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Ecological Genomics Institute

URM Mentors | Ecological Genomics | Kansas State University

Loretta Johnson (Biology) - Response of Native Grass to Changes in Precipitation. The Johnson lab uses reciprocally transplanted genotypes of Andropogon gerardii established under ambient and reduced rainfall across a precipitation gradient to test for local adaptation to climate variation. URM scholars will have the opportunity to 1) characterize the ecophysiological and morphological response of ecotypes of big bluestem to drought, 2) characterize and quantify candidate genes involved in drought, 3) measure aboveground productivity differences of ecotypes in the reciprocal transplant gardens, and 4) characterize genetic diversity of source big bluestem populations across the geographic range. For more information visit: http://www.k-state.edu/johnsonlab/

Ted Morgan (Biology) - Ecological Genomics of Adaptive Trait Variation. The Morgan lab uses Drosophila melanogaster as a model system to address larger questions in evolutionary and ecological genomics. Potential URM projects include: 1) linking functional genetic variation to phenotypic variation, 2) documenting the presence or absence of standing level of functional genetic variation among locally adapted populations for thermal stress phenotypes, 3) documenting clinal phenotypic differentiation and local adaptation among populations. Each of these projects will involve a combination of whole organism and molecular genetic analysis. For more information visit: http://www.k-state.edu/morganlab/Morganlab/lab.html

Chris Toomajian (Plant Pathology) – Next-generation sequencing of genome and transcriptome variation. The Toomajian lab studies the population and evolutionary genetics and genomics of plants and pathogens. We focus on genome-enabled science that emphasize computational and bioinformatic approaches, but also maintain an active experimental lab. URM scholars may participate in one of two projects that involve the bioinformatic analysis of genetic variation: 1) a systems-biology project aimed at characterizing variation in the transcriptome of Arabidopsis thaliana, or 2) a population genetic study of the plant pathogen Fusarium graminearum. For either project, the scholar will learn to use software to map millions of nucleic acid sequence reads to reference genome sequences. The Arabidopsis project involves the analysis of gene expression differences with potential relevance to ecological stressors, while the Fusarium project includes characterizing how population structure relates to the location and host plant of each sampled isolate. The URM scholar will receive bioinformatics training critical to modern ecological genomics research. For more information visit:https://sites.google.com/site/toomajianlab/

Mark Ungerer (Biology) – Genome evolution in wild sunflowers. The genomes of flowering plants are remarkably variable in nuclear DNA content, with greater than 1000-fold differences among some taxa. It is now recognized that differential accumulation (and loss) of genomic parasites known as transposable elements (TEs) accounts for much of this variation. Long terminal repeat (LTR) retrotransposons are a class of TE related to infectious retroviruses that are capable of autonomous transposition via an RNA intermediate. The large size and proliferative ability of these elements make them important contributors to genome size evolution, especially in plants, where they can accumulate to exceptionally high copy numbers and contribute substantially to variation in genome size even among closely related taxa. My laboratory recently discovered a fascinating example of retrotransposon proliferation that involves three wild sunflower species (Helianthus anomalus, H. deserticola, and H. paradoxus) that arose via ancient hybridization events between the same two parental taxa (H. annuus and H. petiolaris). The hybrid species are all independently derived but yet each has undergone massive proliferation events of LTR retrotransposons. Currently, we are investigating the likely environmental and genomic conditions that could have triggered these proliferation events. We also are interested in understanding the role that LTR retrotransposon proliferation may have played in the evolutionary events that took place in this group of sunflowers. For example, have TE proliferation events helped to facilitate hybrid speciation and the ecological transitions of these species to the environmentally extreme habitats in which they’re now found? Or have these evolutionary events occurred independently of, and in fact, notwithstanding the massive transposable element bombardments that took place in each hybrid species' genome? Support for either alternative would deeply impact our understanding of the role of transposable elements in organismic evolution. For more information visit: http://www.k-state.edu/ungererlab/UngererWeb/Home.html

