Theses and Dissertations

Permanent URI for this collectionhttps://hdl.handle.net/10217/100425

Of special note are theses cited in James R. Meiman's Little South Poudre Watershed and Pingree Park Campus (Colorado State University, College of Forestry and Natural Resources, 1971).

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Response of roosting aerial insectivores to ongoing climate change quantified by weather surveillance radar
(Colorado State University. Libraries, 2025) Deng, Yuting, author; Horton, Kyle G., advisor; Bailey, Larissa, committee member; Kendall, William, committee member; Ruegg, Kristen, committee member
Aerial biotas encompass species that feed on airborne insects while in flight, including various bird species (e.g., swallows, martins, nightjars, and flycatchers), bats, and insects (e.g., dragonflies). This community inhabits aerial habitats and occupies a critical interface between terrestrial and aquatic ecosystems. Because these ecosystems provide essential food resources and habitats, aerial insectivores' responses to climate change are closely tied to shifts at these ecological boundaries. As climate change intensifies, these habitats are increasingly unpredictable due to long-term climate shifts and more frequent extreme weather events, like cold snaps. These environmental changes may have driven biological changes at varying levels across aerial trophic food webs, potentially leading to trophic mismatches—where the timing of consumer demand no longer aligns with the availability of their food resources. As a result, aerial insectivores are particularly vulnerable to these shifts, and many are experiencing acute population declines. As key predators in the aerial trophic system, aerial insectivores help maintain ecosystem balance and health. They also provide ecosystem services, such as pest population control and the reduction of insect-borne diseases. Despite their ecological and agricultural importance, knowledge gaps remain regarding how aerial insectivores respond to environmental changes at a macrosystem scale—particularly regarding shifts in phenology and population dynamics. Addressing this knowledge gap is crucial for understanding and mitigating the cascading effects of these changes on ecosystems. Therefore, there is a need to monitor changes in aerial insectivore populations and phenology. In North America, some aerial insectivore species form large roosting aggregations—sometimes numbering in tens of thousands—during certain life cycle stages. These roosts appear on Next Generation Weather Radars (NEXRAD) as expanding "angel rings," providing a unique opportunity to quantify their occurrence across broad spatial and temporal scales. To leverage this, I integrated decades of radar data with other remote sensing datasets and machine learning tools to quantify phenological and population changes and to investigate their drivers in two taxonomic groups of roosting aerial insectivores: swallows and bats. My dissertation centers around the key question: How has the phenology and population of these aerial insectivores changed in response to changing climate? To address this, I first focused on roosting swallows in the Great Lakes region, primarily Tree Swallows and Purple Martins. Chapter 1 asks How swallow roosting phenology changed over the past two decades? Chapter 2 asks Which aspects of climate change, during which periods, at what locations, impact swallow roosting phenology at the Great Lakes? In Chapters 3 and 4, I shifted my focus to Mexican free-tailed bats in south-central Texas. Chapter 3 asks Has phenology and population of Mexican free-tailed bats changed in this region? Chapter 4 asks Can I predict the intensity of nightly emergence events of Mexican free-tailed bats? The goal of my work is to provide ecological evidence of these changes and uncover the underlying mechanisms, offering insights that can inform conservation policies and actions.
Open Access
Spatial and temporal patterns of abundance of swallow and martin communal roosts
(Colorado State University. Libraries, 2025) Belotti, Maria Carolina Tiburcio Dias, author; Horton, Kyle G., advisor; Bailey, Larissa, committee member; Koons, David, committee member; Ross, Matthew, committee member
During their non-breeding period, many species of swallows and martins (family: Hirundinidae) congregate in large communal roosts, which can gather hundreds of thousands of individuals. These roosts are well-known within local birdwatching communities; however, monitoring them at large spatial scales and with day-to-day temporal resolution is challenging. Due to the high densities of birds within these aggregations, however, their early morning dispersals can be systematically detected by nearby weather radars, which can be used to collect data about roost timing, size, and location. Nonetheless, finding roost signatures amongst the millions of rendered reflectivity images is extremely time-consuming — a fact that has limited the spatial and temporal scopes of previous radar-based studies. We leveraged the recent advances in computer vision and high-performance computing to partially automate this task and build a dataset of 22 years of roost detections captured by 12 radar stations in the Great Lakes region. We first verified that these detections correspond to swallow and martin roost dispersals, comparing the phenology of our findings with that obtained from eBird data. We then describe changes in the roost size distribution throughout the season and discuss the relationship between a roost's size and its persistence in the landscape. We also obtained trends of roost activity, comparing those with breeding population trends from eBird and the North American Breeding Bird Survey. Lastly, we used two years of data (2014-2015) collected by an operational weather radar in Manaus to describe, for the first time, the phenology of swallow and martin aggregations in the Low Negro-Solimões region of the Amazon Rainforest. We compared roosting behavior in the Amazon with what we observed 6,000 km away, in the Great Lakes region, regarding the daily number of birds and the roost size distribution. Our work demonstrates how weather radars offer us a unique opportunity to monitor and study swallow and martin populations at an unprecedented transcontinental scale, something that can rarely be achieved for any other taxa.
Open Access
Whole genome sequencing to characterize Cutthroat Trout populations across the Continental Divide
(Colorado State University. Libraries, 2025) Clark, Noël, author; Wells, Caitlin, advisor; Kanno, Yoichiro, advisor; Funk, William Chris, committee member
Cutthroat Trout (Oncorhynchus spp.) are a biological icon of western North America with the largest native range and species diversity of all North American trout. Currently, there are six recognized lineages believed to be native to the Southern Rocky Mountains. Despite almost a decade of genetic and morphological studies, clarity on the phylogenetic history and evolutionary differences between all lineages of Colorado's Cutthroat Trout remains to be resolved and has implications for future management of populations in this species group throughout the Southern Rocky Mountains. Previous molecular studies have used genetic markers representing only a small portion of the genome, such as with ND2 mitochondrial DNA haplotypes, microsatellites, and amplified fragment length polymorphisms (AFLPs), and have not included a comprehensive nuclear DNA assessment from all extant lineages of Cutthroat Trout found in Colorado. To address this knowledge gap, we used whole genome sequencing to analyze DNA samples from all extant lineages of Southern Rocky Mountain Cutthroat Trout, as well as from five other Cutthroat Trout lineages across North America. Using whole genomes, we have confirmed the nuclear distinctiveness of the "blue" and "green" lineages of former Colorado River Cutthroat Trout, as well the form from the San Juan basin. We additionally identified the persistence of ancestral and unique spatial genetic diversity despite widespread historic stocking. These findings, along with an analysis of long-term effective population sizes, provide key insights into possible natural and anthropogenic drivers of population migration, separation, and speciation. Taken together, our results inform conservation management of Cutthroat Trout lineages across their native range in the Southern Rocky Mountains.
