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Research Experiences for Undergraduates Program

Proposed Summer Projects

A major objective of the REU Program is to give undergraduate students an opportunity to conduct independent research.  Mentors for the REU Program have expertise in a broad range of ecological and evolutionary disciplines, and could advise on a range of topics related to the ecology and genomics of organisms of the tallgrass prairie.  Mentors have been invited to describe specific projects that would be available to students participating in the REU Site program.  

Proposed Summer Projects (listed alphabetically by mentor's last name)

Grassland Restoration Ecology (Mentor: Blair).
REU students may participate in ongoing long-term restoration projects at the Konza LTER site that addresses the application of basic ecological principles to restoration ecology.   For example, on-site grasslands restoration experiments in former agricultural fields provide opportunities for students to investigate the recovery of plant communities and/or ecosystem properties and processes.  Studies of the use of fire to reverse the spread of woody vegetation and enhance recovery of herbaceous grassland communities are also possible.  Many opportunities exist for student research in plant, soil and invertebrate ecology within the context of restoration ecology, and I am willing to work with students to design specific research projects that address their interests.
Ecosystem Responses to Fire and Grazing (Mentor: Blair).

The structure and function of tallgrass prairies is strongly affected by three interacting drivers - fire, grazing by large herbivores, and climate.  As part of an ongoing project to assess the interactive effects of fire and grazers in grasslands, we have established grazing exclosures in areas grazed by bison and that are burned either annually, every four years or every twenty years.  REU students may participate in research that addresses the combined effects of grazing and different fire frequencies on a suite of plant and soil responses.  Potential areas of interest include effects on soil nutrient availability, soil C dynamics, and plant nutrient status.  I am also willing to work with students to develop projects that address other specific questions within this general research area.

Behavioral ecology and physiological ecology of birds (Mentor: Boyle).

I'm interested in the underlying ecological causes of animal behavior.  A full understanding integrates evolutionary processes down to individual physiological responses. My projects at the Konza primarily focus on Grasshopper Sparrows. These are relatively common but declining birds distributed through grasslands of North America. This work seeks to elucidate the basis for variation in dispersal behavior, habitat choice, and nest success.  Grasshopper Sparrows and other small birds nesting at the Konza are hard-hit by nest parasitism by Brown-headed Cowbirds and I am also collaborating with a team investigating the evolutionary and physiological ecology of cowbird nestling behavior.  Potential student research topics might focus on a range of topics: e.g., the correlates of within-season dispersal, nestling physiology and behavior, spatial patterns of song variation. Depending on the project, students may gain experience in one to several of the following techniques: mist-netting, color-banding and resighting of marked birds, territory mapping, nest searching, blood sampling, lab assays, telemetry, and song recording and analysis. Project development will be a collaborative process building on student goals and interests.  With appropriate guidance, students will be expected to take primary responsibility for the design and implementation of all aspects of their project.

Biogeochemistry and Ecology of Intermittent Grassland Streams (Mentor: Dodds).

Intermittent streams carry about 1/3 of terrestrial runoff and as such are an extremely important determinant of downstream water quality, as well as central locations for aquatic biodiversity. Grasslands cover large areas of the global terrestrial surface and commonly feature numerous small intermittent streams. Students will be involved with projects on the effects of woody invasion on streams, or cattle effects on streams under patch-burn grazing regimes. Response variables could include whole-system metabolism, breakdown rates of organic materials, alterations of water quality metrics (including coliform bacteria and nutrient export), or responses of the algal community. 

Polyploidy and Diversity in the Genus Phlox (Mentors: Ferguson and Mayfield).

A current research focus in the Ferguson lab and the KSU Herbarium centers on polyploidy and diversity in the plant genus Phlox. Polyploidy, the condition of having more than two sets of chromosomes, is well known in plants. Although polyploidy is considered to play an important role in plant evolution, our current knowledge of ploidy level variation relative to aspects of diversity is limited. In Phlox, some recognized species exhibit variation in ploidy level, occurring as diploid, tetraploid and even hexaploid populations (with sporophytic cells having two, four and six sets of chromosomes). We are documenting patterns of ploidy level variation in some of these polyploid complexes (including grassland species of the Great Plains and of the arid southwestern U.S.; using flow cytometry and chromosome counting techniques), and corresponding geographic and ecological patterns. We are further investigating these patterns relative to genetic, morphological and taxonomic diversity. An REU scholar will apply laboratory, field and museum (herbarium) approaches to the study of diversity in this system; and will also gain a sense of the breadth of research opportunities in the field of plant systematics. More information is available at www.ksu.edu/fergusonlab and www.ksu.edu/herbarium. 