Sue Brown (Biology) - Beetle Ecological Genomics. The Brown lab uses comparative genomics approaches to understand how genome evolution and life histories are shaped by ecological forces. Flour beetles in the genus Tribolium are pests of stored grain. This lab sequences the genomes of multiple Tribolium species with divergent life history traits. URM scholars will 1) use comparative genomic approaches to analyze the amount, content and organization of repetitive DNA in Tribolium spp. genomes, and 2) investigate gene synteny and chromosome rearrangements that led to the change in chromosome number in the T. confusum clade. For more information visit: http://www.k-state.edu/tribolium/

Carolyn Ferguson (Biology) – Ecological Genomics of Emerging Phlox Species. Current research in the Ferguson lab focuses on polyploidy and species boundaries in the plant genus Phlox. Polyploidy, or whole genome duplication (e.g., diploids may have 2n=14 chromosomes, tetraploids 2n=28, and so on) is an important process in plant evolution, and our appreciation of the prevalence, patterns and evolutionary significance of polyploidy continue to increase. Polyploidy accompanied by hybridization between distinct species (allopolyploidy), is a textbook case of sympatric speciation. Yet much polyploidy is cryptic, and may arise within single species (autopolyploidy), or may have a more complex origin. The implications of polyploidy for inference of species boundaries are intriguing, because we must explore the extent to which cytotypes (populations of a particular ploidy level within a recognized species) are distinctive in terms of their evolutionary history, levels of interbreeding, morphology and ecology. The plant genus Phlox is known for hybridization and polyploidy, and includes several polyploid assemblages (from the prairies of the eastern U.S. and central Great Plains to the arid southwest) that include diploid, tetraploid and hexaploid populations. URM scholar projects can take advantage of laboratory, field and herbarium resources to: characterize ploidy level variation in particular polyploid assemblages; apply DNA sequence data to infer allelic relationships (placed within a larger phylogenetic framework for Phlox); and investigate morphological and ecological correlates of ploidy level variation. More information on research in the Ferguson lab is available at www.ksu.edu/fergusonlab.

Jeremy Marshall (Entomology) – The Process of Species Formation in Crickets. UMR scholars in the Marshall laboratory will be trained in the use of comparative proteomic techniques to identify proteins that underlie postmating, prezygotic phenotypes in the Allonemobius socius complex of crickets. Students will conduct experiments that investigate the effects of male age on ejaculate composition and fertilization success with RNAi techniques. Students will be introduced to the basic concepts of comparative proteomics, including experimental design, tissue choice, protein gel methods and analyses, as well as protein identification via mass spectrometry (i.e., MALDI MS and MS/MS analyses). More information is available at: http://www.k-state.edu/cricketlab/Marshall_Lab_Page/Home.html

Michael Herman (CoPI, Biology) – Ecological Genomics of Soil Nematodes. Research projects in the Herman lab use native prairie microbial-feeding soil nematode populations to link organismal responses to environmental change. URM scholars will be involved in three new exciting projects. Students will 1) characterize candidate genes identified in C. elegans and native species of nematodes, 2) document and quantify specific microbial-nematode interactions in a field setting, and 3) test the relative contributions of ecological mechanisms (‘mass effect’ vs. ‘species sorting’ paradigms) to habitat selection. For more information visit: http://www.k-state.edu/hermanlab/