Embargo
Evaluating the role of North American scavengers in the transmission of chronic wasting disease prions to cervids
(Colorado State University. Libraries, 2025) Bye, Kelly, author; Wittemyer, George, advisor; VerCauteren, Kurt, advisor; Titcomb, Georgia, committee member; Zabel, Mark, committee member
Many scavenging species have been categorized as pests or potential disease vectors, and as a result, management actions toward scavengers are frequently focused on removal. However, scavengers can play important ecological roles, and there is a growing need to define their impact on ecological systems and processes. In the context of disease ecology, their influence is inherently complex, as their interactions at and with carcasses can either mitigate or facilitate the pathogen transmission. Chronic wasting disease (CWD) is a transmissible prion disease afflicting cervids – a taxon that is important to multiple stakeholders. The disease is invariably fatal, and prions persist in the environment for years. Scavengers have been implicated in CWD transmission due to their interactions with infected carcasses, and recent studies have begun to quantify the extent of their involvement. In Chapter 1, we explored scavenger activities at 20 cervid carcasses in northern Colorado, USA using data gathered from camera traps from January 2022 to May 2023. Specifically, we characterized the species community at cervid carcasses, described carcass utilization patterns, identified landscape factors associated with scavenger diversity at carcass sites, and determined correlates of scavenger foraging duration. Black-billed magpies (Pica hudsonia) and coyotes (Canis latrans) comprised 63.9% of species detections at carcasses. We found that site-level species diversity decreased as human modifications to the landscape increased and foraging bout duration decreased as carcasses aged and as temperatures increased. Foraging time at carcasses varied by species, with common ravens (Corvus corax) and black bears (Ursus americanus) spending the greatest time foraging on carcasses. While observability of carcass tissues consumed was limited, we found that most scavengers consumed muscle (tissue with relatively low prion loads), except for turkey vultures (Cathartes aura) who preferred abdominopelvic cavity organs. This chapter underscores the complex interplay between temporal, environmental, and species-specific factors in determining scavengers' role in transmission dynamics, with broader implications for understanding the cascading effects of scavenger activity on ecosystem health. In Chapter 2, we explored the contributions of coyotes to CWD epidemiology. This species is of particular interest in this system given their ubiquity across North America, proclivity for scavenging from cervid carcasses, and the retention of prion infectivity post-passage by coyotes. To further quantify coyotes' role in CWD ecology, we conducted controlled feeding experiments to examine the fate of three concentrations of CWD prions post-passage through the digestive tracts of eight adult coyotes. We utilized real-time quaking induced conversion (RT-QuIC) to serially determine the relative amount of prions in coyote feces after three levels of exposure: low (0.1% [4 Log10LD50/g] CWD positive brain homogenate [BH]), moderate (1% [6 Log10LD50/g] CWD positive BH), and high (10% [8 Log10LD50/g] CWD positive BH). We found that coyotes are remarkably efficient neutralizers of CWD; we recovered less than 1% of ingested prions from fecal samples across all tested exposure levels. Additionally, we found no evidence of prion seeding activity in the tissues of study animals after necropsy, indicating that coyotes neutralize, rather than sequester, ingested prions. Our findings demonstrate that coyotes provide an important ecosystem service by consuming CWD-positive tissues, effectively mitigating the environmental accumulation of one of the most environmentally robust pathogens known at carcass sites.
Open Access
Breeding season habitat use of Conservation Reserve Program (CRP) land by lesser prairie-chickens in west central Kansas
(Colorado State University. Libraries, 2004) Fields, Tamara Leigh, author; White Gary, advisor; Leininger, Wayne, committee member; Savidge, Julie A., committee member
Lesser prairie-chicken (Tympanuchus pallidicinctus) populations have drastically declined throughout their range since the 1800's. In Kansas, counts of leks and individual birds indicate that populations have experienced significant declines since 1964. The primary cause of range-wide and statewide declines has been deterioration of suitable habitats. Recently, populations of lesser prairie-chickens have expanded northward and westward in Kansas. The range expansion has been attributed to an increase in CRP (Conservation Reserve Program) lands. This study assessed the importance of CRP and the interseeding of forbs in CRP to lesser prairie-chickens. Invertebrate sampling was conducted in June, July, and August 2001 to determine whether interseeding increased invertebrate biomass and diversity. Sweepnet samples were collected on five grassland CRP fields that were successfully interseeded with alfalfa and sweet clover in alternating strips on 50% of the field. Total invertebrate biomass and diversity were greater on interseeded CRP plots compared to grass CRP plots. There was no evidence of a treatment effect on orthoptera, lepidoptera larvae, hemiptera, hymenoptera, and coleoptera biomass. However, differences in orthoptera biomass between grass and interseeded plots suggest that the majority of the treatment effect on total biomass could be attributed to this order. Greater total invertebrate biomass and count diversity was attributed to the abundance of forbs found within interseeded fields. Seventy-one female lesser and greater prairie-chickens (Tymanuchus cupido) were equipped with transmitters during the 2002 and 2003 breeding seasons to monitor habitat selection and survival. Fields were classified into five habitat types: native rangelands, croplands, grassland CRP (GCRP), interseeded CRP (ICRP), and forb CRP (FCRP). Habitat selection of pre- and post-nesting hens (n = 68), nesting hens (n = 60), and hens with broods (n = 27) was determined by comparing use to habitat availability within the southwest quarter of Gove County. Hens used cropland less than expected and ICRP more than expected. Nesting hens used FCRP, rangeland, and cropland less than expected and GCRP and ICRP more than expected. Greater use of ICRP and GCRP fields was attributed to the abundance of invertebrates and cover provided by ICRP and GCRP, respectively. Lastly, hens with broods used cropland less than expected and demonstrated no habitat selection for any habitat types. The lack of selection by hens with broods is most likely a product of small sample sizes in my study. Lack of selection was also a product of high rangeland brood use and the high availability of this habitat type. Additionally, habitat type was not considered the most important determinant of a brood's location. Instead, broods were frequently located in heterogeneous fields characterized by grassy cover interspersed with an abundance of forbs. A number of nest and brood statistics were computed as an index of reproductive success. Nesting rate was 89. 7%, hatchability was 76.5%, renesting rate was 19.1 %, and mean clutch size was 11.2 eggs. Apparent brood success (~ 1 chick survived) to 14 days was 65.6%, and 53.8% of these broods survived to 60 days. Only 28% of tracked broods survived from hatch to 60 days post-hatch. In addition to complete brood loss, the number of chicks per brood declined from 9.6 (SE= 0.7) at hatch to 5.0 (SE= 3.7) 60 days post-hatch. Mean recruitment at 60 days post-hatch was 0.59 chicks per hen (SE = 0.10), overall chick survival for pre-fledge broods was 0.433 (SE= 0.03), overall chick survival for post-fledge broods was 0.372 (SE = 0.05), and overall chick survival over the entire period was 0.161 (SE= 0.02). Survival rate of hens, nests, and broods were estimated using Program MARK. The known fate data type was used to model weekly survival probabilities of hens as a function of eight time-specific and individual covariates. The same data type was used to evaluate the effects of 13 sources of variation on the daily nest survival probabilities. To model daily brood survival probabilities as a function of 14 sources of variation, the nest survival data type available in Program MARK was used. All candidate models within each survival analysis were ranked based on a small sample Akaike's Information Criteria {Al Cc)- In addition to evaluating the effects of different sources of variation, the best model within each analysis was used to estimate model-conditional survival estimates. The level of model selection uncertainty within the hen survival analysis indicates that none of the models approximated weekly hen survival probabilities well. However, the best model suggested a positive association between survival and weekly precipitation. The probability of a female prairie chicken surviving the breeding season was 0.62 (SE= 0.14) and 0.66 (SE= 0.12) in 2002 and 2003, respectively. Daily survival probabilities of nests were a function of a quadratic time trend, nest age, and temperature. Daily nest survival probabilities declined as the season progressed. Nest age and temperature were also negatively correlated with daily nest survival. The probability of a nest surviving from May 10 to June 1 was 0. 