Master of Science / Department of Biology / Brett K. Sandercock / Samantha Wisely / In birds, the offspring of females in socially monogamous species can be sired not only by their social partner (within-pair mating) but also by other males (extra-pair mating), resulting in broods of mixed paternity. Several hypotheses have been proposed which attempt to explain the adaptive significance of this behavior, including the genetic diversity hypothesis, the good genes hypothesis, the genetic compatibility hypothesis and the fertility insurance hypothesis. I report results of a 5 year population study of the Upland Sandpiper (Bartramia longicauda) at Konza Prairie Biological Station in northeast Kansas. My objective was to determine the genetic mating system of this socially monogamous shorebird, and determine which of the genetic hypotheses best explains the patterns of extra-pair paternity (EPP) in the population. As part of the analysis, I optimized laboratory protocols for genetic sexing of our monomorphic study species. Potential errors in molecular sexing have been previously described but usually result in females being misidentified as males. Here, I report evidence that events in PCR reactions can lead to the opposite error, with males misidentified as females. I recommend the use of multiple primer sets and large samples of known-sex birds for validation when designing protocols for molecular sex analysis. I genotyped birds and tested for the existence of EPP in 58 family groups of Upland Sandpipers. I found 15% of chicks and 30% of broods were the result of extra-pair paternity in this population, which is high in comparison to other socially monogamous shorebirds. Only 2% of chicks and 2% of broods were attended by females unrelated to the young. I tested ecological covariates known to influence EPP in other birds including relatedness of mated pairs, morphology of the within-pair male, and nest initiation date, as well as variables which signify genetic benefits, including morphology of the offspring and offspring heterozygosity, but found no significant relationships. None of the prevailing genetic hypotheses can fully explain the high rates of EPP in this population of Upland Sandpipers. However, the discovery of fine-scale genetic structure in female birds, but not in males, suggests female natal philopatry or male-biased dispersal. This sex-specific genetic structure could be a mechanism of inbreeding avoidance, thereby eliminating the need for females to choose mates based on relatedness. This study provides the first estimates of EPP for the socially monogamous Upland Sandpiper, and provides evidence that the inbreeding avoidance mechanism of engaging in extra-pair copulations does not seem to be as important in Upland Sandpipers as in other socially monogamous shorebirds. Future research should include the identification of extra-pair males and the determination of offspring fitness after departure from the nest.

Doctor of Philosophy / Department of Biology / Philip S. Gipson / Understanding factors that influence genetic variability, demographic vital rates, and resource selection is important for conservation and management of wildlife populations. I examined factors influencing microsatellite variability, demographic vital rates, and habitat use for a reintroduced elk (Cervus elaphus) population at Fort Riley, Kansas based on data collected from 2003 – 2007. Levels of allelic richness, observed heterozygosity, and expected heterozygosity for the Fort Riley population were intermediate to other North American elk populations. Genetic variability in restored North American elk populations was not well explained by founding population size, number of founding populations, or number of years since the last translocation. I examined the influence of demographic vital rates on the rate of population change to test the hypothesis that variability in calf survival has a greater influence on rates of population change than adult survival. Survival for prime-age adult elk had the highest stage-specific elasticity value, but life-stage simulation analysis indicated that variation in calf survival had the highest correlation with variation in population growth rate. These results suggest that calf survival varies temporally and is the vital rate most directly related to variation in population growth rate for this population. I assessed the relative influence of risk-related and resource-related factors on elk habitat selection by comparing predictor variables included in top resource selection function models at the landscape and home range scales. All predictor variables, with the exception of fall and spring prescribed burns, were included in top models across seasons at both spatial scales. Elk selected low elevation areas, gentle slopes, edge habitat, and areas close to streams at both spatial scales. At the landscape scale, elk generally avoided roads and preferred areas on or near Fort Riley. At both spatial scales, elk used riparian woodlands more frequently than grasslands and selected for agricultural crops when seasonally available. These findings do not support the idea that risk-related factors are the primary determinant of elk habitat use at the landscape scale as has been found for ungulates in areas with natural predators.

