Master of Science / Department of Biology / John M. Briggs / Woody encroachment has altered the vegetative structure of grasslands worldwide and represents a potentially irreversible shift in grassland dynamics and biodiversity. Clonal woody species appear to be one of the greatest contributors to the shift from graminoid to woody dominance in the tallgrass prairie. Part of the high success rate of clonal species may be attributed to an ability to circumvent recruitment filters through the integration of environmental heterogeneity and acropetal translocation of resources from mother to daughter ramets. The clonal shrub Cornus drummondii persists in a tension zone of the graminoid-dominated tallgrass prairie, where the dominance structure is primarily maintained through the direct and indirect effects of fire. The competitive displacement of native herbaceous vegetation associated with the establishment and expansion of C. drummondii causes a major alteration in the fuel dynamics responsible for the propagation and sustainment of fire, potentially contributing to biofeedback mechanisms that facilitate shrub expansion. The goal of this research was to quantify fire behavior parameters (temperature, intensity, rate of spread, and heat flux) in relation to C. drummondii invasions and to test physiological integration as a mechanism driving encroachment, using manipulation experiments at the Konza Prairie Biological Station. We observed a significant decrease in fireline intensity associated with the encroachment of C. drummondii, which was amplified by the effects of stem density and shrub island area. This alteration in fire behavior also led to reduced heat flux at stems within shrub islands, reducing the likelihood of tissue necrosis and top-kill. With additional fuel, temperatures and fire intensities were higher, similar to open grasslands. In severing rhizomes, and effectively severing the integration of clonal ramets, we observed a higher risk of mortality of daughter ramets. These rhizome severed ramets were more water stressed, had lower photosynthetic rates, and lower woody and foliar biomass production. These results indicate that C. drummondii significantly alters fire behavior, releasing ramets from the fire trap of successive top-killing, while the integration of intraclonal ramets allows daughter ramets to survive mid-summer drought and increases the likelihood of successful establishment and further clonal reproduction.

Master of Science / Biology / Michael Tobler / Environmental variation can shape phenotypic variation in organisms. Most evidence for trait differentiation along environmental gradients comes from analyses of dichotomous habitat types that differ in only one or few environmental factors. In reality, however, environmental variation is often more subtle, gradual, and multifarious. I investigated geographic variation in body shape, trophic resource use, and individual diet specialization in two species of darters (Etheostoma spectabile and E. flabellare; Percidae) that occur along river gradients. I explicitly tested how abiotic and biotic environmental factors shape trait variation within and between species. Results indicated significant among population variation in the body shape of both species. Population differences in body shape were correlated with variation in substrate composition. Although body shape analyses revealed a small but significant signal of convergent evolution of body shape when both species occur in sympatry, E. spectabile and E. flabellare mostly exhibited unique responses to shared sources of selection. The analyses of darter trophic resource use uncovered significant resource partitioning between the two species and geographic variation in diets that is likely driven by differences in resource availability. Furthermore, the majority of populations exhibited significant individual specialization. Variation in individual specialization in populations of E. flabellare was related to invertebrate density and competitor richness, and in E. spectabile to the combined effects of invertebrate density and invertebrate diversity. My results indicate substantial variation in trophic resource use among individuals, populations, and species of small-bodied fishes that are typically assumed to be generalist insectivores. Variation in diet specialization may be more widespread than previously considered, and ecological opportunity is an important factor in shaping trophic resource use of individuals and populations. Overall, the results indicate that even subtle and gradual environmental variation can induce substantial variation in phenotypes on a relatively small spatial scale.

Master of Science / Division of Biology / Martha E. Mather / A flexible distribution is an adaptive response that allows animals to take advantage of spatial variation in the fluctuation of resources. Distribution of mobile organisms is complex so multi-metric patterns derived from dynamic distribution trajectories must be deconstructed into simpler components for both individuals and populations. Tagging and tracking fish is a very useful approach for addressing these fisheries research questions, but methodological challenges impede its effectiveness as a research tool. Here, I developed and evaluated a high-retention, high-survival tagging methodology for catfish. Then, I integrated multiple distribution metrics to identify if sites within an ecosystem function differently for mobile predators. Finally, I determined if distinct groups of individuals existed, based on distributional patterns. In the appendices, I test sources of variation in system-wide detections (i.e., season, diel period, size, and release location) and provide additional details on methods and interpretation of the results. To address these objectives, I tracked 123 acoustically tagged (VEMCO V9-V13) Blue Catfish (Ictalurus furcatus mean: 505.3 mm TL; SE: 12.3 mm; range: 300-1090 mm) from June through November, 2012-2013, in Milford Reservoir, KS. Across the five months, 85.4-100.0% of the tagged Blue Catfish were detected at least once a month by an array of 20 stationary receivers (VR2W), a detection rate much higher than rates reported in the literature for catfish (38%). Blue Catfish were consistently aggregated in the northern portion of the middle region of Milford Reservoir. Using three metrics (population proportion, residence time, and movements), I found four types of functional sites that included locations with (i) large, active aggregations, (ii) exploratory/transitory functions, (iii) small, sedentary aggregations, and (iv) low use. I also found that tagged Blue Catfish clustered into three groups of individuals based on distribution. These included (1) seasonal movers, (2) consistent aggregations across seasons, and (3) fish exhibiting site fidelity to Madison Creek. Sites with different functions and groups of individual fish were related but not the same. My approach to looking at multiple responses, functions of sites, and individual groupings provided new insights into fish ecology that can advance fisheries management of mobile predators.