Ari Jumpponen (PI, Biology) – Microbial genomics in the urban environment. Human activities in the urban areas alter microbial communities and reduce their diversity. However, the reasons for these changes are poorly understood. An on-going research program in Jumpponen’s laboratory aims to pin-point the mechanisms that best explain the reduced microbial diversity and altered community composition in urban centers. Using a combination of pure-culturing and cutting edge molecular tools, this program specifically tests i) if the urban trees are more susceptible to microbial diseases than those outside of urban centers; ii) if the microbial communities in urban and non-urban areas differ in their tolerance to heavy metals or nutrient enrichment; iii) if the soils in urban areas reduce microbial activity and change their community composition; or, iv) if isolation of the sites within the urban grid leads to reduced microbial loads. Ultimately, the combination of these studies will provide insights to fundamental questions about controls of microbial community assembly and test specifically how human-induced controls operate in conjunction with urban land use. For more information visit:http://www.k-state.edu/fungi/Greeting/Fungal_Ecology_Lab.html

Dorith Rotenberg (Plant Pathology) – Genomics of Tomato Spot Wilt Virus (TSWV) in two ecologically distinct hosts: the plant and the insect vector. If you are curious about complex ecological and molecular interactions between viruses, plants, and insects that transmit plant-pathogenic viruses, then the Rotenberg lab group has a research project for you. This diverse and interactive lab team aims to identify, quantify, and determine the function of molecular components (RNA and protein) associated with viral infection of two ecologically distinct hosts: the insect vector which provides an environment for virus to replicate in various insect tissues without comprising the health of the vector, and the plant host which provides an environment for virus replication, but unlike the vector, succumbs to irreversible disease leading to early death. They invite you to join their team to address the question “How do the host (plant and vector) and virus components (RNA and protein) interact to result in successful transmission of a plant-pathogenic virus by the vector without compromising the health of the vector?” Your research project will be to 1) quantify expression levels of several key host defense genes and TSWV transcripts (RNA) in the two TSWV hosts (western flower thrips vector and tomato); 2) characterize the relationship between defense gene expression levels and viral RNA in the two hosts; and 3) learn how to design biological experiments, analyze quantitative data, and master current molecular biology techniques. For more information visit: http://www.plantpath.ksu.edu/p.aspx?tabid=410&ItemID=411&mid=74&staff_category=Faculty

Anna Whitfield (Plant Pathology – Ecological genomics of insect defense responses to viruses. Our lab uses the Peregrinus maidis-Maize mosaic rhabdovirus (MMV) system as a model to study vector-virus interactions. URM scholars will 1) quantify gene expression and viral infection concomitantly using real-time quantitative RT-PCR (qRT-PCR) on individual insects fed on MMV-infected corn, 2) quantify expression of key genes from the insect immune system (members of the Toll, Imd, JAK/STAT, and siRNA pathways), and 3) conduct RNA-silencing experiments to knock-down target gene expression in P. maidis to investigate the functional significance of correlations between insect gene expression and virus titer. For more information visit: http://www.plantpath.ksu.edu/p.aspx?tabid=410&ItemID=410&mid=74&staff_category=Faculty

Brett Sandercock (Biology) – Conservation genomics of globally migrating sandpipers Shorebirds as a group are imperiled by habitat loss, degradation and pollution. We will use genome scan approaches to investigate population structure, pathogen load, and conservation status. For more information visit: http://www.k-state.edu/bsanderc/

Bradley Olson (Biology) - Genomic basis of the evolution of multicellularity in gree agae. The Olson laboratory is focused on understanding how multicellular organisms evolved from single cells.  We utilize the Volvocine algae as a powerful model system for multicellular evolution.  Volvocacean member species include organisms with well developed molecular genetics such as singled celled Chlamydomonas reinhardtii, and multicellular Volvox carteri.  Despite significant evolutionary and morphological changes between unicellular Chlamydomonas and multicellular Volvox, their genomes are very similar, suggesting few genetic changes are required for multicellular evolution.  Currently the lab is using a systems biology based approach toward determining genes that are important for multicellular evolution.  In addition these organisms are commonly found in many freshwater aquatic environments, including ponds and lakes in Kansas, Thus, we are utilizing results from our systems based approaches to understand the interplay between ecological habitat and the genomics of of multicellular evolution.  For more information visit http://www.k-state.edu/olsonlab/