Master of Science / Department of Biology / David C. Hartnett / Perennial grasses on tallgrass prairie primarily reproduce vegetatively via the belowground bud bank, yet the production, dynamics, and morphology of belowground buds is largely unexplored. Since the two main photosynthetic pathway guilds (C3 and C4) on tallgrass prairie vary in their aboveground phenology, their belowground phenology would also be expected to vary. Differences in bud production, development, and spatial arrangement result in different growth forms. Therefore, an extensive biweekly examination of a dominant tallgrass prairie C4 rhizomatous grass Andropogon gerardii and C3 caespitose grass Dichanthelium oligosanthes was conducted over an entire year. Andropogon gerardii and D. oligosanthes have multiple distinctive bud developmental stages. Andropogon gerardii was synchronous in its bud development and its bud bank was composed of multiple annual cohorts. The bud bank of D. oligosanthes was developmentally asynchronous and was comprised of a single bud cohort since its bud bank underwent a complete turnover in early summer. The different roles of buds in the life history of each species reflected their differences in bud longevity, quality, and dormancy. In D. oligosanthes, belowground buds enabled plant survival over the C3 summer dormant period whereas juvenile tillers overwintered during the longer winter dormant period. In contrast, A. gerardii survived its single, winter dormant period as dormant buds. The higher-order bud production observed in D. oligosanthes multiplied its tiller production potential and, along with its shortened internodes, contributed to its caespitose growth form. The rhizomatous growth form of A. gerardii resulted from its lack of higher-order bud production and its elongated internodes. Differences in production of buds per vegetative and flowering tiller were quantified in A. gerardii. Flowering tillers of A. gerardii produced larger numbers of buds per tiller and transitioned a larger proportion of their buds to tillers than did vegetative tillers. Therefore, no tradeoff between sexual and vegetative reproduction was evident. Developmental constraints likely prevented such a tradeoff. Bud bank dynamics offer insight into the control of grass population dynamics, production, and ultimately aboveground net primary production (ANPP) and will be useful in understanding the underlying mechanisms by which management practices and environmental change can alter perennial grasslands.

Master of Science / Department of Biology / Walter K. Dodds / Human-induced stressors such as increased nitrogen (N) loadings, altered watershed land-use, and biodiversity losses are a few of the numerous threats to aquatic systems. Prairie streams experience natural disturbances, such as flooding and desiccation, which may alter responses to anthropogenic stressors. Denitrification, the dissimilatory reduction of NO3- to N gas (N2O or N2), is the only permanent form of N removal from terrestrial or aquatic ecosystems, and is important in mitigating N pollution to streams and downstream waters. Little is known about the relationships between denitrification and riparian prairie vegetation or large consumers. In the first chapter, I used outdoor mesocosms to determine the impact of a grazing minnow, Campostoma anomalum, on structural and functional responses of prairie streams to a simulated flood, focusing on denitrification. In terrestrial ecosystems, grazing can stimulate denitrification, but this has not been studied in streams. Ammonium (NH4+) enrichments, used to simulate fish excretion, alleviated N limitations on denitrification. Both fish and NH4+ affected algal biomass accrual, but only fish affected algal filament lengths and particulate organic matter. In a second experiment, I examined the impact of woody vegetation expansion, a primary threat to tallgrass prairie, on riparian and benthic denitrification. Expansion of woody vegetation in these grasslands is due primarily to altered fire regimes, which historically inhibited woody vegetation growth. To determine the effect of woody vegetation expansion on benthic and riparian denitrification, woody vegetation was removed from the riparian zone of a grazed and an ungrazed watershed. Both soil and benthic denitrification rates from this removal buffer were compared to rates in grassy or woody riparian zones. Riparian soil denitrification was highly seasonal, with greatest rates occurring during early spring, and rates being low throughout the remainder of the year. Benthic denitrification was also temporally variable but did not exhibit seasonal trends, suggesting benthic denitrification is driven by factors other than water temperature. Removal of woody vegetation stimulated soil and benthic denitrification rates over rates found in naturally vegetated riparian zones. Elevated N loadings will continue to affect aquatic ecosystems, and these effects may be exacerbated by biodiversity losses or changing riparian vegetation.