70. Daily brood survival probabilities were a function of a quadratic time trend, brood age, hen age, forb composition and precipitation events. Daily brood survival declined as the season progressed. Brood age and forb composition were positively associated with daily survival, whereas precipitation was negatively correlated with daily survival. Broods tended by adult hens had higher daily survival probabilities than broods of juvenile hens. The probability of a brood surviving from June 1 to July 30 (hatch to 60 days post-hatch) was 0.52 and 0.06 for a brood reared by an adult and juvenile, respectively. The habitat selection analyses indicate that ICRP and GCRP may be beneficial to prairie chickens during the breeding season. Although there was no evidence that hen, nest, and brood survival were a function of habitat, the long-term benefit of CRP was evident. From field observations it was apparent that CRP may be allowing these birds to persist in dry years. In contrast, rangeland may be adequate when drought and the compounding effects of grazing do not decrease cover and food sources.
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
Spring and autumn stopover resources and land use patterns for the Rocky Mountain population of sandhill cranes in the San Luis Valley, Colorado
(Colorado State University. Libraries, 2024) Vanausdall, Rachel Ann, author; Kendall, William L., advisor; Collins, Daniel P., committee member; Koons, David N., committee member; Sueltenfuss, Jeremy, committee member
Stopover areas are important to migrant birds for resting and refueling on long journeys to and from their breeding grounds. Many birds use spring stopover areas to obtain adequate energy reserves to aid in reproduction, and the quality of habitat used during both spring and autumn migration can have cross-seasonal effects on vital rates, such as survival probability, later in the annual cycle. The Rocky Mountain Population of greater sandhill cranes (Antigone canadensis tabida) is a migrant population that stages in several western regions during the migratory period, but most of their time is spent on a single stopover area during the autumn and spring. While this population breeds throughout states within and around the Rocky Mountains and winters throughout parts of New Mexico, Arizona, and Mexico, over 90% of the RMP stopover in the San Luis Valley (SLV) in southcentral Colorado. Additionally, a smaller number of lesser sandhill cranes (A. c. canadensis) from the Midcontinent Population use the SLV during autumn and spring migration. During this time, sandhill cranes utilize riverine corridors, wetland complexes, wet meadows and pastures, and agricultural fields in the SLV on both private and public lands. A high proportion of their diet includes spilled barley and other grains leftover after harvest in autumn and before planting season the following spring. The Monte Vista National Wildlife Refuge (MVNWR) also provides supplemental barley for sandhill cranes in spring and manage water to provide emergent wetland and shallow water habitats for roosting and loafing. However, the SLV has experienced landscape changes that threaten important habitat for sandhill cranes, and most of these changes center around the availability of water. As a semi-arid and snowpack driven region, the hydrology of the SLV relies mostly on precipitation that comes from the surrounding mountains and on aquifers that provide irrigation water and recharge other water sources. Over the years, efforts to divert surface water and pump water from aquifers have led to overappropriation of water rights and reduced water availability. In addition, increasing temperatures and a changing climate are contributing to increasing water scarcity. These changes will likely influence the land use patterns, which could ultimately affect the supply of energy on the landscape and energetic demand of sandhill cranes. In turn, this could affect abundance and distribution. Understanding migration phenology, along with their bioenergetics and land use patterns while at a primary stopover area, are important for informing management on both public and private land and for estimating the carrying capacity of an area for migrant species. While the timing of RMP sandhill crane migration in the SLV has been documented previously, our first objective was to formally quantify their migration phenology in and out of the SLV and determine if there were weather or habitat covariates influencing their persistence probability. Migrant birds are thought to optimize migration timing and energy use by balancing the speed of migration with energetic consumption and expenditure. For example, migrating faster in the spring (i.e., time-minimization), and thus arriving earlier at the breeding grounds, may improve reproductive performance for some species. On the other hand, reducing the amount of energy (i.e., energy-minimization) used during migration may be preferred in autumn under reduced time constraints, so birds may take longer to migrate at this time of the year. Various factors will also influence how long birds remain at a stopover area, including weather patterns and habitat availability. As large birds, sandhill cranes may take advantage of various weather patterns, such as strong tailwinds or high wind speeds, to aid in flight and overall migration. These factors may reduce the probability that a sandhill crane will remain at a stopover if they incur a higher energetic cost. We examined the arrival probability and persistence probability of RMP sandhill cranes in the SLV using data across eight years from birds fitted with global system for mobile communication (GSM) platform transmitter terminal (PTT) tags or Global Positioning System (GPS) units. Using an open robust design mark-recapture model, we examined the influence of temperature change, barometric air pressure, tailwinds, crosswinds, wind speed, and surface water on the persistence probability of RMP sandhill cranes. Stopover duration was longer in autumn than in spring and had higher variability across years. Arrival probability to the SLV peaked on 13 October in autumn and 21 February in spring. Persistence probability declined around mid-December in autumn and mid-March in spring. We found that several weather covariates influenced persistence in both seasons. In autumn, sandhill cranes departed the SLV with higher tailwinds, lower crosswinds, and higher surface water availability. In spring, sandhill cranes departed the SLV with lower crosswinds and higher barometric air pressure at the surface and higher wind speeds at altitudes of about 3,000 m. The effect of wind speed was stronger later in the spring. Given the lower variability of arrival and persistence probability and shorter stopover duration in spring compared to autumn, we suspect that RMP sandhill cranes are using a time-minimization strategy during spring. However, given the use of supportive winds and weather conditions ideal for soaring, RMP sandhill cranes appear to be using strategies that save energy in both seasons. This study identified the optimal timing of water management and surveys for RMP sandhill cranes and confirms that weather influences their persistence. Understanding differences in migration patterns between seasons and the factors that influence persistence at stopover sites will also be important for anticipating phenological impacts from climate change and land use alterations. Next, we focused on how RMP sandhill cranes select habitat and use the SLV during their stopovers in autumn and spring. Sandhill cranes tend to show predictable movement patterns during migration in the SLV. They