Conservation biology and ecology of prairie stream fishes (Mentor: Gido). 

REU students are invited to participate in a variety of project focused on the conservation of prairie stream fishes.  This research might include studies addressing how climate change will impact the distribution and abundance of stream fishes.  Examples of previous research in this area involved measuring species thermal biology as well as experiments testing how populations might recover from disturbances such as flooding and drought, which are predicted to increase in intensity under current climate change scenarios.  We also are interested in food web dynamics of aquatic systems, with specific studies on how invasive species might influence the success of native species.  Access to Kings Creek, an unmodified prairie stream, and the experimental stream facility at the Konza Prairie Biological Station (see my webpage) provides the necessary resources to rigorously to test a variety of research questions relevant to the conservation of aquatic systems in prairie streams.

A Multi Scale Analysis of the Habitat-Use Patterns and Metapopulation Dynamics of the Regal Fritillary (Mentors: Haukos and Albanese). 

The Regal fritillary (Speyeria idalia) was once an abundant butterfly species of the prairie biome. The historic range of this species extended from the Canadian border to Oklahoma and east to the Atlantic coast.  Populations have declined by ≈ 99% in the prairie region and are nearly extirpated from the eastern portion of the former range.  Causes of decline remain largely undetermined but habitat loss and the subsequent breakdown of metapopulation dynamics are generally suspected.  However, populations within northeastern Kansas remain relatively abundant and are considered stable.  This offers a unique opportunity to understand the habitat- use patterns and metapopulation dynamics of an integral population of this imperiled species. The goal of this project is to provide baseline data on the distribution of Regal fritillary subpopulations and its larval host plant within the Konza Prairie, gather information on the spatiotemporal extent of the disturbance regime within the study area, assist in the assemblage of a geographic information system (GIS), and to conduct a comprehensive literature review of issues related to the focal species.  Students will be trained in experimental design, standard butterfly and vegetation monitoring methodology, basic use of GIS and GPS technologies, and literature review practices.

Statistical methods for predicting population dynamics (Mentor: Hefley)

Broadly, my research focuses on developing and applying statistical methods to inform wildlife conservation and management decisions. I am also interested in applied statistics, specifically, how other disciplines such as engineering, biology, ecology and computer science utilize the large amounts of data that are currently available for decision making. For more information see my website

Ecological Genomics of Soil Nematode Community Responses: Model and Non-model Approaches (Mentors: Herman). 

This research project will use native prairie microbial-feeding soil nematode populations sampled from the Konza Prairie Biological Station to link organismal responses to environmental change. Extensive genomic tools are currently available for one model species of soil nematode, C. elegans. Our group has shown that microbial-feeding nematode and bacterial communities differentially respond to altered disturbance regimes and nutrient enrichment. We have modeled interactions in the lab and used transcriptional profiling to identify C. elegans candidate genes involved in bacterial interactions. Moreover, functional tests were used to determine which induced genes have the greatest impact in a changing bacterial environment. REU students will be involved in two new exciting projects. One lab-based project will involve functional characterization of candidate genes identified in C. elegans and native species of nematodes. The second project will be field-based and will involve use of molecular methods to document and quantify specific microbial-nematode interactions.

Small Mammal Parasite Diversity and Community Interactions in the Tallgrass Prairie Ecosystem (Mentor: Hope).

