K., committee member
This dissertation research on genome evolution focuses on understanding the mechanisms that drive the evolution of mitochondrial genome size, content, and organization in animals. This research uses a combination of empirical and computational approaches to examine the evolution of mitochondrial genomes in vertebrates, focusing on salamanders as an exemplar clade. Chapter One analyzes mitochondrial genome sequences of vertebrate lineages that differ in metabolic rates. Salamanders, which have the lowest metabolic requirements among tetrapods, experience weaker purifying selection on protein-coding sequences than do frogs, a comparable amphibian clade with higher metabolic rates. In contrast, there is no evidence for weaker selection against mitochondrial genome expansion in salamanders. Together, these results suggest that different aspects of mitochondrial genome evolution (i.e. nucleotide substitution, accumulation of non-coding sequences) are differently affected by metabolic variation across tetrapod lineages. Chapter Two describes the correlation between gene rearrangement/genome expansion and increased rates of substitution in salamander mitochondrial genomes. Most protein-coding genes maintain their position along the mutation gradient in rearranged/expanded mitochondrial genomes, and the genes that do move are unaffected by their new position because the mutation gradient in salamanders is weak. Additionally, genomic rearrangements/expansions occur independent of levels of selective constraint on genes. Together, these results demonstrate that large-scale changes to genome architecture impact mitochondrial gene evolution in predictable ways; however, despite these impacts, the same functional constraints act on mitochondrial protein-coding genes in both modified and normal genomes. Chapter Three reports the phylogenetic relationships among lineages of Aneides, sampling both within and among all six species, based on three nuclear markers and describes mitochondrial genome sequences for nine of the taxa represented in the phylogeny. Mitochondrial gene order and level of mitochondrial sequence divergence were estimated for these sequences and two previously published sequences. Two genome duplication events resulting in mitochondrial gene rearrangements were detected, the first rearrangement occurring in the common ancestor of Aneides and the second rearrangement existing across different populations of a single species, A. hardii. Comparisons of A. hardii genomes show that duplicated protein-coding and rRNA genes are lost more rapidly than other duplicated mitochondrial sequence (i.e. tRNAs, non-coding sequence) and suggests that these large scale changes can occur across very shallow levels of genetic divergence.
Open Access
Demography and parental investment in orange-crowned warblers: testing life history theory
(Colorado State University. Libraries, 2012) Sofaer, Helen R., author; Ghalambor, Cameron K., advisor; Noon, Barry R., committee member; Sillett, T. Scott, committee member; Webb, Colleen T., committee member
Understanding the diversification of life history strategies is a major goal of evolutionary ecology. Research on avian life history strategies has historically focused on explaining variation in clutch size, and most studies have tested whether this variation can be explained by variation in a single ecological factor, such as food availability or mortality risk. However, relatively few studies have evaluated whether the causes of variation within populations are distinct from or similar to the causes of variation between populations. In my dissertation, I compare the life history strategies of orange-crowned warbler (Oreothlypis celata) populations and study the causes of variation in clutch sizes, incubation behavior, nestling provisioning rates, nestling growth rates, and breeding phenology. I tested alternative hypotheses for the ecological causes of divergent life histories, and assessed the consequences of these different reproductive strategies for parents and offspring. My results indicate that no single ecological factor can explain life history variation either within or between populations. Instead, life history and behavioral traits differ in their sensitivities to different ecological factors, and while differences between nearby populations can reflect plastic responses to ecological variation, populations that are more geographically and evolutionarily distant can differ in both their responses to ecological variation and in the consequences of variation in parental behavior for offspring growth and development.
