Browsing by Author "Noon, Barry, committee member"
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Item Open Access Adjusting for capture, recapture, and identity uncertainty when estimating detection probability from capture-recapture surveys(Colorado State University. Libraries, 2015) Edmondson, Stacy L., author; Givens, Geof, advisor; Opsomer, Jean, committee member; Kokoszka, Piotr, committee member; Noon, Barry, committee memberWhen applying capture-recapture analysis methods, estimates of detection probability, and hence abundance estimates, can be biased if individuals of a population are not correctly identified (Creel et. al., 2003). My research, motivated by the 2010 and 2011 surveys of Western Arctic bowhead whales conducted off the shores of Barrow, Alaska, offers two methods for addressing the complex scenario where an individual may be mistaken as another individual from that population, thus creating erroneous recaptures. The first method uses a likelihood weighted capture recapture method to account for three sources of uncertainty in the matching process. I illustrate this approach with a detailed application to the whale data. The second method develops an explicit model for match errors and uses MCMC methods to estimate model parameters. Implementation of this approach must overcome significant hurdles dealing with the enormous number and complexity of potential catch history configurations when matches are uncertain. The performance of this approach is evaluated using a large set of Monte Carlo simulation tests. Results of these test vary from good performance to weak performance, depending on factors including detection probability, number of sightings, and error rates. Finally, this model is applied to a portion of the bowhead survey data and found to produce plausible and scientifically informative results as long as the MCMC algorithm is started at a reasonable point in the space of possible catch history configurations.Item Open Access Assessing wildlife habitat suitability for ecological sites and state and transition models(Colorado State University. Libraries, 2011) Hibbs, Willow Bo, author; Roath, Roy, advisor; Fernandez-Gimenez, Maria, committee member; Noon, Barry, committee memberWildlife habitat is an important component of rangeland management plans. Unfortunately, there are few practical tools to assist managers in understanding how management and environmental variation affects habitat suitability. Ecological site descriptions (ESDs) have the potential to fill this role because they contain information on the biophysical features of the land and contain state-and-transition models (STMs) which describe ecological sites in terms of their potential vegetation dynamics. These characteristics can be the primary indicators of suitable wildlife habitat. Researchers and managers using ESDs and STMs have suggested that information on other aspects of ecosystem functions should be included so that they can be evaluated along with soils and vegetation. I developed greater sage grouse (Centrocercus urophasianus) and mule deer (Odocoileus hemionus) habitat models using published literature and a fuzzy logic knowledge representation and evaluation system. The resulting outputs were 0-1 scaled indices representing the relative suitability of habitat based on measured habitat attributes in different states of two ecological sites common in NW Colorado, claypan and mountain loam. In Chapter 1, I tested hypotheses related to the habitat suitability of differing states in these two structurally divergent ecological sites. Results support the hypotheses that states with degraded attributes or that were associated with aerial herbicide spraying are generally lower in habitat suitability, and that states with similar components as the reference state do not have significantly different habitat suitability than the reference states. In Chapter 2, I developed sage grouse habitat maps and compared the results with current habitat mapping procedures. The ecological site/STM framework allowed for an understanding of the distribution, abundance, and value of habitat to be linked to management and environmental variation. This work is an important contribution towards incorporating wildlife habitat information into ESDs and understanding trade-offs in wildlife habitat suitability associated with different vegetation states.Item Open Access Big fish start small(Colorado State University. Libraries, 2020) Leach, Clinton, author; Webb, Colleen, advisor; Poff, LeRoy, committee member; Hooten, Mevin, committee member; Noon, Barry, committee memberIndividuals of the same species often participate in substantially different predator-prey interactions. In many species, these differences are driven by individual size and the ontogenetic niche shifts that occur as an individual grows. This intraspecific size-structure can have profound consequences for our understanding of food web structure and community dynamics. These consequences are particularly important in exploited marine ecosystems where fisheries often target the largest individuals and size-structured feedbacks have been implicated in preventing collapsed fisheries from