generally spend nights roosting in areas with shallow water (e.g., emergent wetlands, rivers, creeks, ponds) and leave the roosts around sunrise to forage primarily on grain fields. They spend midday loafing (i.e., resting and engaging in other behaviors) in various habitats, usually near or in water, and then return to feed one more time close to sunset before returning to the roost. This movement around a focal roosting point characterizes central place foragers. Given the risk of increasing water scarcity in the SLV and the potential for future landscape changes, quantifying the selection patterns of RMP sandhill cranes during their roosting, foraging, and loafing periods provides valuable information for habitat management. We used GSM/GPS data to examine the effects of water, sandbar, vegetation height, distance to the nearest grain field, landcover type, and ownership on roosting, loafing, and foraging habitat selection by RMP sandhill cranes. We found that sandhill cranes selected for areas with a high amount of water, relatively short vegetation (<5 m in autumn, <10 m in spring), close to grain fields (<5 km), and areas identified as open water for roosting. Loafing sandhill cranes also selected for areas with short vegetation and close to grain fields but that had less water and more sandbar than roosting areas and were identified as pastures or wetlands. While selection was higher for private land overall, we found evidence of avoidance of private lands and a stronger preference for public lands with increasing surface water for roosting in spring. For foraging areas, selection was highest for barley in both seasons, but triticale and other grains had relatively high selection in autumn. Our finding confirms the importance of providing roosting and loafing areas on both private and public lands close to foraging areas and provides evidence that roosting and loafing opportunities may be most limited on public lands in the SLV. We then examined foraging selection patterns more closely to define RMP sandhill crane distribution during migration and determine factors, in addition to habitat type, that affect selection for foraging areas. Flying is energetically expensive, so understanding some of the drivers of foraging preferences can inform management to aid in reducing the amount of energy required to find food. Greater sandhill cranes tend to forage within 2-5 km of their roost from the previous night. As food items in patches decline due to consumption and deterioration, sandhill cranes will move farther from their roost to forage. Other factors may motivate birds to switch patches. Tilling, for example, is a practice that takes place after harvest in many fields in the SLV and can also reduce seed availability. We sought to understand how tillage intensity in grain fields, along with crop type, distance to the nearest roost, and time, influence foraging selection by both greater sandhill cranes and lesser sandhill cranes. The same covariates were also used to examine their effects on the number of greater sandhill cranes. We completed roadside surveys to count greater and lesser sandhill cranes in autumn and spring and identify field-specific covariates. Lesser sandhill cranes were more concentrated in specific areas in the SLV, while greater sandhill cranes were more variable in their distribution. Selection in autumn was most influenced by an interaction between time and crop type for both subspecies, while spring selection was influenced by an interaction between crop type and roost distance. The probability of presence was highest on barley fields or other grains for both subspecies in mid-October and mid-March, but it declined as distance to the nearest roost increased for both subspecies. We only modeled covariates on abundance for greater sandhill cranes and found that an interaction between time and roost distance was the most influential model in autumn. The interaction between time and crop type most influenced abundance in spring. The effect of roost distance was negative early in the autumn season but became positive later in the season. Greater sandhill cranes also showed a higher abundance in other crop types in spring compared to autumn. We found that both greater and lesser sandhill cranes were more likely to be on fields with idle or low intensity tillage practices than those with high intensity tillage practices. Overall, our results suggested that sandhill cranes are variable in their use of the SLV for foraging and prefer to fly farther from roosts to their preferred forage type but may also switch to other crop types. While documenting phenology and selection patterns is useful for prioritizing areas for conservation and determining the appropriate habitat types to provide during migration, researchers and managers are lacking an understanding of how many sandhill cranes the SLV could theoretically support. Changing landscape and climate conditions in the SLV are contributing to increasing water scarcity, which may eventually reduce the amount of barley grown in the SLV or alter the juxtaposition of foraging and roosting areas. To understand how changes in barley tillage practices and amounts may influence RMP sandhill crane numbers in the SLV, our goals were to examine the influence of tillage intensity on barley availability, determine the energy demand of RMP sandhill cranes during autumn and spring, calculate the supply of energy available on the landscape from barley, and estimate current and potential carrying capacity under varying barley amounts. Idle fields (i.e., fields not tilled) had the greatest density of barley than fields that had low or high tillage intensity practices, and RMP sandhill cranes that used more tilled fields spent more time searching for forage. We also found an increase in lipid gain during spring migration, which increased the daily energetic expenditure (DEE) of RMP sandhill cranes during spring compared to autumn. Overall, we found that individual RMP sandhill cranes required between 458 to 566 kcal per day, which equated to 0.129 to 0.160 kg of barley per day, with a greater amount required during spring. The total energy demand required by the population for autumn was approximately 284.9 x 106 kcal (0.08 x 106 kg of barley), and this value increased to 435.4 x 106 kcal (0.1 x 106 kg of barley) for spring. The average energy supply was 5905.5 x 106 kcal (1.7 x 106 kg of barley) for early autumn and 1589.9 x 106 kcal (0.4 x 106 kg of barley) in late spring for the entire SLV. Overall, the supply of energy exceeded sandhill crane demand throughout both seasons. Based on bioenergetics models using the TRUEMET model, most scenarios also showed that energetic supply exceeded demand. Under all scenarios, barley declined by approximately 90% or more between early autumn to late spring, but supply was still greater than demand at the end of spring. While we made several assumptions using these models that could not be validated, we are confident that we provide evidence that there is currently enough barley in the SLV to support more sandhill cranes than the present population. Tillage intensity, particularly barley left idle in autumn and spring, appears to play a bigger role in barley availability than the presence of barley on public over private land. Overall, our findings provide information that can aid in practical management objectives in the face of climate and land use challenges and describe baseline information on how current conditions influence the energetics of the RMP. While the RMP appears to be relatively stable and increasing, several environmental changes in the SLV are likely to impact the distribution, timing of migration, and habitat selection patterns of the population. In turn, these factors will affect how sandhill cranes use and expend energy, which may lead to reduced reproduction or survival. Current objectives for the RMP include providing suitable habitat to support a population goal of 17,000 – 21,000 individuals. Our results indicate that habitat is sufficient for the current population and potentially a larger population. However, given the role of water in the movement and selection of sandhill cranes, increasing water scarcity is likely to temper the benefits of available forage over time, which may make meeting population objectives more challenging. Continued management of water and foraging resources on public and private lands are important, but our results also emphasize the need to integrate habitat management on both ownership types to ensure adequate resources are available during migration.