Open Access
Illustrating the post-introduction ecology of Rift Valley fever virus in the United States of America
(Colorado State University. Libraries, 2021) Hartman, Daniel A., author; Kading, Rebekah C., advisor; Ebel, Gregory, committee member; Foy, Brian, committee member; Webb, Colleen T., committee member
Rapid urbanization, increasing international travel, and our changing climate are modifying the existing interspecies interactions at the interfaces between human, wildlife, and livestock interfaces, increasing the potential for outbreaks and transboundary disease introductions. It is more important than ever to maintain proactive research programs that integrate data across disciplines to maintain a working knowledge the potential transmission cycles of high-threat pathogens in novel environments. For vector-borne pathogens, entomological parameters, as well as interactions with the pathogen and host are highly informative, while representing avenues for control prior to an introduction. The work of this dissertation seeks to inform the potential transmission cycles of Rift Valley fever virus (RVFV) in the United States. Currently restricted to Africa and the Arabian Peninsula, RVFV infects domestic ruminants and humans with substantial degrees of morbidity and mortality. Throughout its current range, transmission involves a diversity of vectors, which are capable of transmitting the virus horizontally between vertebrates and vertically to mosquito progeny. The ecology of RVFV presents a great deal of complexity, with many unknown factors such as the roles of wildlife hosts, and relative contributions of vectors to transmission. To gain some insight into the potential ecology of RVFV in the United States, we first performed extensive sampling of mosquitoes at feedlots in northern Colorado to explore the potential for these operations to act as amplification foci after an introduction. We discovered that the most competent mosquito in Colorado that has been tested to date is highly abundant, and feeds readily on cattle, making these operations high risk for an epizootic. In this previous study we also identified blood-feeding on deer for some mosquitoes (Ae. vexans, Ae. melanimon, Ae. dorsalis) as well as domestic ruminants. We then set out to determine whether Ae. melanimon is capable of transmitting RVFV biologically, as there were no data to date for this species. We conducted infection experiments with these three Aedes species and others to determine the efficiencies with which they can transmit RVFV horizontally and vertically. We found substantial evidence for horizontal transmission and susceptibility of ovaries to infection, a prerequisite for vertical transmission, in all species but for Aedes increpitus. For these data we also developed a model to estimate the infection susceptibilities and barriers in mosquito organs in a functional manner. Finally, we sought to investigate the potential for transmission of RVFV in white-tailed deer by describing the community of mosquitoes in a riparian woodland habitat. We revealed some interesting patterns in the abundances of some mosquito species which stood in contrast to those observed at the feedlots. Several mosquito species exhibited the capacity to feed on white-tailed deer, including Ae. increpitus and Ae. vexans, both previously shown the ability to transmit RVFV by bite. By scoring the digestive stage of the blood meals in mosquitoes that were later identified to vertebrate source species, we uncovered an interesting pattern suggestive of interrupted feeding on eastern cottontail rabbits, in contrast to blood meals taken from white-tailed deer, from which mosquitoes fed to repletion. The implications of interrupted feeding for transmission by mosquitoes is unclear, but highlights the important factor of behavioral interactions between mosquito vectors and hosts which is often overlooked.
Open Access
Impact of methanotroph ecology on upland methane biogeochemistry in grassland soils
(Colorado State University. Libraries, 2011) Judd, Craig R, author; von Fischer, Joseph C., advisor; Butters, Gregory, committee member; Webb, Colleen T., committee member
Molecular assays of soil environments reveal tremendous microbial diversity, but it remains unclear how this diversity might be mechanistically linked to the ecology of the organisms and their biogeochemical function. Methane consumption in upland soils is arguably the simplest biogeochemical function, and there are emerging patterns in the diversity and biogeography of the organisms that carry out soil methane consumption. This simplicity may allow methane uptake in upland soils to be a model system for merging microbial ecology, diversity and biogeochemistry. Five key traits appear critical for methanotroph ecology: enzyme kinetics, nutrient demand, pH tolerance, ammonium sensitivity and desiccation tolerance. Unfortunately, few studies to date have examined the functional consequences these traits may have on methane consumption. Here, I present analysis of methanotroph community composition and Michaelis-Menten kinetics of methane uptake across three North American temperate grassland sites of differing soil moisture regimes. Across this gradient, I observed distinct variation in community composition, and significant changes in enzyme kinetics. In addition, I find that differences in field estimates of methane activity parallel the patterns of Michaelis-Menten assays, which in turn correlate with differences in methanotroph community composition. These correlations suggest that methanotroph community composition alters ecosystem function.