recovering. In this dissertation, we explored the consequences of this size-structure for the Scotian Shelf and Gulf of Alaska ecosystems. To understand how the collapse of the cod stock on the Scotian Shelf may have fed back on the demographic landscape of cod, we developed a model to estimate how the length-dependent growth and survival of cod changed before and after the collapse. We found that forage fish, released from top-down control, likely played an important role in limiting cod access to food, with consequences for cod survival and the potential for long term recovery. To better understand the community context of these changes, we developed a multivariate autoregressive model to capture how shifts in species' size distributions may have driven changes in the interspecific interaction landscape on the Scotian Shelf. This study found further evidence for the role of forage fish in preventing cod recovery, and linked the corresponding changes in interaction structure to an increase in the overall instability of the system. Lastly, we explored the community structure of ontogenetic niche shifts in the Gulf of Alaska by developing a model to identify trophic groups — collections of individuals with similar interaction patterns — in an individual-level food web assembled from stomach contents data. The identified trophic groups revealed substantial overlap in the ontogenetic trajectories of Gulf of Alaska predator species and the low-dimensional structure of the individual-level food web. This work represents a step toward incorporating individual-level processes into modeling frameworks that can be used to both inform existing theory with data and to inform fisheries management. Specifically, this research highlights the different trophic roles that individuals of a species occupy as they grow, and the importance of growth in moving individuals up the food web and maintaining community structure and stability. Our findings suggest that disruptions to this flow and the resulting loss of large individuals can generate a cascade of effects through the system, leading to fundamental reorganization and increased instability.Item Open Access Bird and mammal response to large-scale habitat mitigation for game species in the oil and gas fields of northwest Colorado(Colorado State University. Libraries, 2016) Gallo, H. Travis, author; Pejchar, Liba, advisor; Noon, Barry, committee member; Paschke, Mark, committee member; Wittemyer, George, committee memberTo view the abstract, please see the full text of the document.Item Open Access Grazing for grassland birds: assessing how management and environmental conditions affect abundance in Colorado's shortgrass steppe(Colorado State University. Libraries, 2018) Davis, Kristin Petersilia, author; Aldridge, Cameron, advisor; Augustine, David, advisor; Skagen, Susan, committee member; Noon, Barry, committee memberRangelands are temporally and spatially complex socio-ecological systems on which the predominant land use is livestock production. In North America, rangelands also contain approximately 80% of remaining habitat for grassland birds, a guild of species that has experienced precipitous declines since the 1970s. Some evidence suggests livestock grazing can be managed to benefit certain grassland bird species by generating the vegetation structure/density they prefer. These benefits, however, appear to be ecosystem-specific, are equivocal even for species predicted to benefit from grazing (e.g., those that prefer short, sparse vegetation), are rarely considered in conjunction with the full suite of environmental factors known to influence grassland birds (e.g., precipitation, vegetation composition), and are poorly understood for species breeding in the shortgrass steppe. To address these research gaps, I evaluated how two grazing management systems – continuous, season-long grazing and adaptive, rest-rotational grazing – and environmental characteristics (e.g., vegetation structure, vegetation composition, precipitation and topography) affected grassland bird abundance in Colorado’s shortgrass steppe. I fit hierarchical distance sampling models that accounted for temporary emigration in a Bayesian framework to five years of point count data (2013-2017) for five focal grassland bird species collected from an ongoing grazing experiment on the Central Plains Experimental Range, a USDA experimental range site, in northeastern Colorado. I first examined grazing impacts on grassland bird abundance in conjunction with ecological sites, which represent local soil and plant characteristics. When grazing management was evaluated in conjunction with spatial variation in ecological sites, I found two of our five focal bird species responded to grazing management: McCown’s longspur abundance decreased and grasshopper sparrow abundance increased in pastures rested from grazing for the entire previous year. In addition, abundances of all focal species varied across ecological sites. To evaluate environmental influences on grassland bird abundance, I first used model selection (deviance information criterion; DIC) to identify temporal scales of precipitation and spatial scales of topography that best