With ongoing climate shifts, small mammals are experiencing significant range changes resulting in community turnover. Where different communities collide, such as at the interface of woodland and grassland biomes, there exists a broad array of potential biotic interactions, including hybridization of closely related species or lineages within species, competition for space and resources, and potential spread of micro- and macro-parasites. Small mammals harbor internal parasites that may constitute diverse communities occurring within individual hosts and although these parasite loads may significantly affect host population size and health, very little is yet known of the basic diversity, distribution, and host specificity of these organisms. REU students will have options for a number of research questions within this system including basic biodiversity discovery and description, host-parasite associations, and interspecific interactions. Work will be specimen based with a strong field component and lab processing of specimens, including preparation of study skins and museum voucher materials to develop existing synoptic teaching collections. Potential exists for molecular lab work associated with using DNA to characterize novel biodiversity. The Konza Prairie Biological Station has a long history of small mammal demographic experimentation that will form a background for developing a contemporary sampling framework.

Behavioral Ecology of Amphibians and Dragonflies (Mentor: Horne).

Male cricket frogs (Acris crepitans) in this area have recently been discovered to display visually as well as acoustically. Projects with these small frogs would include observations of displays in the field and lab to determine the function of displays and whether they make males more successful. For projects involving dragonfly behavior, I have discovered males of the Plains clubtail (Gomphus externus), a species that lays eggs in rivers, evenly spaced along high, dry, rocky areas far from their breeding grounds. I hope to be able to individually mark these males and, through observation, discover if they are defending feeding territories or perhaps forming leks to display for females. Males of another species of dragonfly, the common whitetail (Plathemis lydia), defend oviposition sites on the banks of ponds. Males appear to prefer to defend sites where a branch or other piece of debris extends partially into the water. A good project here would be to manipulate the sizes of debris, individually mark males, and then record reproductive success and number of aggressive encounters with other males as correlated with characteristics of oviposition sites.

Phenotypic Variation and Local Adaptation to Drought in Big Bluestem (Andropogon gerardii) Ecotypes Across the Great Plains (Mentor: Johnson).  
My ecological genomics lab studies natural variation in drought tolerance in an ecologically dominant prairie grass along the cline of the Midwest precipitation gradient and seeks to identify the mechanisms (physiological, genetic) to account for the observed adaptation. The research is an exciting mix of basic biology, ecology, and genetics with strong implications for conservation and restoration ecology. The questions we are addressing include: Are ecotypes of big bluestem Andropogon gerardii broadly or locally adapted along a sharp precipitation gradient, how will ecotypes from different places across the gradient respond to precipitation change (natural and experimentally induced with rainout shelters). What is the genetic basis for these drought adaptation? How can these results inform land managers about how to restore tallgrass prairie? Can results tell us which ecotypes to plant where in the face of climate change? Our approach is a reciprocal garden platform arrayed across the precipitation gradient from Illinois to western KS. You can get more information at the project website at http://bluestemecotype.ksu.edu and lorettajohnsonlab.weebly.com.
Conceptualizing and Quantifying Fish Movements (Mentor: Mather). 

Fundamental questions about animals and their relationship to the environment, at a landscape level, require an understanding of where animals are, how often, and how far they move. Telemetry, especially acoustic-radio-pit tag arrays in underwater environments, is an emerging technology that can provide spatially-explicit information on fish habitat use and movements. Factors that control populations, processes that structure communities and the role of higher trophic levels in ecosystem fluxes are fundamental questions in ecology that will change with the underlying distribution of animals. Consequently, identifying sources of heterogeneity in fish distribution through movement is critical for a basic understanding of stream and river networks. I am presently determining home range, residency, site fidelity, activity, and movements of (a) top predators in reservoirs, (b) threatened stream fish in river networks, and (c) an abundant stream macroinvertebrate (crayfish) in the Kings Creek watershed. Using stationary and mobile arrays, my colleagues and I seek to understand the commonalities of underwater motile organism's use of wintering, spawning and feeding areas and link distribution and movement to ecosystem structure and function.

Ecological Genomics of Adaptive Trait Variation (Mentor: Morgan). 