Open Access
Influence of urban environments on black bear populations and foraging behaviour
(Colorado State University. Libraries, 2013) Lewis, David Laurel, author; Wilson, Kenneth R., advisor; Breck, Stewart W., advisor; Webb, Colleen T., committee member; Crooks, Kevin R., committee member
For most large carnivores, the impact of human development on their population is poorly understood. American black bears (Ursus americanus) use urban environments to forage, often resulting in negative human-bear interactions and management removal of conflict bears. There is a general consensus that available human food sources are the underlying cause of human-bear conflict, but the subtle patterns of how bears use urban resources and the impact that using these resources has on the population is poorly understood. My research focused on understanding how available human foods and management actions in urban environments influence black bear foraging behavior and populations. The National Wildlife Research Center, Colorado Parks and Wildlife and Colorado State University collaborated six year urban bear study in Aspen, Colorado. The overall goal of the study and the objectives of my research questions were to better understand how bears use urban food resources and the influence that these resources have on their population, so that better management practices can be developed. In Chapter 1, I focus on the impacts that natural food failure, available human food, and management removal of conflict bears has on population. Chapter 2 describes general foraging patterns and models resource use in the urban environment at a fine spatial scale. A brief chapter summary, finding, and then management implications are given below. In Chapter 1, we developed a stochastic projection matrix model parameterized with data from the literature and the 6 years of study (2005-2011) in Aspen, Colorado to evaluate the positive and negative influences of urban environments on bears. We modeled the influence that failure of natural food sources, available human food, and different levels of conflict-bear removals could have on a bear populations by comparing a scenario where bears to not benefit from human food sources or experience conflict-bear removals with two urban scenarios where bears have access to human foods, but conflict-bears are removed. Perturbation analyses were used to evaluate consequences that changes to population vital rates could have. We found that the benefit increased cub production from after natural food failure years from available human food sources was quickly negated if conflict-bear management removals reduced adult female survival. Increasing frequency of natural food production failure years resulted in greater impacts from available urban food and conflict-bear removals. Our findings suggest that managers may need to utilize non-lethal practices in managing conflict-bears and municipalities will need to secure human food sources to avoid management removals and population declines. In Chapter 2, we used GPS radio-telemetry data and information obtained from visiting bear foraging locations in Aspen, Colorado from 2007-2010 to determine the food resource bears were using and what factors influenced anthropogenic foraging events. We used a resource selection study design to evaluate fine-scale foraging behavior during prehyperphagia and hyperphagai. Overwhelmingly garbage was the main resource bears used and modeling efforts determined that selection of foraging sites was not only influenced by the presence of garbage but also by the proximity to riparian habitat and presence of ripe fruit trees. We documented inter- and intra-annual foraging patterns of bears foraging extensively in urban areas when natural food sources were not available and switch back to natural food sources when they became available. These patterns suggest that bears balance an energy budget and individual safety when making foraging decision. We suggest management action focus on reducing available human foods to make the urban environment less energetically beneficial for foraging than natural habitat. Management efforts should be prioritized and focus on securing garbage and replacing anthropogenic fruit trees with non-fruiting varieties especially near riparian habitat.
Open Access
Parsimony and complexity in epidemiological models for decision support in animal health
(Colorado State University. Libraries, 2012) Zagmutt, Francisco J., author; Dow, Steven W., advisor; Hill, Ashley, advisor; Webb, Colleen T., committee member; Wagner, Bruce A., committee member
To view the abstract, please see the full text of the document.