Embargo
Riverscape features and isolation-by-distance shape spatial genetic structure of Brook Trout in a Colorado headwater stream network
(Colorado State University. Libraries, 2024) Stack, Taylor, author; Kanno, Yoichiro, advisor; Winkelman, Dana, advisor; Oyler-McCance, Sara, committee member; Fairchild, Matthew, committee member; Funk, William Chris, committee member
Understanding the influences of riverscape characteristics on gene flow in stream networks is crucial for managing population connectivity in freshwater species. In this study, we examined the fine-scale genetic structure of non-native Brook Trout (Salvelinus fontinalis) in a headwater stream network proposed for future reintroduction of native trout. Using 12 microsatellite loci, we genotyped 757 individual Brook Trout from 22 sampling sites throughout the dendritic stream network and modelled the effects of physical riverscape features on gene flow. Genetic clustering analysis identified four distinct tributary groups, indicating fine-scale population structure, while pairwise genetic differentiation estimates (mean FST = 0.04; mean Jost's D = 0.06) revealed some genetic connectivity across the network. Riverscape genetics models identified vertical barriers and steep stream gradients as key factors impeding gene flow, whereas higher order mainstem streams were more conducive to trout movement. Gene flow was stronger in the downstream direction, and models with interaction terms revealed that asymmetries between upstream and downstream gene flow were more pronounced in stream reaches with barriers and steep gradients. Mantel tests confirmed that both waterway distance between sites and riverscape resistance significantly influence genetic connectivity across the network. Overall, this study demonstrates that spatial genetic patterns in stream networks are shaped by a combination of isolation-by-distance, riverscape resistance, and asymmetric stream flow. Our findings suggest that this reintroduction area provides sufficient genetic connectivity to support a metapopulation of native trout.
Open Access
Movement ecology of mule deer in partially migratory herds
(Colorado State University. Libraries, 2024) Hart, Anneke R. M., author; Kendall, William, advisor; Alldredge, Mat, committee member; Wittemyer, George, committee member; Boone, Randall, committee member
The purpose of animal movement can be broadly partitioned into two categories of factors that either push or pull animals to move (Loe et al. 2009). Animals will move towards resources, such as food or mates, that are necessary to complete their life cycle. Likewise, they will move away from threats, such as predators or inclement weather, to survive. Movement therefore helps augment an animal's ability to access resources and avoid threats because these variables are typically also moving and changing across space and time. There is great diversity across taxa in how animals move. There is huge variation in the distances, regularity, and area over which animals move – certainly across species but often also within species. In all cases, we can expect that the strategy of movement that animals develop will have been shaped by selective processes where animals made choices about how to access resources and avoid threats that subsequently affected their fitness. In ungulates, a type of movement evolved independently across 17 different lineages (Abraham et al. 2022) that is thought to help them access high-quality forage throughout the annual cycle – i.e., migration. Ungulates that live in mountainous regions can typically maximize their nutrition by spending their winters at low elevation then following the green up as it progresses to higher elevations in the summertime. Selective pressures have shaped herbivore behavior so that they can learn to track food resources as they change in quantity and quality across a landscape. Migratory ungulates typically time their migrations to maximize access to high-quality food resources. Mule deer (Odocoileus hemionus) are unique among ungulates in that they tend to be extremely habitual in their seasonal movements. Like other cervids, they are plastic in terms of timing their movements but exhibit strong fidelity to their seasonal ranges and choice of movement strategy. Mule deer typically establish migratory or resident tactics as adults and stick to that behavior life-long. They also adhere closely to established migration routes and utilize the same extents of seasonal ranges year after year. Mule deer therefore can respond to a seasonally changing environment but are limited in doing so within a fixed spatial extent. In this work, I examined how migratory strategies of mule deer affect 1) resource selection of irrigated lands and 2) survival of adult females and fawns. The two chapters I produced were unified by an aim to understand the nuances of mule deer movement ecology in two partially migratory herds in south-central Colorado. In my first chapter, I examined how fluctuations in natural forage abundance influence the movements of mule deer in an agricultural system, where irrigation provides enhanced foraging opportunities for ungulates. Mule deer tended to increase their selection for alfalfa when their native forage was poor in quality. In my second chapter, I assessed how migratory strategies influenced survival of fawns and adult female mule deer. I detected apparent tradeoffs in survival of mule deer relative to their migratory strategy. Migrant fawns tended to have higher early survival while residents had higher overwinter survival. Additionally, there was interannual variation in the benefits of migration on survival of adult female deer. My research contributes to a broader understanding of how fluctuations in forage abundance drives mule deer movement and how the movement strategies that deer choose to obtain forage then influences their survival. Abraham, J. O., N. S. Upham, A. Damian-Serrano, and B. R. Jesmer. 2022. Evolutionary causes and consequences of ungulate migration. Nature Ecology & Evolution 6:998–1006. Loe, L. E., A. Mysterud, V. Veiberg, and R. Langvatn. 2009. Negative density-dependent emigration of males in an increasing red deer population.
Embargo
Determining the impact of harvest and climate change on the demography of black brant (Branta bernicla nigricans)
(Colorado State University. Libraries, 2024) Blommel, Caroline, author; Koons, David, advisor; Aubry, Lise, committee member; Webb, Colleen, committee member
As a coastal long-distance migrant, black brant (Branta bernicla nigricans) are vulnerable to climate and land-use change while also facing harvest pressure from sport hunting along the Pacific Coast. To examine impacts of harvest pressure and environmental change on brant survival and reproductive components of fitness, I combined band-recovery data with live recapture and resighting data from 1990 to 2023 for the Tutakoke River breeding colony of brant on the Yukon-Kuskokwim Delta in western Alaska. I fit multiple Bayesian multistate mark-recapture models to these data to estimate temporal changes in cause-specific mortality and breeding probabilities over the last 33 years. Harvest rate increased over time and is significantly impacted by bag limit across sex and age groups. Adult non-harvest mortality has remained stable over the study period but is higher in years of extreme El Niño and Aleutian Low Beaufort Sea Anticyclone events. Breeding probability for previous breeders increased over time while breeding probability for previous non-breeders decreased, driven largely by differing responses to spring timing. My work describing brant demographic response to environmental change and harvest provides valuable information on how to manage brant most effectively across their migratory range.