Research in my lab is motivated by the fact that most species are subdivided into finite systems of subpopulations and that the pattern of phenotypic and genetic variation within and among populations provides crucial information about evolutionary processes in nature. Determining the relative roles of diverse evolutionary processes in population differentiation and local adaptation has and remains one of the central questions in evolutionary biology. My lab currently uses Drosophila melanogaster as a model system to address larger questions in evolutionary and ecological genomics. These broad questions include what are the genes that underlie ecologically-relevant phenotypic variation? What evolutionary processes have influenced (and currently influence) the molecular genetic variation at these functional loci? And how does molecular variation in these loci and networks influence ecologically relevant phenotypic variation in nature? Potential summer projects that fit under the umbrella of my lab include: a study that seeks to link the role of functional genetic variation to phenotypic variation via a candidate gene approach, a study documenting the presence or absence of standing level of functional genetic variation among locally adapted populations for thermal stress phenotypes, as well as project investigating the level of phenotypic differentiation and local adaptation among populations sampled along a latitudinal cline. Each of these projects would involve a combination of whole organism and molecular genetic analysis. No prior experience is necessary for success in these summer REU projects!

Drought impacts on woody encroachment (Mentor: Nippert). 

In many grasslands, woody plant species have increased in frequency and abundance over the past 30 years, shifting the system from grass-dominated to shrub or tree-dominated.  At the Konza Prairie, we have investigated physiological, community, and ecosystem drivers and consequences of woody encroachment.  Yet, we lack a complete understanding of how climate change will impact woody shrubs and their interactions with grasses in tallgrass prairie.  Here, the REU student will work on a large collaborative climate change experiment that is simulating changes in rainfall variability and intensity to quantify woody shrub responses to altered climate. The REU student will get to design a project focused on physiological, community, or ecosystem responses to these climate changes, based on personal preference. These results will be useful for parameterizing mathematical and statistical models that forecast future ecosystem changes in tallgrass prairie. 

The molecular-genetic basis of multicellular evolution (Mentor: Olson). 

Despite the biological and ecological importance of major evolutionary sate transitions such as multicellular evolution, very little is known about their molecular-genetic basis.  REU students in the Olson lab will work on projects aimed at discovering what genes are important for multicellular evolution in a green algal model system for multicellular evolution - the volvocine algae.  Projects are student led and may include using next-generation sequencing technologies to decode and compare the genomes of several key volvocales species as part of the international Volvocales Genome Project.  Students could also combine laboratory and field work to make important contributions toward our understanding of the ecological basis of multicellular evolution in the volvocine algae.

The evolution and ecology of pathogen cooperation and virulence (Mentor: Platt). 

Pathogens exhibit tremendous life history variation which helps shape the epidemiology of the diseases they cause. Despite this, the ecological and evolutionary forces driving pathogen evolution are often poorly understood. For example, though facultative pathogens cause many important human and agricultural diseases most epidemiology models do not capture basic features of their ecology. These organisms maintain significant populations in non-host environments and consequently are subject to heterogeneous selective pressures. Our group works to understand how ecological trade offs and social evolution influences the evolution and epidemiology of a common facultative plant pathogen. Depending on their interests, REU students will design a research project related to the maintainance and dynamics of cooperative pathogenesis, the evolution of virulence, or the adaptive significance of the horizontal transmission of virulence genes

Effects of Patch-Burn/Grazing on Grassland Songbirds (Mentor: Sandercock). 

Rangeland management in the Flint Hills of eastern Kansas is primarily for cattle production.  Widespread use of annual spring burning, coupled with intensive grazing, reduces the biomass and vertical structure of herbaceous plants.  Loss of vegetative structure can have negative impacts on prairie animals that require ground cover for protection of dormant stages overwinter, or for food resources or concealment during the summer breeding season.  Experimental units on the east side of Konza Prairie have been developed as two large-scale replicates of a new patch-burn/grazing experiment.  Each replicate is subdivided into four experimental units: one site is set aside as an annually burned control and three sites are burned on a rotational basis, which creates a chronosequence of sites that are either burned, rested for one year, or rested for two years.  Prescribed burns are completed in early spring and grazing is conducted with cow/calf stocking.  The combination of rotational fire and grazing creates heterogeneity in vegetative structure, which may benefit grassland animals by mimicking the historical patterns of grazing by bison.  The focus of this REU project will be to investigate the effects of patch-burn/grazing on grassland songbirds as one core part of the prairie community.  The REU student will receive training in the techniques of field ornithology, including line transect sampling, nest searching and monitoring of reproductive success.  Standardized sampling procedures will be used to examine the effects of patch-burn grazing on species diversity, species abundance, and demographic performance of common species. 