Master of Science / Entomology / Ming-Shun Chen / Robert "Jeff" J. Whitworth / MicroRNA (miRNA) plays a role in nearly all the biological pathways and therefore may provide opportunities to develop new means to combat the Hessian fly, Mayetiola destructor, a destructive pest of wheat. This study presents a comprehensive analysis of miRNA species via deep-sequencing samples from Hessian fly second instar larvae, pupae and adults. A total of 921 unique miRNA species were identified from approximately 30 million sequence reads. Among the 921 miRNA species, only 22 were conserved among Hessian fly and other insect species, and 242 miRNA species were unique to Hessian fly, the remaining 657 share certain sequence similarities with pre-miRNA genes identified from various insect species. The abundance of the 921 miRNA species based on sequence reads varies greatly among the three analyzed stages, with 20 exclusively expressed in adults, two exclusively expressed in pupae and two exclusively expressed in second instar larvae. For miRNA species expressed in all stages, 722 were with reads lower than 10. The abundance of the remaining 199 miRNA species varied from zero to more than eight-fold differences among different stages. Putative miRNA-encoding genes were analyzed for each miRNA species. A single putative gene was identified for 594 miRNA species. Two putative genes were identified for 138 miRNA species. Three or more putative genes were identified for 86 miRNA species. The three largest families had 14, 23 and 34 putative coding genes, respectively. No gene was identified for the remaining 103 miRNA species. In addition, 1516 putative target genes were identified for 490 miRNA species based on known criteria for miRNA targets. The putative target genes are involved in a wide range of processes from nutrient metabolism to encoding effector proteins. Analysis of the expression patterns of miRNA and pre-miRNA for the miRNA family PC-5p-67443, which contains 91 genes, revealed that miRNA and pre-miRNA were expressed differently in different developmental stages, suggesting that different isogenes are regulated by different mechanisms, or pre-miRNAs had other functions in addition to as an intermediate for miRNA biogenesis. The large set of miRNA species identified here provides a foundation for future research on miRNA functions in Hessian fly and for comparative studies in other species. The differential expression patterns between a pre-miRNA and its encoded mature miRNA in a multigene family is an initial step toward understanding the functional significance of isogenes in dramatically expanded miRNA families.

Master of Science / Department of Biology / John M. Blair / Anthropogenic activities impact ecosystems in numerous direct and indirect ways, affecting the cycling of carbon (C) and nitrogen (N) on local, regional and global scales. North America tallgrass prairie is an ecosystem profoundly altered by anthropogenic activities, with most native prairie converted to alternate land uses or heavily impacted by other environmental changes. While aboveground responses to anthropogenic drivers have received much attention, the responses of belowground biota, ecological processes, and nutrient allocation to land management and environmental change are poorly documented, especially over long timeframes. This research builds upon a long-term experiment (the Belowground Plot Experiment) initiated in 1986 at Konza Prairie Biological Station (Manhattan, KS). I utilized a subset of treatments to address the effects of annual burning vs. fire suppression and/or chronic N additions on soil C and N dynamics and microbial communities in tallgrass prairie. I measured a suite of soil variables related to C and N cycling during the 2012 growing season, including total soil C and N, microbial biomass C and N, in situ net N mineralization, potential N mineralization, in situ CO2 efflux, and potentially mineralizable soil C. I also assessed changes in microbial community composition using microbial phospholipid fatty acids (PLFA) profiles. Annual burning significantly (p≤0.05) increased the soil C:N ratio and in situ CO2 efflux, while decreasing potential ammonification and nitrification rates. Annual burning also increased total PLFA mass and relative abundance of fungi. Chronic N addition (100 kg N ha-1 year-1) significantly reduced the soil C:N ratio, while increasing total soil N and potential nitrification and ammonification rates. Chronic N addition reduced potential C mineralization, microbial biomass C and N, and altered microbial community composition by increasing abundance of bacterial PLFAs and reducing fungal PLFAs. Sampling date also significantly affected many variables. These results indicate that different fire regimes and chronic N enrichment over decades affects soil C and N pools and transformations, as well as microbial biomass and composition. In total, this study highlights the importance of long-term ecological research and identifies likely changes in tallgrass prairie nutrient dynamics and soil microbial communities under increased N and frequent burning.