Doctor of Philosophy / Department of Biology / Michael A. Herman / Determining the genetic mechanisms involved in organismal response to environmental change is essential for understanding the effects of anthropogenic disturbance. The composition of the bacterial-feeding nematode community is an excellent biological indicator of disturbance, particularly in grassland ecosystems. We have previously shown that grassland soil nematodes are responsive to perturbations in the field including the addition of nitrogen fertilizer. We are interested in how this perturbation affects the microbial community and downstream effects on the next trophic level, the bacterial-feeding nematodes. To determine the effects of disturbance on soil bacterial communities we used massively parallel sequencing and found that chronic nitrogen addition on tallgrass prairie significantly impacts overall bacterial community diversity and the abundance of specific bacterial taxa. Because native soil nematodes lack well developed genomic tools, we employed Caenorhabditis elegans as a model for native soil nematode taxa and used transcriptional profiling to identify 204 candidate genes regulated in response to altered bacterial diets isolated from grassland soils. To biologically validate our results we used mutations that inactivate 21 of the identified genes and showed that most contribute to fitness or lifespan in a given bacterial environment. Although these bacteria may not be natural C. elegans food sources, this study aimed to show how changes in food source, as can occur in environmental disturbance, has large effects on gene expression and those genes whose expression are affected, contribute to fitness. Furthermore, we identified new functions for genes of unknown function as well as previously well-characterized genes, demonstrating the utility of this approach to further describe C. elegans genome. We also investigated the function of previously well-characterized C. elegans defense pathways in our grassland soil bacterial environments and found that some are environment specific. Additionally, we found that cuticular collagen genes are important for lifespan, and appear to function downstream of known defense pathways. Overall, our results suggest that anthropogenic disturbance in grasslands alters the most basal components of the soil food web, bacteria and bacterial-feeding nematodes through the genes they possess and how they are expressed, and resultant bottom-up effects could have profound consequences on ecosystem health and function.

Master of Science / Department of Psychology / Jerome Frieman / Male and female Phodopus campbelli were investigated for kin recognition abilities, assessed by kin discrimination of bedding, urine, fecal, or midventral glandular secretion odors. Using a habituation-discrimination paradigm, subjects were presented either the odors of a pair of their own brothers (C[subscript 1]) or a pair of brothers that were unrelated to them (C[subscript 2]). All subjects were then presented with a final test discrimination odor from a male donor unrelated to themselves or the first donors. All subjects differentiated between the bedding and glandular odors of two unrelated males, regardless of condition assignment. Subjects did not statistically differentiate between the odors of two brothers. These results suggest Phodopus campbelli are capable of recognizing kin based on bedding and midventral gland odors.

Master of Science / Department of Entomology / David C. Margolies / James R. Nechols / The study of how extrinsic factors affect the foraging efficiency and behavior of predaceous arthropods like Phytoseiulus persimilis is important to understand their various processes of acquiring prey, mates, refuges, oviposition sites, and overcoming obstacles posed by the environment. Many intrinsic and extrinsic factors affect predator foraging efficiency and behavior. One of the most influential extrinsic factors may be the host plant on which herbivorous prey are found. Recent studies suggest that plant architecture plays an important role in tritrophic interactions. In this work, I studied the effects of cucumber plant architecture and prey distribution on the foraging efficiency (prey-finding time and prey-consumption rate) and behavior (time allocated between moving, resting and feeding) of P. persimilis. Plant architecture represented differences in leaf number and size; however, all plants had the same total surface area. Plants with 6 small leaves (ca. 82.98 square cm each) were considered as complex architecture, whereas plants with only 2 large leaves (ca. 240.60 square cm each) were considered as simple. The prey distributions were: prey patch on a single basal leaf (closest leaf to the soil) and prey patch on all leaves. The foraging efficiency was assessed by measuring prey-finding time and prey-consumption rate, whereas the behavior was assessed by conducting observational studies on specific foraging activities. When placed either on the top or at the base of the plant P. persimilis encountered prey more rapidly (interval 0-30 minute) on complex and simple plants with prey patches distributed on all leaves. Differences in prey density (number of prey per leaf) had no effect on the prey-finding time of P. persimilis. The predator consumed more eggs on complex plants with prey patches distributed on all leaves. Phytoseiulus perismilis tended to find prey patches more quickly as well as consume more eggs on leaves close to its release point. Furthermore, the predator was observed to lay more eggs on leaves where it had consumed higher number of prey eggs. The dimensions of individual parts of the plant e.g., stem, petiole and leaf, affected the time allocated by P. persimilis between searching, resting and feeding. The predatory mite spent more time foraging on the stems and petioles of the simple plants whereas on complex plants it spent more time foraging on the leaves.