Open Access
Restoration of scaled quail to historic ranges in the Rolling Plains ecoregion of Texas
(Colorado State University. Libraries, 2024) Ruzicka, Rebekah Elizabeth, author; Doherty, Paul F., Jr., advisor; Rollins, Dale, committee member; Kendall, William L., committee member; Otis, David L., committee member; Webb, Colleen T., committee member
Scaled quail (Callipepla squamata) are a gallinaceous game bird native to the grasslands and deserts of the southwestern United States and northcentral Mexico experiencing range contraction and population decline due to habitat fragmentation and degradation. Once abundant in the Rolling Plains ecoregion of Texas dating back to the 1880's, scaled quail were locally extinct throughout most of the ecoregion by the late 1980's primarily due to brush encroachment and spatial aggregation of row crop agriculture. Despite state and federal landowner habitat restoration programs (e.g., Landowner Incentive Program, Environmental Quality Incentives Program) scaled quail populations in the Rolling Plains ecoregion failed to respond, likely because the same fragmentation that contributed to decline also prevented effective natural recolonization to restored habitats. Translocation of wild-caught quails to reestablish self-sustaining populations gained popularity during the 2000's, particularly due to success reestablishing northern bobwhites (Colinus virginianus) in fragmented habitats of the southeastern United States. However, many translocations in arid, western climates were either poorly documented or failed outright. Understanding factors that influence translocation outcomes and form best practices is critical for translocation to be used effectively as a management tool. I examined long-term, seasonal survival in a population of scaled quail successfully reestablished on the Rolling Plains Quail Research Ranch in Fisher County, Texas in the context of drought and demographics (Chapter 1). Competing hypotheses predict that scaled quail populations are either resistant to drought or that annual survival is negatively correlated with precipitation amounts. My findings supported the hypothesis that scaled quail are drought sensitive. Additionally, I found survival was lower during non-breeding season, for females, and adults. Scaled quail survival estimates reported here are the most comprehensive for the species and the longest-term study of a translocated scaled quail population to date. I conducted a field experiment to test the effects of source population and variation in delayed release strategy (1–9 weeks) on mortality, dispersal, nest initiation, renesting rate, and nest survival of wild-caught, translocated scaled quail (Chapters 2 and 3). I trapped and translocated quail over 2 years (2016–2017) from source populations in the Edwards Plateau and Rolling Plains ecoregions to a large (>40,000 ha), contiguous release site in Knox County, Texas. Data were analyzed using two multi-state mark-recapture models with state uncertainty to incorporate uncertainty in the process of observing location and nest initiation in radio-marked birds. The framework I used to model reproductive processes is a novel method for obtaining estimates of nest initiation and renesting rate (Chapter 3). I found that scaled quail translocated within the Rolling Plains were more likely to exhibit philopatry to the release site, but that source population did not influence reproduction. Quail with longer holding times had higher mortality, but lower dispersal rates. Additionally, increased length of holding time decreased renesting effort. Yearlings were more likely to initiate nests than adults and the probability of renesting was lower during drought conditions. Finally, I compiled estimated demographics from chapters 1–3 to inform a matrix population model (MPM) that compared asymptotic and transient dynamics under wet and drought conditions (Chapter 4). While traditional MPM analyses focus on asymptotic dynamics, transient dynamics are more relevant for modeling short-term dynamics in translocated or unstable populations. My findings showed divergence between transient and asymptotic dynamics, with asymptotic projections potentially overestimating population growth by 14%. Asymptotic growth rates were most sensitive to renesting rate changes, while transient growth rates were affected by changes in hatchability and renesting rates. The results from my research will inform management decisions and I summarize my recommendations in Chapter 5. I suggest managers avoid initiating translocations in years projected to have drought conditions. Improved accuracy of El Nino–Southern Oscillation cycle-based long-range forecasts has made predictions a useful tool for managers considering translocation. Even so, translocated populations can persist long-term in drought conditions despite the negative impacts to survival and reproduction. Longer holding times for translocated scaled quail result in lower dispersal but higher mortality and lower renesting rates, presenting a decision tradeoff for managers. Managers can hold scaled quail on the release site (up to 9 weeks) when limiting dispersal is a priority (e.g., when in habitats surrounded by a high degree of fragmentation) or holding birds makes the translocation more feasible. However, when considering all factors a holding time of 2–3 weeks is ideal (Chapter 5). The Edwards Plateau is a suitable source site for translocations in the Rolling Plains. Managers should consider transient dynamics when modeling populations where short-term outcomes are relevant such as translocation. By doing so, I show that prioritizing the translocation of yearlings, the stage class with the highest reproductive value, can result in a 16% larger population after one year compared to translocating only adults.
