Projects

 

On the application, students are required to rank up to three projects that interest them. Projects should be checked for possible prerequisites and/or the amount of computational work involved. Not all projects are appropriate for students at all stages of education. Possible projects for 2018 are:

Modeling/Bioinformatics

Modeling and bioinformatics projects are ideal for both biology and mathematics/computer science majors.

Dr. Folashade Agusto, Models of Disease Transmission

Background Paper. The REU student will learn how to develop mathematical models for transmission of an infectious disease of public health interest such as Methicillin-resistant Staphylococcus aureus (MRSA), and vector borne diseases (such as malaria and Zika). The student will then investigate basic properties of the models in order to determine conditions under which the disease will be eliminated or will persistence. These analyzes require writing computer codes either in Matlab, R or Python. The student will also learn parameter estimation using relevant data. No programming knowledge is required, some programming will be learnt in the course of the project. The project is suitable for a student with a mathematical background or an apt for quantitative study.

Dr. Maria Orive, Modeling Evolutionary Genetics

Background PaperThe research experience will closely integrate evolutionary biology and mathematics. through numerical analyses of models using analytical software, using computer programming to develop simulations for model testing and parameter exploration, and/or statistical analyses of genetic data collected by collaborators. The student may choose one of two different research projects. 1) Patterns of host-endosymbiont associations. Symbioses between multi-cellular hosts and their endosymbionts are widespread throughout marine and many terrestrial systems. We focus on corals and their photosynthetic dinoflagellates by developing new theoretical models allowing interpretation and analysis of genetic data for both hosts and symbionts. 2) Effects of life history stage and clonal structure on the rate of evolution and the amount of evolutionary lag (the difference between current mean population fitness and optimum mean fitness). Models that describe how genetic and life history structure affect the rate of evolution are crucial for predicting patterns of evolution and extinction under changing selective conditions.

Prerequisite: A course in genetics OR computer programming

Dr. Jamie Walters, Molecular evolution and genome biology of butterflies

Background PaperThe REU student will use computational and bioinformatic methods to investigate patterns of molecular evolution in butterflies. Possible research topics include tests of selection on reproductive proteins, proteomic analysis of spermatophores, characterization of transposable elements in lepidopteran genomes, or population genomics of sex-linked genes. A common theme of these projects is that the REU student will be performing computational analyses of existing genomic datasets. This REU position would be well-suited to students coming from either biological or computer science backgrounds. The specific research project will be tailored to fit the interests and skills of the successful applicant.

Dr. Mark Holder, Analyzing sources of conflict in phylogenetic estimates.

Background paper. Estimates of phylogenetic relationships for a set of species can differ for a number of reasons: each of the estimates can be wrong due to random, sampling error; the statistical models used to analyze the data could be inadequate; the computational methods approaches used may have been insufficient; or the differing estimates could reveal real discordant genealogies for different portions of the genome. The Open Tree of Life project gathers phylogenetic estimates from many sources together. The project aligns them to a common taxonomy and then produces "synthetic" supertree estimates of the full tree. These estimates also highlight the discordance between the input phylogenetic estimates. Currently, the software tools from the project do not attempt to diagnose the cause of the discordance. The project would benefit for more tools for helping researchers analyze the causes of incongruence. Alternatively, a student could develop some "case studies" of identifying parts of the tree of life that show a large number of conflicting estimates, and then going to the source data for these estimates to try to find the cause of the discordance.

Dr. Terry Locke: see below under Ecology

Dr. Pamela Sullivan: see below under Ecology

Evolution

Evolution projects are primarily lab based

Dr. Jim Bever: see below under Ecology.

Dr. Jennifer Gleason, Drosophila courtship behavior

Background Paper. Animals use many different types of signals that stimulate different senses to communicate with one another. The Gleason Lab is interested in the evolution of courtship in different groups of Drosophila. The REU project will examine courtship in one of the lab’s focal groups, likely the Drosophila suzukii group, which uses visual signals or Zaprionus indianus, which has far less courtship behavior than most other species. The student will be involved in observing courtship behavior to identify elements important for courtship success. Some use of video and auditory recording equipment may be necessary, depending on the research question. As a project with great flexibility, the hypotheses tested may be directed by student interest. The project can be adapted for students at any level of education.

Dr. Rich Glor, Lizard speciation

Background Paper. How and why do new species form? Members of the Glor Lab investigate these questions with lizards by combining field studies of animals in nature with experimental studies of animals in a captive colony. Potential REU projects include a diverse range of questions about phylogenetics, speciation, and the genetic basis of species differentiation. Previous undergraduate researchers in the Glor Lab have used phylogenetic and population genetic analyses to delimit species boundaries with genomic data, investigated the role of behavioral divergence in reproductive isolation, and characterized the heritability of phenotypic traits like dewlap color and pattern. Please visit KU Herpetology's research page to learn more about research conducted by the Glor Lab and others.

Dr. Kirsten Jensen: see below under Systematics

Dr. Deb Smith, Native Bee Ecology or Social Spider Biogeography 

Background Paper. The Deb Smith lab focuses on social arthropods and their relatives.  Students may choose between two major project areas: (1) Native bees nest in surviving patches of original tallgrass prairie (remnant prairie), one of the most endangered habitats in North America. Students participating in this project could investigate hypotheses about bee size and response to habitat fragmentation. (2) Cyrtophora citricola (Araneidae), the tent-web spider, may live in solitary webs or form colonies of two to hundreds of individuals, each with its own web. Are new expansion populations established by migrants from many populations, or descended from one or a few individuals from a single source. Students participating in this project will address this question by comparing mtDNA of “expansion” and established populations.