Doctor of Philosophy / Department of Biology / David A. Haukos / Mottled ducks (Anas fulvigula) are dabbling waterfowl species native to coastal wetlands of the Gulf of Mexico of the United States and Mexico. Although closely related to common waterfowl species such as the mallard (A. platyrhynchos) and American black duck (A. rubripes), the mottled duck exhibits unique behavior, mainly in its life history as a non-migratory species. As such, because of population declines caused by predation, habitat destruction, and environmental contaminants, this species requires specialized conservation concerns and species-specific management to protect population numbers. The goal of this study was to assess ongoing effect of observed lead (Pb) contamination and exposure issues in mottled ducks and their habitats, which I achieved by conducting assessments that will provide managers habitat and organism level metrics to detect and mitigate lead in mottled ducks and their environments. My field study was conducted at the Texas Chenier Plain National Wildlife Refuge Complex (TCPC), which was the area of greatest mottled duck density on the Texas Coast. I first created a body condition index to provide managers a tool to monitor population health, and a proxy for lead exposure and avian health without destructively sampling individuals. I then used presence-only maximum entropy (MaxENT) and multivariate statistical modeling procedures in conjunction with mottled duck movement data to elucidate sets of habitat conditions that were conducive to predicting the occurrence of mottled ducks and environmental lead “hot spots”. MaxENT analyses suggested that lead in the top portion of the soil column is similarly related to all environmental variables considered, may be increasingly available after large-scale environmental disturbances. Lack of variation in coarse-scale habitat use between breeding and non-breeding seasons may further point to a food-based exposure pathway for lead as mottled ducks switch from an invertebrate to plant diet, either as a result of changing age classes or normal adult phenology, during the period of increased lead exposure. Using stable isotope ratio analysis, I then tested environmental samples of soil and vegetation as well as mottled duck blood to determine isotopic signatures that were consistent with particular sources of lead deposition (e.g., lead shot pellets, leaded fossil fuel combustion, industrial effluents). Comparisons suggested a great deal of similarity to lead shot reference values in vegetation and blood samples, especially in blood samples with higher concentrations of lead present. Last, I conducted a formal Ecological Risk Assessment (ERA) procedure to quantify the risk to mottled ducks from lead exposure in their current habitat and direct managers towards effective mitigation and habitat management strategies to reduce exposure in the future. One scenario suggested that mottled ducks were at greatest risk from eating an invertebrate-based diet, but lead content values at the TCPC suggest that a plant-based diet may provide a higher lead exposure risk for mottled ducks, depending on true levels of bioavailability in environmental media. Overall, I determined that mottled ducks experience greatest lead exposure risk from lead shot pellets on the TCPC or in nearby habitat, while potentially also experiencing low levels of exposure from several other sources. Additionally, management efforts that focus on plants that do not provide food resources for mottled ducks as a potential environmental sink for lead contamination, such as phytoremediation, may prove effective in reducing the overall lead load from historical activities that likely deposited much of the lead in this ecosystem.