Master of Science / Department of Biology / Craig Paukert / Improperly designed stream crossings may prohibit movement of stream fishes by creating physical or behavioral barriers and may alter the form and function of stream ecosystems. A mark-recapture and geomorphological study was conducted to evaluate fish passage and stream morphology at three types of vehicle crossings (compared to control sites) located on streams in the Flint Hills of Northeast Kansas. We investigated five concrete box culverts, five low-water crossings (concrete slabs vented by one or multiple culverts), and two single corrugated culverts. A total of 6,433 fish were marked April to May 2007 and 709 were recaptured June to August 2007. Fish passage occurred at all crossing types, but upstream movement of recaptured fish was higher at controls (41.1%) than at crossing reaches (19.1%) for low-water crossings. Control sites had more species in common upstream and downstream than did crossings. There was reduced overall abundance of fish upstream at low-water crossings, commonly percids and centrarchids. A comparison of channel and road crossing dimensions showed that box culverts and corrugated culverts would be more effective than low-water crossings at transporting water, sediments, and debris during bankfull flows, and fish passage at base flows. Upstream passage of Topeka shiner (Notropis topeka), green sunfish (Lepomis cyanellus), red shiner (Cyprinella lutrensis), and Southern redbelly dace (Phoxinus erythrogaster) was tested through three simulated crossing designs (box culverts, round corrugated culverts, and natural rock) across 11 different water velocities (0.1 m/s to 1.1 m/s) in an experimental stream. Upstream movement did not differ among designs, except natural rock crossings had lower movement than box or corrugated culverts for red shiners. A greater proportion of Topeka shiners moved upstream at higher velocities. These results suggest that crossing type affects fish passage and the morphology of the stream, although water velocity in different crossing designs alone may not be a determining factor in fish passage. Low-water crossings had the greatest impact on fish community and movement, but barriers to fish movement are likely caused by other variables (e.g. perching). Use of properly designed crossing structures has great promise in conserving critical stream habitat and preserving native fish communities.