Open Access
Effects of a non-lethal chemical repellent on airport bird communities
(Colorado State University. Libraries, 2024) Urchek, Kathleen, author; Pejchar, Liba, advisor; Werner, Scott, committee member; Kendall, William, committee member; Bright, Alan, committee member
Human-wildlife conflicts are likely to occur wherever the interests and activities of humans and wildlife overlap. Airport environments are a prime example of where such conflict is pervasive because wildlife can view airports as habitat, yet the presence of wildlife increases the risk of collision. As humans increase our reliance on air travel and development encroaches on natural areas, conflicts between humans and wildlife will continue to be prevalent in airport settings, thus creating the need for effective management tools. To assess the effectiveness of one such tool, we evaluated the effect of a non-lethal chemical repellent on bird abundance, species richness, movement, and behavior in airport settings. Following a Before After Control Impact Paired study design we compared the changes among each variable from a period of pre-treatment to a period of active treatment, in both treated and control sites. Using Poisson and zero-inflated mixed effects models we found that the repellent is likely effective in shifting birds from treated to untreated areas within airports, and that the abundance of two common species, Bobolinks and European Starlings, declined following treatment. We also found that the repellent does not change the frequency in which birds move out of treated plots and intersect with runways, but may be altering the within-plot behavior of Eastern Meadowlarks, Red-winged Blackbirds, and Sandhill Cranes. Our mixed findings highlight the need for continued study of the mechanisms behind avian response to chemical repellents in airport settings. Although a diverse set of approaches will always be needed to alleviate the many human-wildlife conflicts associated with airports, here we show that, to promote co-existence with wildlife, this chemical repellent can be a part of that toolset.
Open Access
Occupancy dynamics of barred owls on a spotted owl landscape
(Colorado State University. Libraries, 2024) McGee, Kaitlin R., author; Doherty, Paul, Jr., advisor; Franklin, Alan B., advisor; Bailey, Larissa, committee member; Hart, Sarah, committee member
Invasive barred owls (Strix varia) pose a significant threat to native northern spotted owls (Strix occidentalis caurina) in western North America. Barred owls compete with northern spotted owls for resources and habitat, leading to displacement and subsequent declines in northern spotted owl populations. This impact highlights the need for conservation efforts to mitigate the negative consequences of barred owl presence in spotted owl habitats. In my thesis, I explored barred owl habitat use in northern California using data on both lethal removals of barred owls and barred owl occupancy of non-removal areas from long-term studies. These studies provided a unique opportunity to study associations of barred owl land use both during initial colonization and over time. Barred owl land use was influenced by landscape factors such as topographic water accumulation, forest age, tree composition, and canopy cover as well as interspecific effects of northern spotted owls. I used these results to predict variation in barred owl use of landscapes, which can then focus barred owl management efforts in California.
Open Access
Home range estimates, habitat selection, and nesting behavior of Ferruginous Hawks (Buteo regalis) in western Wyoming
(Colorado State University. Libraries, 2024) Ramirez, Sarah Kathleen, author; Pejchar, Liba, advisor; Koons, David, committee member; Angeloni, Lisa, committee member
Oil and gas development has the potential to negatively impact wildlife, but the consequences for some raptor species are less well understood. Ferruginous Hawks could be particularly susceptible to negative effects due to their large habitat requirements and sensitivity to anthropogenic disturbance. Given the rapid expansion of oil and gas development in many parts of the range of Ferruginous Hawks, it is critical to evaluate habitat use in both a pre-construction and post-construction environment. Understanding selection of habitat resources and nest sites, as well as the factors that contribute to home range estimates, nest success and nest productivity could help inform efforts to mitigate against potential negative effects of land use change. In my first chapter, I aimed to investigate factors associated with breeding Ferruginous Hawk home range estimates and habitat selection in a landscape slated for energy development. In a sagebrush-steppe study site in western Wyoming, I captured breeding hawks and used radio and satellite-telemetry to collect location data, estimate home range estimates, and model habitat selection. Home range estimates were smaller for females and hawks with egg-laying breeding status, and larger with increasing numbers of producing wells. Ferruginous Hawks selected habitat with high terrain ruggedness, low shrub cover, and areas closer to primary prey, and avoided areas with high density of wells. The relationship between lagomorph density and distance to development was dependent on scale. My findings show that home range estimates are smaller in my study relative to other parts of the species' range, and that future energy development is likely to reduce habitat quality and availability for Ferruginous Hawks. In my second chapter, I investigated the factors associated with nest site selection, success, and productivity in the same study site in western Wyoming. I used an existing dataset on nest site locations, nest success, and productivity, and collected new data on these response variables between 2019 and 2023. I used a resource selection function model (RSF) to evaluate nest site selection and used generalized linear mixed models (GLMMs) to evaluate nest success and productivity. Ferruginous Hawks selected nest sites in developed-open space landcover (e.g., areas cleared of vegetation with little or no infrastructure), higher topographic position index (TPI), and in closer proximity to producing wells (km). In contrast, breeding hawks avoided nest sites in areas with higher densities of producing wells (per km2) and more shrub cover (%). Nest success and productivity of egg-laying pairs was positively associated with artificial nesting platforms (ANPs) and negatively associated with anthropogenic structures and rocky outcrops, developed-open space landcover, TPI and year. These findings suggest that Ferruginous Hawks may be subject to an ecological trap when they nest on anthropogenic structures, but that ANPs are a potentially viable tool for mitigation.