Doctor of Philosophy / Department of Biology / Craig Paukert / River discharge influences fish and invertebrate communities and understanding how hydrologic variables contribute to fish and invertebrate composition can provide information for restoration and management. This study examines the relationship between several flow regime metrics that may influence fish and invertebrate community structure in large river systems such as the Kansas River. First, I examined how hydrology influences macroinvertebrate (drifting and benthic) density and fish communities before, during, and after flooding in both main and secondary channels. I found that drifting invertebrate density increased during flooding potentially providing increased prey opportunities for fishes. I also found that fluvial dependent and generalist fish species use inundated habitats more than fluvial specialists. My results suggest that the flux of water into inundated habitats supports a unique subset of invertebrate and fish communities of the main channel. Next, I examined the importance of lateral connectivity on fish and invertebrate composition by examining differences in seasonally and permanently inundated secondary channels in relation to main channel reaches. I found that drifting and benthic invertebrate assemblages and fish assemblages differed between seasonally inundated and permanently connected secondary channels. These results suggest that maintenance of diverse secondary channel connections is useful in preserving native biota in the Kansas River. Finally, I tested if hydrologic variables influenced recruitment of four native Kansas River fishes. I found that recruitment for two of the four fish species (flathead catfish, Pylodictis olivaris, and shovelnose sturgeon, Scaphirhynchus platorynchus) increased in high flow years. These results indicate that a natural and variable flow regime may be important for maintaining fish community structure in the Kansas River. The results of this study have implications for management strategies that include the use of high flows to provide a pulse of insect prey to the main channel for fishes, restoration of natural high and low flow variability as important to fish recruitment, and diversity in secondary channel connectivity (seasonal and permanently connected) that promotes unique fish and invertebrate communities.

Master of Science / Biology / David A. Haukos / The lesser prairie-chicken (Tympanuchus pallidicinctus) is an endemic North American prairie grouse once widely distributed in the southwestern Great Plains. Recent population declines and continued threats to lesser prairie-chicken populations prompted the U.S. Fish and Wildlife Service to list the species as “threatened” under the protection of the Endangered Species Act of 1973 in May 2014. The northern extent of the species range in Kansas and Colorado supports 2/3 of the remaining range-wide population of lesser prairie-chickens, but has thus far been relatively understudied. Concern for species viability has created a need to fill current knowledge gaps in lesser prairie-chicken ecology, provide more recent demographic information, and develop appropriate conservation actions. I evaluated female survival, movement, space use, and effects of anthropogenic features during the breeding seasons of 2013 and 2014. I captured and radio-tagged 201 females with satellite GPS (N = 114) and VHF (N = 82) transmitters within the three ecoregions of Kansas and Colorado. Mean daily movement varied by region, year, and breeding season period but the amount of space used was consistent between ecoregions and years. On average, females moved 1352 m ± 12 [SE] per day. Females moved the greatest distances during the lekking period of the breeding season with females moving 2074 m ± 36 per day. Females were most sedentary during the brooding period moving only 780 m ± 14 per day. Mean breeding season home range size was estimated to be 340 ha ± 27. The lekking period had the greatest amount of movement as a result of females visiting leks to find mates, copulate, and search for nest locations. Female’s movements were reduced during the brooding period because of physical limitations of the brood mobility. Variation in movement between ecoregions was most likely a product of fragmentation as females moved 10-30% more in northwest Kansas compared to the study sites, which was characterized by northwest Kansas having the greatest degree of fragmentation. Survival varied by ecoregion with females in northwest Kansas having the lowest probability of surviving the 6-month breeding season compared to other ecoregions. Estimated 6-month breeding season survival during 2013 and 2014 was 0.455 (95% CI = 0.38 – 0.53). Survival was lowest during the nesting period, which claimed 59.5% of all observed mortalities. Survival increased from 2013 to 2014 in northwest Kansas as grassland habitats recovered from extreme drought conditions in 2013. Drought was less severe in south-central Kansas and survival rates remained fairly consistent across years. Avian and mammalian predators caused 45.7% and 34.3% of breeding season mortalities, respectively. Other mortalities were either cause by snakes or were unknown (5.7%, 14.3%). Overhead cover may have been limited from drought conditions causing nesting females to be more visible to avian predators during incubation. When pooled across years and ecoregions, rump-mounted GPS transmitters did not adversely affect female survival when compared to commonly used necklace style VHF transmitter (VHF: 0.48 95% CI = 0.39 – 0.58; GPS: 0.50 95% CI = 0.38 – 0.64). Distance to distribution power lines and lek were significant predictors of female space use within their home range with females behaviorally avoiding distribution power lines and using space closer to leks. Space use decreased with increasing oil well density. Females avoided areas that had well densities of 23 wells/250 ha. Observed female locations were further from anthropogenic features but closer to leks on average than at random. Avoidance behavior of anthropogenic features may result in functional habitat loss and reduce the amount of suitable habitat available; compounding previously fragmented landscapes. Anthropogenic features may limit movement by acting as barriers on the landscape and potentially disrupt population connectivity. Furthermore, habitats selected for nesting and brooding may result in potential ecological traps because of reduce breeding success when impacted by increased occurrence and densities of anthropogenic features. Reduced breeding success can have significant negative impacts on population persistence. Average home range size across all ecoregions indicated that female lesser prairie-chickens need at least 340 ha of habitat to fulfill her life-history requirements during the breeding season. Brooding habitats need to be in close proximity (≤ 750 m) to nesting cover to reduce distance traversed by newly hatched broods. Reducing grazing pressure will ensure that sufficient vertical habitat structure is available during the nesting period and increase female survival; especially in times of drought. Mangers should restrict construction of anthropogenic features near or within suitable lesser prairie-chicken habitat with emphasis on distribution power lines. Well densities should not exceed 1 well/60 acres (11 wells/section) for a >10% probability of use. However, because the affect that density of wells has on demographic rates of lesser prairie-chickens has yet to be determined, a conservative approach where well densities in or adjacent to grassland patches should be minimized as much as possible is best.