Molecular Evolution of Land Plants (Mentor: Schrick). 

Plants are photosynthetic factories that produce a plethora of small metabolites critical to life on earth. Studies in our lab are focused on steroids and other lipids and how they regulate plant growth using the Arabidopsis model system. Plant-specific homeodomain transcription factors that contain lipid-binding motifs are master regulators of cell-type differentiation. The goal of this project is to examine the evolution of these transcription factors that first appeared in Charophycean green algae, an ancestral lineage to the land plants. Their emergence accompanied adaptations in specialized cells of the epidermis to protect against water loss and ultraviolet radiation, in addition to cell wall modifications to combat environmental factors such as microbial pathogens and insect predation. A phylogenetic analysis will be performed to determine the occurrence of these transcription factors among five major Charophycean green algae groups. In addition, the student will characterize of one or more of the transcription factor genes from the green algae species, Penium margaritaceum, using molecular techniques. Studying the evolution of these key regulatory proteins will provide insight into the molecular toolbox that was required for mosses and higher plants to colonize land, with implications for plant survival and adaptation in changing environments.

Adaptation to extreme environments. (Mentor: Michi Tobler). 

Extreme habitats are characterized by the presence of extreme physiochemical stressors that require costly adaptations that are absent in closely related species. Some organisms are able to cope with extreme environmental conditions and thrive in places that are hostile for most others, proving life’s capacity to adapt to extreme conditions. The Tobler lab investigates freshwater fishes of the family Poeciliidae, which have colonized hydrogen sulfide-containing springs, as a model to study ecological and evolutionary consequences of living in extreme environments. Current research projects investigate patterns and mechanisms of local adaptation and ecological speciation. Using genomic, physiological, and morphological tools, the Tobler lab is investigating how fish cope with physio-chemical stressors, whether and how living under extreme conditions leads to adaptive trait divergence and reproductive isolation, whether similar traits evolved independently in different phylogenetic groups occurring along similar environmental gradients, and what genomic changes underlie adaptation in sulfide spring fishes. REU students will design independent research projects focused on the genomic or physiological basis of adaptation and speciation. 

Population Genomics of Fungal Secondary Metabolite Production (Mentor: Toomajian).

The Toomajian lab studies the population and evolutionary genetics and genomics of plants and pathogens. We focus on genome-enabled science that emphasizes bioinformatic approaches. Recently, we have pursued several evolutionary and population genetic questions related to variation in the capabilities of pathogenic fungi to produce different secondary metabolites, investigating variation at both the interspecies and intra-population levels. We are testing the hypothesis that variation in the genes underlying secondary metabolite production is due to different selective pressures, and that this variation plays a key role in the adaptation of different pathogen populations and species. REU scholars may participate in one of multiple projects that involve the bioinformatic analysis of fungal genetic variation, using this variation to infer evolutionary processes or map genes involved in population or species differentiation. For most projects, the scholar will learn to use software to map millions of nucleic acid sequence reads to reference genome sequences for polymorphism discovery, and will learn techniques for the downstream analysis of these polymorphisms. Example projects include: 1) A population genetic study of the plant pathogen Fusarium graminearum, investigating divergence population genetics of closely-related species or scanning for adaptive divergence among populations using a reverse-ecology approach. 2) A comparative genomics study contrasting the gene content of multiple isolates of two closely related Fusarium species, with a special focus on secondary metabolite gene clusters. 3) A fungal pathogen quantitative trait mapping study of traits such as secondary metabolite levels and host specificity using progeny from an interspecific cross between two Fusarium species. In the Toomajian lab, the REU scholar will receive bioinformatics training critical to modern ecological genomics research.

Population Genomics and Transcriptome Variation (Mentor: Toomajian). 