Open Access
Developing rock ramp fishway criteria for fishes of regional conservation concern
(Colorado State University. Libraries, 2024) Paik, Kira, author; Myrick, Christopher A., advisor; Kanno, Yoichiro, committee member; Wohl, Ellen, committee member
Rivers and streams in the United States have been greatly fragmented by the construction of instream structures such as dams, diversions, and culverts to meet the growing needs of human populations. Many of these structures inhibit upstream movement by fish species, negatively affecting abundance as well as overall survival. Conservation efforts are looking at restoring connectivity through the installation of fish passage structures or fishways. To improve effectiveness and functionality of these fish passage structures, the swimming abilities of the target species should be considered when creating the design. Rock ramp fishways are becoming increasingly utilized because they can allow passage of a large assortment of species with variable swimming abilities and are highly customizable. Creating cast concrete fishways in this style can also help to reduce the cost of construction of passage structures. We evaluated the passage success of five fish species of conservation concern using an experimental rock ramp fishway at slopes of 2-10%, in 2% increments. This study focused on species of national or regional conservation concern including Topeka Shiner Notropis topeka, Suckermouth Minnow Phenacobius mirabilis, Rio Grande Chub Gila pandora, Rio Grande Sucker Catostomus plebeius, and Mottled Sculpin Cottus bairdii. Our results showed that decreased slope and distances would lead to higher passage success for the five species. For the entire length of the fishway (6.1 m), all species had very high passage probabilities (> 0.9) at the lowest slopes 2 and 4%, and for all species except the Topeka Shiner, the 6% slope also had high passage probabilities (> 0.8). At 8% and 10% slopes, passage success for these species decreased drastically (< 0.31) and would not be recommended for longer fishways (> 2.03 m between resting areas). Based on these results, managers designing fishways for these species should be able to pick ideal combinations of slope and length to successfully allow passage of an acceptable proportion of the fish to attain management goals.
Open Access
Assessing the swimming and jumping performance of Wyoming fishes with implications for fishway design
(Colorado State University. Libraries, 2024) Garvey, Chase, author; Myrick, Christopher A., advisor; Kanno, Yoichiro, committee member; Wohl, Ellen, committee member
To successfully begin to solve the complex problems facing native fish conservation efforts, we need to seek a deeper understanding of the fish that inhabit the communities that we hope to conserve. With regards to the issue facing the fragmentation of our lotic ecosystems, and the effects that dams and similar structures can have on fish communities, fishways are a common tool used to restore the connectivity of streams by allowing the uninhibited passage of fish. In these experiments we studied the swimming and jumping abilities of Hornyhead Chub (Nocomis biguttatus), Bigmouth Shiner (Notropis dorsalis), Iowa Darter (Etheostoma exile), and Brook Stickleback (Culaea inconstans) in order to provide fisheries managers with criteria for fishway design that will allow the passage of desirable target species, and potentially block the spread of invasive Brook Stickleback. We did this by testing the jumping abilities of each species at various temperatures using artificial waterfalls. After testing groups of fish at various waterfall heights, we used logistic regression to predict the probability of individual fish passage under various conditions. To test the swimming ability of each species, we used swim tunnels to determine the maximum swimming velocity of each species, and estimate their endurance at various swimming velocities. Our results show that a vertical barrier greater than 15 cm will block the upstream movement of nearly all individual Hornyhead Chub. Heights greater than 8.4 cm will block the upstream passage of Bigmouth Shiner, and barriers taller than 6.0 cm will block the upstream passage of Iowa Darter and Brook Stickleback. Given this information, if vertical drops and pool designs were to be incorporated into fishways designed for these species, drops between fishway pools should remain within these thresholds if successful passage is to be achieved. The results of the swimming performance experiments show that each species' swimming abilities are unique relative to their raw maximum swimming abilities and overall endurance. The problem facing engineers and biologists is that many different species that make up these communities are unique, and have characteristics that pose specific challenges or advantages to assisting their movements. Additionally, fisheries scientists must remain cognizant that fishways that allow native fish movement will likely allow the movement of non-target species (including potential invasives) present in the same systems. Managers must balance the trade-offs between restoring native ecosystems and protecting areas that have not been invaded.
Open Access
Avian conservation and ecology in northern Vietnam
(Colorado State University. Libraries, 2009) Vu, Thinh Tien, author; Doherty, Paul F., Jr., advisor; Huyvaert, Kathryn, advisor
Due to the rapid rate of biodiversity loss in Vietnam conserving the avian biodiversity is a contemporary issue of concern and my dissertation was aimed at several issues focused on avian conservation. Recently, the number of non-native tree plantations has increased but the conservation potential of such plantations remains unknown. In Chapter 1, I estimated bird species richness to be highest in mature natural forest, lower in second-growth natural forest, and lowest in pine plantation. I suggest that natural forest types should receive priority for conservation in Vietnam. In Chapter 2, I compared bird movement over a paved road (6-8m wide) and within forest interior plots. The probabilities of approaching the playback for ground species at the road site were lower than those in the forest interior. The road seems to moderately affect the ability for ground-feeding bird species to cross gaps. Roads in the natural reserves should be designed to be as narrow as possible. In Chapter 3, to investigate the effects of logging on biodiversity, I modeled the recovery of avian communities following a variety of potential logging schemes. I found that, to conserve 80% of the species pool, logging schemes with either cycle length > 40 years or wood volume left after harvest > 55% should be implemented. Wildlife diseases are raising concerns with respect to human and domestic animal health, as well as the persistence of wildlife populations. Chapter 4 was aimed at characterizing the sample prevalence of avian malaria in wild land birds. The prevalence of avian malaria was 45.85%. However, higher parasite prevalence was observed in flocking species compared to solitary species and higher parasite prevalence was observed in adult birds compared to juvenile birds. In Chapter 5, I focused on surveillance for the presence of avian influenza virus nucleic acids and antibodies in wild land birds. Serum samples from four birds out of 197 birds sampled were antibody positive for the H5 subtype. Sample prevalence for avian influenza virus nucleic acids was 7.25%. This result suggests that attention should be given to land birds in AI surveillance and monitoring programs.
Open Access
Generalized mixed effects models for estimating demographic parameters with mark-resight data
(Colorado State University. Libraries, 2008) McClintock, Brett Thomas, author; White, Gary C., advisor
Mark-resight methods constitute a slightly different type of data than found in traditional mark-recapture, but they are in the same spirit of accounting for imperfect detection towards reliably estimating demographic parameters. Compared to mark-recapture, mark-resight can often be a less expensive and less invasive alternative in long-term population monitoring programs. However, the mark-resight estimators developed to date do not provide a flexible framework allowing the efficient use of covariates in modeling the detection process, information-theoretic model selection and multimodel inference, and the joint estimation of abundance and related demographic parameters. Here I develop a series of mark-relight models for the sampling conditions most often encountered in these studies that address this need for a more generalized framework. In Chapter 1, I introduce the the logit-normal mixed effects model (LNE) for estimating abundance when sampling is without replacement and the number of marked individuals in the population is known exactly. I compare the model to other mark-resight abundance estimators when applied to mainland New Zealand robin (Petroica australis) data recently collected in Eglinton Valley. Fiordland National Park. I also summarize its relative performance in simulation experiments. It can often be difficult to achieve sampling without replacement or to know the exact number of harked individuals in a population. In Chapter 2, I address these limitations of LNE by introducing the (zero-truncated) Poisson-log normal mixed effects abundance model, (Z)PNE. I demonstrate the use and advantages of (Z)PNE using black-tailed prairie dog (Cynomys ludovicianus) data recently collected in Colorado. I also investigate the expected relative performance of the model in simulation experiments. In Chapter 3, I extend (Z)PNE to a full-likelihood robust design model analogous to that used in mark-recapture for the simultaneous estimation of abundance, apparent survival, and transition probabilities between observable and unobservable states. I illustrate the use of the model with additional New Zealand robin data collected in Fiordland National Park, New Zealand. I also report on a series of simulation experiments evaluating the performance of the model under a variety of sampling conditions.