Master of Science / Division of Biology / Martha E. Mather / Understanding how and why fish distribution is related to specific habitat characteristics underlies many ecological patterns and is crucial for effective research and management. Blue Catfish, Ictalurus furcatus, are an important concern for many fisheries agencies; however, lack of information about their distribution and habitat use remains a hindrance to proper management. Here, over all time periods and across months, I quantified Blue Catfish distribution and environmental correlates of distribution in Milford Reservoir, the largest reservoir in Kansas. I tested relationships among acoustically tagged Blue Catfish and three groups of variables postulated to influence Blue Catfish distribution in the literature (i. localized microhabitat variables, ii. larger-scale mesohabitat variables, iii. biotic variables). Blue Catfish were consistently aggregated in two locations of the reservoir across five months during summer and fall, 2013. Using multiple linear regression and an information theoretic model selection approach, consistent correlates of distribution included localized, microhabitat variables (i.e., dissolved oxygen, slope) larger-scale, mesohabitat variables (i.e., distance to channel, river kilometer from the dam) and a biotic variable (i.e., Secchi depth). This research identified which 5 of the 12 variables identified in the literature were most influential in determining Blue Catfish distribution. As a guide for future hypothesis generation and research, I propose that Blue Catfish distribution was driven by three ecologically-relevant tiers of influence. First, Blue Catfish avoided extremely low dissolved oxygen concentrations that cause physiological stress. Second, Blue Catfish aggregated near the channel, an area of bathymetric heterogeneity that may offer a foraging advantage. Third, Blue Catfish aggregated near low Secchi depths, shown here to be associated with increased productivity and prey abundance. Building on my results, future research into the distribution and habitat use of Blue Catfish should incorporate aggregated distributions of fish into research designs, focus on how both small and large scale relationships interact to produce patterns of distribution, and explore further the mechanisms, consequences, and interactions among the three tiers of influence identified here.

Master of Science / Department of Biology / Samantha M. Wisely / Nearly 30% of emerging infectious diseases are caused by vector-borne pathogens with wildlife origins, posing a risk for public health, livestock, and wildlife species of conservation concern. Understanding the spatial patterns of exposure to dipteran vectors and their associated pathogens is critical for epidemiological research to target prevention and control of vector-borne infectious diseases. In recent years, Western Equine encephalitis, St. Louis encephalitis, West Nile Virus encephalitis and avian malaria have not only been a public health concern but also a conservation concern, specifically the conservation of grassland nesting birds. Although the central Great Plains is the most specious region for grassland nesting birds, their role in the enzootic (primary) amplification cycle of infectious diseases may lead to further population depressions, and could potentially result in spill-over events to humans and livestock. The goals of my thesis were 1) to identify the underlying causes of spatio-temporal abundance patterns of mosquito vectors within the grasslands of the eastern Smoky Hills, and 2) to create probabilistic distributions of functional disease vectors, to evaluate disease risk in Greater Prairie-chicken (Tympanuchus cupido, surrogate species for other grassland nesting birds). First, I found that temporal dynamics in mosquito abundances were explained by maximum and minimum temperature indices. Spatial dynamics in mosquito abundances were best explained by environmental variables, such as curvature, TWI (Topographic Wetness Index), distance to woodland and distance to road. Second, the overall predictive power of the ecological niche models of important vector species in the grasslands of the Smoky Hills was better than random predictions, indicating that the most important predictor variables in their distribution were: distance to water, TWI, AASHTO (soil particle size distribution), and mean temperature during the coldest quarter. Furthermore, the spatial analysis indicated that Greater Prairie-chicken nest in areas with a higher probability of vector occurrence than other potentially available habitats within the grasslands. However, I failed to detect a significant difference in the probability of vector occurrence at nest of infected versus uninfected females. Understanding the distribution and abundance patterns of vectors of infectious diseases can provide important insights for wildlife conservation as well as public health management.