Doctor of Philosophy / Department of Biology / Kimberly A. With / The loss, fragmentation, and degradation of grasslands have resulted in widespread declines in grassland birds. Nest predation is the leading cause of avian reproductive failure; therefore minimizing nest predation can lessen the severity of bird declines. Snakes are important predators of bird nests, but little is known about how snakes may enhance predation risk. To address this issue, I studied the habitat use, movement behavior, population genetic structure, and connectivity of snakes in the grasslands of northeastern Kansas. I addressed the connectivity of eastern yellowbelly racer (Coluber constrictor flaviventris) populations by using a landscape genetics approach at a broad scale (13,500 km2). I also radio-tracked the yellowbelly racer and Great Plains ratsnake (Pantherophis emoryi) at Konza Prairie Biological Station to understand their spatial ecology while simultaneously evaluating nest survival in grassland birds. Individual racers had limited dispersal (<3 km), but substantial admixture occurred within 30 km and populations were in migration-drift equilibrium and had high allelic diversity; therefore, racers must be abundant and continuously distributed for gene flow to be fluid throughout the region. Racers may be more likely to encounter bird nests, as they had more frequent movements and traversed greater distances on average than ratsnakes, which exhibited long periods of inactivity between directed movements. As for grassland birds, nest survival rates decreased with increasing shrubs and decreasing vegetation height. Discriminant function analysis revealed that successful nests were likely to occur in tall vegetation but reduced shrub cover, whereas higher shrub cover characterized snake habitats. Because snakes often use shrubs, nests in areas of increased shrubs may be at higher risk of predation by snakes. Targeted removal of shrubs may increase nest success by minimizing the activity of predators attracted to shrubs. Although predator removal is often a strategy for protecting bird populations, it may not be feasible in this instance, especially since snakes are a native component of the grassland community. Efforts to reduce snake predation on grassland bird nests should therefore focus on managing habitat within grasslands (i.e., shrubs) that influence snake activity, as no natural or anthropogenic habitat barriers currently limit snake movement across the landscape.

Master of Science / Department of Agronomy / Jay Ham / The exchange of water, carbon, and energy between grasslands and the atmosphere is an important biogeochemical pathway affecting ecosystem productivity and sustainability. The eddy covariance (EC) technique directly measures this mass and energy exchange. However, questions remain regarding the accuracy of EC-derived H[subscript]2O and CO[subscript]2 fluxes in landscapes with irregular topography and variable vegetation. These concerns stem from the "energy balance (EB) closure problem" (i.e., measured energy in does not equal measured energy out). My main objectives were to examine EB closure at two topographical positions within an annually burned tallgrass prairie watershed and to examine the effect of landscape position and woody encroachment on carbon and water exchanges. In tallgrass prairie, 14 km south of Manhattan, KS, USA, EC towers were deployed at three sites in 2007 and 2008. One upland and lowland tower were within an annually burned watershed dominated by C[subscript]4 grasses. Another lowland tower was deployed in a separate quadrennial-burned watershed where significant woody vegetation occupied the tower's sampling area. All towers measured EB components (net radiation, R[subscript]n; soil heat flux, G; sensible heat flux, H; and latent heat flux, [lambda]E). In the annually burned watershed, landscape position had little effect on G, H, and R[subscript]n with differences [less than] 2% between sites. However lowland [lambda]E was 8% higher, owing to larger plant biomass/leaf area and greater soil moisture. Energy balance closure (i.e., [[lambda]E + H] / [R[subscript]n - G]) was 0.87 and 0.90 at the upland and lowland sites, respectively. A nearby large-aperture scintillometer provided good validation of EC-derived H in 2007. Data suggested that underestimates of [lambda]E may have accounted for the closure problem; sample calculations showed that increasing [lambda]E by 17% would have resulted in near prefect closure. Data from this study suggests that EB closure does not strongly correlate with topographical position; however these data raise questions regarding accuracy of the [lambda]E term. Mass exchange analysis shows that the prairie carbon cycle is highly dependent on burning. The lowland and upland annually burned sites saw carbon gains of 281 to 444 g C m[superscript]-[superscript]2 yr[superscript]-[superscript]1 before burning with the shrub lowland showing the least (e.g. 159 and 172 g C m[superscript]-[superscript]2 yr[superscript]-[superscript]1). After the prescribed burn, the upland and lowland sites remained slight carbon sinks (68 to 191 g C m[superscript]-[superscript]2 yr[superscript]-[superscript]1), whereas the unburned shrub site was a carbon sink in 2007 (159 g C m[superscript]-[superscript]2 yr[superscript]-[superscript]1, because no carbon loss was incurred via burning) and a large carbon source in 2008 when it was burned the following year (336 g C m[superscript]-[superscript]2 yr[superscript]-[superscript]1 loss). Evapotranspiration (ET) was highest at the shrub lowland where greater soil moisture and abundance of deep-rooted C[subscript]3 shrub vegetation allowed greater uptake and loss of water.