Open Access
The distribution of lotic insect traits in relation to reference conditions and projected climate change in the western United States
(Colorado State University. Libraries, 2014) Pyne, Matthew Ivern, author; Poff, N. LeRoy, advisor; Bledsoe, Brian P., committee member; Hoeting, Jennifer A., committee member; Webb, Colleen T., committee member
The use of species traits (e.g., life history, morphological, physiological, or ecological characteristics of an organism) to describe community responses to environmental change has become a common practice in stream ecosystems, with over 900 papers describing macroinvertebrate trait-environment relationships in streams. The use of traits provides some advantages over traditional taxonomic metrics, such as providing a mechanistic link between an organism and its environment, but also presents some challenges, such as many traits being correlated with other traits and multiple environmental variables. Various methods have been recommended to address these challenges, such as using multiple traits, posing a priori hypotheses, and evaluating streams across large-spatial scales. The vast majority of studies have not incorporated these recommendations, however, particularly in North America. My research had two general objectives: 1) describe the dominant trait-environmental relationships in natural streams in the western United States and 2) use two distinct traits-based methods to evaluate how stream aquatic insect communities are currently distributed in terms of multiple environmental variables and how species and communities may respond to climate change. Traits are often used to evaluate the ecological integrity of streams and a baseline understanding of aquatic insect trait-environment relationships is needed for the western United States. I used logistic regression, multinomial regression, and redundancy analysis to explore the relationships between 20 trait distributions and 83 environmental variables in 253 least-disturbed streams across 12 western states. Traits had the strongest relationships with regional climate and local stream habitat conditions (e.g., air temperature, conductivity, mean annual runoff) rather than elevation, land use, or measures of extreme hydrological events. Traits such as thermal tolerance, size, swimming strength, rheophily, voltinism, and armoring exhibited strong relationships with the environmental data and would be ideal for large-scale stream assessments. Aquatic insect communities contain many taxa that are sensitive to temperature increases and changes to runoff. Two traits, cold water preference and erosional obligate (i.e., needs to live in fast-water habitat) have been used in the past to estimate the effect of climate change on stream insect communities, but no study has accounted for both climatic and non-climatic effects on these two traits. I developed a Bayesian path analysis describing how the distributions of these two traits respond to multiple environmental gradients, not just temperature, and discovered that the distribution of cold-adapted taxa was strongly correlated with changes in air temperature in the wet, cool ecoregions, but was correlated with thermal buffers and refuges in most dry, warm ecoregions, indicating that temperature-sensitive taxa are likely on the brink of their thermal tolerance in those ecoregions. A second approach to assess community sensitivity to climate change is to determine the specific thermal tolerance of each taxon individually. I computed the thermal and stream runoff thresholds of common stream taxa and compared the World Climate Research Programme's climate model predictions to these thresholds. I found that the stream communities most at risk to climate change were found in some dry ecoregions, concurring with the previous results, and in wet, warm ecoregions with a high proportion of spatially restricted and endemic taxa, such as northern California. These two approaches describe possible mechanisms of climate change resistance and identify sensitive ecoregions.
Open Access
Using community detection on networks to identify migratory bird flyways in North America
(Colorado State University. Libraries, 2012) Buhnerkempe, Michael G., author; Hoeting, Jennifer A., advisor; Givens, Geof H., committee member; Webb, Colleen T., committee member
Migratory behavior of waterfowl populations in North America has traditionally been broadly characterized by four north-south flyways, and these flyways have been central to the management of waterfowl populations for more than 80 years. However, recent desires to incorporate uncertainty regarding biological processes into an adaptive harvest management program have underscored the need to re-evaluate the traditional flyway concept and bring uncertainty in flyways themselves into management planning. Here, we use bird band and recovery data to develop a network model of migratory movement for four waterfowl species, mallard (Anas platyrhnchos), northern pintail (A. acuta), American green-winged teal (A. carolinensis), and Canada Goose (Branta Canadensis) in North America. A community detection algorithm is then used to identify migratory flyways. Additionally, we compare flyway structure both across species and through time to determine broad applicability of the previous flyway concept. We also propose a novel metric, the consolidation factor, to describe a node's (i.e., small geographic area) importance in determining flyway structure. The community detection algorithm identified four main flyways for mallards, northern pintails, and American green-winged teal with the flyway structure of Canada geese exhibiting higher complexity. For mallards, flyway structure was relatively consistent through time. However, consolidation factors and cross-community mixing patterns revealed that for mallards and green-winged teal the presumptive Mississippi flyway was potentially a zone of high mixing between flyways. Additionally, interspersed throughout these major flyways were smaller mixing zones that point to added complexity and uncertainty in the four-flyway concept. Not only does the incorporation of this uncertainty due to mixing provide a potential alternative management strategy, but the network approach provides a robust, quantitative approach to flyway identification that fits well with the adaptive harvest management framework currently used in North American waterfowl management.