predicted grassland bird abundance. I then fit two environmental models – 1) a full environmental model with the best topographic and precipitation scale and vegetation structure and composition covariates for each species, and 2) a full environmental model where I replaced the precipitation scale with a categorical effect of year. Finally, I used model selection (DIC) to evaluate the predictive capacity of my grazing models compared to my environmental models for each species. I found precipitation had the largest magnitude of effect on the abundance of lark bunting and grasshopper sparrow. Vegetation structure had the largest magnitude of effect on the abundance of McCown’s longspur, and vegetation composition had the largest magnitude of effect on the abundance of western meadowlark. Vegetation structure and precipitation had the largest magnitude of effect on horned lark abundance. Precipitation strongly and positively affected the abundance of all focal species except western meadowlark, where the effect was strong but negative. Vegetation structure strongly affected the abundance of all species except grasshopper sparrow, and characterized species by their preferred vegetation structure/density (e.g., sparse grass-preferring species’ abundances decreased and dense grass-preferring species’ abundances increased with vegetation structure). Responses to vegetation composition were generally species specific, but cover of standing dead vegetation and shortgrass affected the abundance of two of my five focal species. Only McCown’s longspur responded to topography. Although my focal species responded to multiple environmental characteristics considered in my environmental models, the grazing models had greater predictive capacity than the environmental models for some of my focal species that prefer more moderate to tall/dense vegetation on the landscape – lark bunting and western meadowlark – and the grazing and environmental models had equal predictive capacity for grasshopper sparrow. This study suggests the factors influencing grassland bird abundance in the shortgrass steppe are complex and diverse. Grazing management alone can predict patterns in grassland bird abundance, but these species also responded to specific components of vegetation composition, vegetation structure and precipitation. Thus, grazing impacts on grassland birds may be context-dependent and managers should consider local environmental conditions (e.g., ecological sites, precipitation conditions, vegetation composition) when developing grazing management for grassland birds. My study occurred during historically wet and average precipitation years, so repeating these analyses in drought would reveal additional and important insight into drivers of grassland bird abundance in the shortgrass steppe. Ultimately, my results suggest cattle production on rangelands can continue to support human economic needs while also supporting grassland bird populations in the shortgrass steppe.Item Open Access Impacts of elk management and riparian condition on songbirds in Rocky Mountain National Park(Colorado State University. Libraries, 2015) Craig, Apryle Dawn, author; Pejchar, Liba, advisor; Aldridge, Cameron, committee member; Noon, Barry, committee member; Bobowski, Ben, committee memberThe widespread loss of apex predators from the western U.S. is having cascading effects on ecosystems. As in other western parks, riparian willow (Salix spp.) communities in Rocky Mountain National Park (RMNP) are declining as a result of a trophic cascade involving the local extinction of wolves (Canis lupus) and an exponential increase in elk (Cervus elaphus). In 2008, RMNP began installing elk exclosures to protect and restore willow communities and the diverse taxa that depend on riparian ecosystems from heavy browsing. Using point counts, I evaluated the effect of elk exclosures and riparian shrub condition on songbird density and occupancy. I found little support for a direct effect of elk exclosures on bird communities, with the exception of shrub nesting birds which occurred at higher densities within exclosures. However, the density and occupancy of some riparian bird species and guilds was positively correlated with particular vegetation conditions in this ecosystem. Shrub height positively related to both density and occupancy of Dusky Flycatcher. For the Lincoln Sparrow and shrub-nesting guild, occupancy also had a positive relationship with shrub height. The percent of shrub cover within 15 m of the survey point was an important positive predictor of density for Lincoln's Sparrows, Song Sparrows, and Wilson's Warblers, and foliage-gleaner and shrub-nesting guilds. The percent of riparian shrub cover within 300 m was an important positive predictor for the density of Wilson's Warblers. American Robin, a habitat generalist, and ground-nesting and foraging guilds did not respond strongly to shrub cover or height at any scale. These results reflect the variable shrub conditions inside and outside exclosures, and affirm that managing for mid to high density shrub cover and height will be beneficial for some riparian specialists. My findings provide park managers critical