The Toomajian lab studies the population and evolutionary genetics and genomics of plants and pathogens. We focus on genome-enabled science that emphasizes computational and bioinformatic approaches, but also maintain an active experimental lab. REU scholars may participate in one of several projects that involve the bioinformatic analysis of genetic variation, using this variation to infer evolutionary processes, map genes involved in population or species differentiation, or understand the genetic basis of gene expression variation. For most projects, the scholar will learn to use software to map millions of nucleic acid sequence reads to reference genome sequences for polymorphism discovery, and will learn techniques for the downstream analysis of these polymorphisms. Example projects include: 1) a systems-biology project investigating the evolution of gene expression levels between Arabidopsis thaliana and its close relatives. This project also involves the analysis of within-species variation in gene expression changes under ecologically-relevant abiotic stress in Arabidopsis. 2) A population genetic study of the plant pathogen Fusarium graminearum, investigating divergence population genetics of closely-related species or scanning for adaptive divergence among populations using a reverse-ecology approach. 3) A pathogen quantitative trait mapping study of traits such as secondary metabolite levels and host specificity using progeny from an interspecific cross between two Fusarium species. In the Toomajian lab, the REU scholar will receive bioinformatics training critical to modern ecological genomics research.

Population genetics and social interactions of the Konza Prairie bison herd (Mentors: Ungerer, Joern, and Briggs). 

The Konza Prairie Biological Station (KPBS) is situated 10 miles south of Kansas State University and is home to a resident bison herd of approximately 300 animals. This herd was established in 1987 to study interaction effects of grazing and fire frequency on the tallgrass prairie ecosystem in long-term ecological research. Ongoing stewardship of this herd involves monitoring its genetic health, conducting molecular parentage analysis for each seasonal cohort of new calves, and leveraging these data to better understand social interactions among individuals and optimal herd management practices. Opportunities for REU student involvement in this project include training in extraction of DNA from bison hair follicles, generation of genetic marker data (i.e., nuclear microsatellite loci), and the use of population genetic and molecular parentage software packages. Students also will have ample opportunities for field-based observational study of social interactions and group dynamics within the herd. This REU opportunity thus has both lab-based and field-based components.

Evolutionary Developmental Biology of the chordate body plan (Mentor: Veeman).

Research in the Veeman lab centers on the development and evolution of the chordate body plan, with specific interests in the morphogenesis of key chordate structures such as the notochord and the hollow dorsal neural tube. Our model system is the ascidian chordate Ciona, which has a particularly small, simple embryo that can be imaged in toto with fine subcellular detail. The ascidians are part of a group called the tunicates that are the closest outgroup to the vertebrates, thus providing a valuable evolutionary perspective. We use modern imaging and image analysis methods to quantify cell and tissue dynamics in these remarkable embryos, with the goal of resolving questions in both the cell biology of morphogenesis and the evolution of morphogenetic mechanisms.

Lipids and Plant Response to Environmental Stress (Mentors: Welti). 

Plants undergo major changes in metabolite levels when exposed to environmental stresses.  Our group studies changes in non-water soluble metabolites, i.e. lipids, in plants responses to abiotic stressors, including mechanical damage, heat, cold, freezing, and drought.  To understand the molecular basis for lipid changes and their role in plant adaptation to environmental stress, mutations and natural variation in genes putatively responsible for wounding-induced lipid changes are analyzed.  Lipid variation is measured using mass spectrometry.  An REU project may focus on analysis of stress-induced lipid metabolism and its underlying mechanisms in the model plant Arabidopsis thaliana, in a crop species, or in another group of plants.

Microbial responses to global change in grassland soils and streams (Mentor: Zeglin).

Bacteria and fungi are diverse and abundant in soils and streams, and their integrated metabolic activity controls soil fertility and water quality. Changes in grassland precipitation patterns, nitrogen and carbon availability affect microbial growth, survival and metabolism, which in turn impact grassland productivity, soil carbon storage and stream nutrient export. A primary goal of work in my lab is to identify the microbial populations and functional groups that respond to changing habitat conditions, in order to provide a mechanistic understanding of microbial function in grassland ecosystems and enable better prediction of microbial activity based on the field distribution of microbial populations and functional genes. For example, current research questions include: Which soil microbial populations show greater growth and activity during and upon relief of drought conditions, and what physiological mechanisms facilitate this drought tolerance? How do short- and long-term changes in nitrogen availability impact microbial communities and microbial potential to metabolize nitrogen compounds in different ways? Field experiments at Konza Prairie provide opportunities to address these questions in the context of various aspects of grassland management, including fire, grazing, fertilization and climate change. REU project specifics will be defined in collaboration with the student to incorporate individual interests and goals.