Ecology

Some ecology projects will involve fieldwork

Dr. Jim Bever, Ecological and evolutionary feedbacks between plants and beneficial fungi

Background paper. Our lab investigates the ecological and evolutionary consequences of plant-microbe interactions.  Much of our work focuses soil fungi (called mycorrhizal fungi) that commonly improve plant growth through increased access to soil resources.  We are particularly interested in how the benefits that plants receive from these fungi change over time and the potential role of these fungi in maintenance of plant species diversity.  We often work in native prairie, where we have found that these fungi play primary roles in plant dynamics and in the restoration of native diversity. Work on this problem could involve work in the field, greenhouse, lab (at microscope work or DNA analysis) or computer (modeling).

Dr. Sharon Billings, Understanding how microbial enzymes function to drive ecosystem nutrient availability

Background paper. We are exploring how key enzymes made by soil microbes function in the soil environment.  They are important, because they induce the decay of organic compounds in soil that contain nutrients important for microbial and vegetation functioning.  As such, they ultimately provide a large fraction of any ecosystem’s nutrient demand.  We do not know how many of them respond to temperature, soil pH, soil mineralogy, or moisture availability.  We have a set of projects exploring these questions.

Prerequisites: Introductory courses in biology and chemistry. A course in ecology is helpful, but not required.

Dr. Bryan Foster, Restoration and plant communities

Background paper. Research in our lab explores how biotic interactions, resource availability, regional processes interact to govern the assembly, diversity, and functioning of plant communities. We are also interested in understanding the impacts of management and human-induced global changes on biodiversity and ecosystem function and applying this understanding to the conservation and restoration of native plant communities. REU projects can be centered around one or more of our long-term field experiments at the KU Field Station by taking advantage of existing long-term data sets and/or by collecting new data.

Dr. Terry Locke, Terrestrial community response to precipitation extremes

Background paper. The student will choose from water and soil analyses or statistical modeling aspects of a project geared toward understanding how plant, soil, and aquatic microorganisms from different environments respond to and interactive with variation in precipitation and land use.

Dr. Ben Sikes, Ecology of Soil Microbes 

Background PaperResearch in my lab explores the diversity and interactions of soil microbes with a focus on fungi. These interactions range from microbes, to plants, and ecosystems. Our ongoing lab projects include the study of disturbance with an emphasis on fire, the effects of restoration on soil communities, and mutualistic networks between pollinators, plants, and mycorrhizal fungi. REU students will develop an independent project while getting hands-on experience with fungal culturing, molecular techniques to characterize microbial communities and field work. Recent undergraduate projects have explored how management decisions and land use history alter soil fungal communities, whether fire alters the microbial decomposition of new litter after fire, and if pollinators and mycorrhizal fungi specialize on the same prairie plants.

Dr. Pamela Sullivan, Understanding how plants, soil and water interact to govern stream water quality

Background paper. In Dr. Sullivan’s Ecohydrology Lab at KU there are multiple opportunities to explore how plants, soil and water interact to govern stream water quality. For example students can choose include varying degrees of field, lab and modeling based research learning everything from collecting samples, harvesting and manipulating data and modeling how future changes in land cover will alter water quantity and quality. We welcome students are excited about how the environment works and how changes to this environment alter the hydrology and biogeochemistry of terrestrial Earth.

Systematics

Systematics projects involving molecular and/or morphological techniques applied to diverse species groups

Dr. Mark Holder: see above under Modeling/Bioinformatics

Dr. Kirsten Jensen, Systematics of tapeworms

Background paper. The major focus of research in the Jensen laboratory has been the global study of metazoan parasite biodiversity. While parasitologists have estimated that parasites comprise over half of all animal species, many regions and ecosystems remain understudied for parasites; this is especially true for the marine environment. Current research focusses on the documentation of macroevolutionary patterns in fish parasites. Patterns of primary interest are those relating to a group’s evolutionary history, host associations, biodiversity, and geographic distribution, as well as the potential cophylogenetic patterns that exist between parasites and their hosts. REU students will become familiar a specific host-parasite system (i.e., tapeworms and their shark and ray hosts), and acquire the necessary skills to distinguish among tapeworms of different orders and prepare the tapeworms as whole mounts for study with light microscopy and scanning electron microscopy. A specific research project centered on description of tapeworm novelty using primarily morphological data will be chosen depending on the interests of the student.

Dr. Mark Mort, Diversification and Evolution Among Micronesian Island Endemic Flowering Plants

Background paper. The Mort lab uses DNA data to study the patterns of evolution among lineages of flowering plants endemic to the islands of Macaronesia (i.e., Canary Islands, Azores, Madeira, and Cape Verde). The resulting phylogenetic trees are used to study morphological and breeding system evolution as well as biogeography. A summer REU student could select a subproject from several ongoing studies, including the following: (1) analyses of genomic data to study the evolution of self compatability and biogeography an endemic lineage in the sunflower family (ie Tolpis); (2) analyses of nuclear and chloroplast data to resolve relationships with in an among three genera of the flowering plant family Crassulaceae; or (3) an empirical study on to test how well current methods of phylogenetic analyses of genome-scale analyses preform under a range of evolutionary models of DNA evolution. A student interested in computer science or mathematics would be ideal for the latter project but the projects can be tailored to the student’s skill levels.


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