information on bird communities in experimental elk exclosures, and insight into the conditions needed to support songbird communities in the park's riparian ecosystems.Item Open Access Implications of movement behavior responses of both Asian and African elephants in changing landscapes of the 21st century(Colorado State University. Libraries, 2023) Chan, Aung Nyein, author; Wittemyer, George, advisor; Leimgruber, Peter, committee member; Noon, Barry, committee member; Aldridge, Cameron, committee memberAn organism moves to fulfil its most fundamental survival and reproductive needs. Studying movement behavior can provide insights into both inter- and intra-specific interactions, how a species interacts with its environment and accesses resources, species distribution, etc. Given human presence affects mammalian movement across the globe, animal movement studies are increasingly important to assess and understand the impacts of humans on wildlife. Movement behavior response to human presence is particularly relevant and important to understand in the 21st century since global human population is projected to reach 9.7 billion by the year 2050. The unprecedented level of human presence and associated land use changes will impact all living organisms on the planet, particularly megaherbivores such as Asian and African elephants which have some of the largest space use requirements among terrestrial mammals. My dissertation research focuses on studying and understanding the movement behavior responses of Asian and African elephants to human-related landscape changes. The Asian elephant (Elephas maximus) which is currently listed as endangered under the IUCN red list of threatened species. The population status of the species is unclear but declining. The species is facing habitat loss and fragmentation due to agricultural expansion, heightened human-elephant conflicts related to human encroachment in previous wilderness areas, and illegal killings, including but not limited to, poaching for skin, ivory, and meat. The largest remaining tracts of wildland (i.e., habitat suitable for wild elephant to exist) among the current extant range countries/states occurs in the country of Myanmar. However, the struggling economy and unstable political climate put unusual amount of stress on the remaining elephant populations across the country. Asian elephant numbers are declining across much of their range in Myanmar, driven largely by serious threats from land use change resulting in habitat loss and fragmentation. To effectively manage and conserve the remaining populations of endangered elephants in the country, it is crucial to understand their movement behavior across the country's agricultural gradient. Chapter 1 provided baseline information on elephant spatial requirements and the factors affecting them in Myanmar. This information is important for advancing future land-use planning that considers space-use requirements for elephants. Failing to do so may further endanger already declining elephant populations in Myanmar and across the species' range. We used autocorrelated kernel density estimator (AKDE) based on a continuous-time movement modeling (ctmm) framework to estimate dry season (26 ranges from 22 different individuals), wet season (12 ranges from 10 different individuals), and annual range sizes (8 individuals), and reported the 95%, 50% AKDE, and 95% Minimum Convex Polygon (MCP) range sizes. We assessed how landscape characteristics influenced range size based on a broad array of 48 landscape metrics characterizing aspects of vegetation, water, and human features and their juxtaposition in the study areas. To identify the most relevant landscape metrics and simplify our candidate set of informative metrics, we relied on exploratory factor analysis and Spearman's rank correlation coefficients. Based on this analysis we adopted a final set of metrics into our regression analysis. In a multiple regression framework, we developed candidate models to explain the variation in AKDE dry season range sizes based on the previously identified, salient metrics of landscape composition. Our objectives were to (1) estimate the sizes of dry, wet, and annual ranges of wild elephants in Myanmar; and quantify the relationship between dry season (the period when human-elephant interactions are the most likely to occur) range size and configurations of agriculture and natural vegetation within the range, and (2) evaluate how percentage of agriculture within dry core range (50% AKDE range) of elephants relates to their daily distance traveled. Elephant dry season ranges were highly variable, averaging 792.0 km2 and 184.2 km2 for the 95% and 50% AKDE home ranges, respectively. We found both the shape and spatial configuration of agriculture and natural vegetation patches within an individual elephant's range play a significant role in determining the size of its range. We also found that elephants are moving more (larger energy expenditure) in ranges with higher percentages of agricultural area. Chapter 2 reveals how elephants interact with agriculture and other important environmental variables such as natural vegetation, roads, and water, etc. Habitat