Open Access
Effects of groundwater withdrawal and drought on native fishes and their habitats in the Arikaree River, Colorado
(Colorado State University. Libraries, 2009) Falke, Jeffrey Arron, author; Fausch, Kurt D., advisor
Great Plains streams are harsh environments for fishes, and are increasingly degraded by human-caused impacts, including overuse of groundwater. Plains stream fishes are in decline, due in part to interactions between natural drought and anthropogenic stream drying. To address these issues, in a collaborative study we developed a model of groundwater and surface water that predicted fish habitat quantity within the Arikaree River basin in eastern Colorado into the future, based upon three scenarios of land and water use (e.g., irrigation pumping). We found that under the status quo of pumping, >50% of remaining refuge habitats in the wettest segment of river will be dry in 35 years, and will be isolated in a 1-km fragment along the river. Loss of critical habitats due to stream dewatering, and subsequent negative effects on native fishes, are not unique to eastern Colorado but are in fact widespread across the western Great Plains. Secondly, to set this research in context, I conducted a review of metapopulation and metacommunity research in the stream fish literature. Stream fish populations and communities are spatially structured at multiple scales, and easily fragmented. To date, this spatial structure has not been incorporated into stream fish population and community models. However, recent research in this area should improve our understanding of processes that regulate stream fish assemblages. Next, I developed a spawning phenology for Arikaree River fishes and found that cumulative growing season degree days had the strongest effect on hatching initiation. Occupancy by larvae of most species was related to local scale spawning habitat characteristics (e.g., habitat size and type). Among years, colonization and extinction rates for individual species differed in segments that were fed by groundwater, versus those that were not, and were influenced by climate variability among years. Last, I investigated when and where the threatened brassy minnow, Hybognathus hankinsoni, spawns, and what environmental factors influence growth and survival of this species within and among years. Interannual variability in climate, and the hydrologic context of segments along the riverscape, had a strong influence on habitat availability and recruitment of brassy minnow in the Arikaree River.
Open Access
Cold summer stream temperatures reduce recruitment of native cutthroat trout populations
(Colorado State University. Libraries, 2007) Coleman, Mark Anthony, author; Fausch, Kurt D., advisor
Translocation is a key strategy for conserving subspecies of native cutthroat trout Oncorhynchus clarkii, which have declined markedly throughout their native ranges in North America. Previous research showed that translocation success in high-elevation southern Rocky Mountain streams was more likely in warmer streams, and suggested that cold temperatures could limit juvenile trout recruitment and explain translocation failures. However, the effects of cold temperature on recruitment had not been previously investigated. I studied these effects using an integrated laboratory and field approach. In the lab, age-0 Colorado River cutthroat trout O. c. pleuriticus were subjected to one of three natural temperature regimes during two years, which averaged 7°C, 8.5°C and 10.0°C during the warmest summer month. From hatching to swimup, mean survival was high during both years, ranging from 97% (warm regime) to 85% (cold). After swimup, warm regime fry had much greater survival and grew more than 60% larger, on average, than cold regime fry by the onset of winter in the 2003 experiment. The pattern of lower survival in colder temperature regimes held through mid-winter, with 76% survival (warm regime), 62% (intermediate), and 29% (cold). Likewise, during the 2004 experiment, survival to early winter ranged from 44% (warm regime) to 10% (cold). Most mortality in all treatments occurred during a recruitment bottleneck encompassing a 4- to 6-week period following swimup. A response surface analysis of percent dry weight data indicated that the energy content of fry at swimup was lower in colder regimes, and declined during the recruitment bottleneck in all regimes. In the field, I monitored temperatures and conducted surveys to estimate densities of age-0 fry at peak emergence in six headwater streams that varied in thermal characteristics. Density and growth increased with Celsius degree days during the growing season. My results indicate a strong recruitment bottleneck after swimup, when temperature-related energy deficits probably cause significant mortality. Fisheries managers in the southern Rocky Mountains may increase translocation success of native cutthroat trout by selecting sites with ≥800-900 degree days during the growing season, and fry grow to ≥30-35 mm by the end of the growing season.
Open Access
Bayesian analysis of age-at-harvest data with focus on wildlife monitoring programs
(Colorado State University. Libraries, 2007) Conn, Paul Bayne, author; White, Gary C., advisor
State and federal agencies often collect hunter harvest data at check stations. When age- and sex-classes can be determined at the time of harvest, such data provide a wealth of information about population structure. For instance, such summaries are used extensively in quantitative fisheries stock assessment. However, statistically defensible approaches for using age-at-harvest data to monitor terrestrial wildlife populations have not appeared until quite recently, and are deficient in several respects. The primary focus of this dissertation is on developing better methods for analyzing wildlife age-at-harvest data, and on applying these methods to real and hypothetical populations. Chapter one starts by developing statistical methods necessary for fitting population dynamics models to age-at-harvest data. As an example, I analyze marking and harvest records from female black bears (Ursus americanus) in Pennsylvania. In chapter two, I describe numerical implementation issues, as well as results from several extensive rounds of simulation testing. I show that Markov chains will typically need to be quite long to accurately summarize the posterior distribution of model parameters. Nonetheless, estimators are shown to display little bias, to have satisfactory credible interval coverage, and to have a high degree of precision. I show that abundance estimators are quite robust to aging errors, although using data from marked animals twice may lead to overstated measures of precision. In chapter three, I conduct a power analysis to determine if it would be feasible to monitor black bear in Colorado with age-at-harvest and radio telemetry data. My focus in this chapter is on detecting and estimating population trend for varying levels of effort. I show that five year studies are typically too short for all anticipated levels of marking effort, but that ten year studies can yield meaningful estimates of population trend. In chapter four, I address methods that can be used to correct age-at-harvest data for misclassification errors. When the aging criterion is inexact, it is possible to correct for errors if additional information is available on error rates. I illustrate proposed methodology with a black bear dataset from Pennsylvania.