loss and fragmentation due to accelerated agriculture expansion is a major threat to existing wildlife populations across Asia. Although it had been shown that Asian elephant space use was correlated with the level of fragmentation on the landscape in Chapter 1, the mechanism underlying this process is not well documented and can serve to help focus conservation efforts. We analyzed selection behavior of wild elephants across three study sites with different levels of agriculture use patterns in Myanmar, assessing the impact of structure in the agriculture- wildlands interface on habitat selection by elephants. Given elephants exhibit heterogeneous spatial behavior, we fitted two types of selection models to gain insight into the diversity of strategies employed at the local- and home-range scale. We used variance partitioning analysis to quantify the explanatory contribution of individual, study site, and sex. We found that the variation in the resource selection behavior was mainly due to individual differences, and the level of agriculture present in an individual's range was the most influential to its selection behavior. Gaining a deeper understanding of habitat selection behavior by elephants across the changing landscapes of Asia can help inform management decisions and conservation actions. As the military coup in 2021 in Myanmar affected my ability to continue working in Myanmar, we decided to transition into assessing the connectivity between Etosha National Park and an adjacent Kunene multi-use conservancies area in Namibia for African elephant (Loxodonta africana) as Chapter 3. This region is of particular importance in African elephant conservation since the population is doing relatively well in the area and could serve as one of the remaining strongholds for the species. The loss of habitat and fragmentation of landscapes could lead to declines in wildlife populations, highlighting the need to identify and preserve critical habitats. Connectivity between populations plays a crucial role in mitigating the risks faced by small populations and ensuring their long-term persistence. As a result, the identification of corridors has become a key objective in wildlife conservation. Various methods have been developed to identify high connectivity locations, including resistance surface modeling and empirical-based approaches using GPS tracking data. We used GPS telemetry data from 66 elephants to empirically quantify connectivity using a graph-theoretic approach and assessed landscape features influencing connectivity. We applied the 'movescape' approach to define and locate different types of corridors and examined how landscape features differed across these corridors. Our results revealed strong variation in connectivity across the landscape, with paths of high connectivity near water sources between the study areas. We found that factors related to water sources and human presence primarily influenced connectivity. The findings of this study provide valuable insights into the connectivity patterns and landscape features influencing connectivity for African elephants in northwestern Namibia. We discussed this findings in the context of future conservation management scenarios. Finally, Chapter 4 assessed the current knowledge on population status of Asian elephants across all 13 range countries or states. We conducted a literature search on Google Scholar using keywords, "Asian elephants", "Population size", "Abundance", and "Density". We found 26 articles and 9 governmental and non-governmental reports from 2000 to 2022 to evaluate the extent of population assessments using statistically robust methods. Our findings indicate that only 4.39% of the current known distribution of Asian elephants had been assessed using robust sampling and statistical approaches. Out of the 13 range states, only 7 had conducted assessments, with only 3 countries performing robust population assessments in the last 5 years. We highlight the urgent need for more comprehensive and up-to-date studies to accurately estimate the population size of Asian elephants. We recommend investing in spatial capture- recapture approaches using fecal-DNA and photographic capture-recapture methods where feasible to improve abundance estimation. The results of this review emphasize the critical role of accurate population knowledge for effective conservation and management actions for endangered species like the Asian elephant. This dissertation provides critical pieces of information regarding movement ecology and conservation of both Asian elephant and African elephant. We present analyses on space use requirements, resource selection behavior and the quantification of sources of variation in the movement behavior for Asian elephant in Myanmar. Chapter 1 and chapter 2 were the first two studies to assess movement behavior in Myanmar using empirical data. Since identifying and conserving corridors is one of the key objectives for African elephant's conservation, chapter 3 provides crucial information for managers on the ground in Etosha National Park and surrounding areas. Finally, we highlighted the research gap in Asian elephant conservation by reviewing studies and reports on population status across the species' range.Item Open Access Managing vernal pool habitats on federal lands: maintaining obligate amphibian species(Colorado State University. Libraries, 2013) Green, Adam Wesley, author; Bailey, Larissa L., advisor; Funk, W. Chris, committee member; Nichols, James D., committee member; Noon, Barry, committee memberTo view the abstract, please see the full text of the document.Item Open Access The selection of species of conservation concern under the USDA Forest Service's new planning requirements for wildlife(Colorado State University. Libraries, 2016) Grimes, Summer Star, author; Schultz, Courtney, advisor; Noon, Barry, committee member; Cheng, Tony, committee memberIn 2012, the USDA Forest Service finalized a planning rule that represents the most significant change in federal forest policy in nearly 30 years. All 155 national forests (and 20 national grasslands) must eventually update their management plans in accordance with the new regulations, which have significant implications for wildlife conservation planning. The agency selected eight “early adopter” forests as the first to implement the new planning rule. Given the contentious history of wildlife planning on national forests, there is a high level of interest amongst many audiences in the implementation of the new rule’s language – specifically for a new category of species: “species of conservation concern” (SCCs). The new rule requires the agency to maintain the viability of SCCs on national forests; however, due to uncertainty regarding the new rule’s language, concern exists regarding the management of and planning for SCCs. This research investigated the process of policy implementation during the early stages of forest plan revision on three adjacent early adopter forests to provide insight into the factors that are likely to influence wildlife planning decisions for SCCs across all national forests. Approximately 20 qualitative, semi-structured interviews with agency staff and external environmental partners revealed that traditional challenges of policy implementation were a continued barrier to wildlife planning; however, interviews also revealed cautious optimism that the agency is experiencing a positive paradigm shift in how they address ecosystem management, enabling them to move beyond administrative borders and see forests as part of a broader ecosystem – potentially resulting in a more integrated approach to wildlife management and habitat conservation. This study provides valuable insight into early-stage procedural determinations for wildlife planning on national forests for at-risk species and can serve as a valuable source of ‘lessons learned’ for subsequent forest plan revisions.Item Open Access Using species functional traits to predict community dynamics(Colorado State University. Libraries, 2012) Ames, Gregory Michael, author; Webb, Colleen, advisor; Poff, N. LeRoy, committee member; Knapp, Alan, committee member; Noon, Barry, committee memberA major goal for community ecology has been to determine a general set of rules to explain the structure and function of communities. Traits-based methods for describing community dynamics have been touted as providing a set of general methods to describe the structure and function of communities based on measurable properties of individual organisms in the community in a changing environment. Validation of traits-based methods that describe changes in community structure as a function of the interaction between functional traits along changing environmental gradients in real systems is needed. Here we present studies of three different plant communities where we use novel applications of traits-based Bayesian hierarchical models and principal component analysis to explain the changes in community structure/function and demonstrate that the communities are primarily structured by traits and their interactions with a changing environment. In a natural tallgrass prairie we were able to explain more than 84% of the variation in community functional diversity and an average of 64% of the cover variation across the ten species in the study over a 25-year span (Chapter 1). Additionally we show that changes in community structure are primarily explained by relative growth rate and its interaction with precipitation. In an experimentally manipulated grassland, our model explains more than 75% of the variation in total plot biomass over the course of 18 years. Further, we found that this system was primarily driven by the same trait/environment interactions as the tallgrass system. Finally, we show that trait/environment interactions allow us to explain 91% of the variation in plot biomass in a restored riparian wetland. Our ability to explain large portions of the variation in community structure and performance of these three distinct types of plant communities, using similar traits and environmental drivers, provides evidence of general laws underlying the structure of plant communities. This work represents a significant step toward understanding those general laws and helping community ecology develop from a largely descriptive science to a predictive science.