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. Projects may be mentored by a faculty member or a team consisting of a faculty member and a graduate student. Possible projects for 2016 are:
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), vector borne diseases (such as chikungunya). 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. Mark Holder, Phylogenetic Models
Background Paper. The 3 primary projects in the Holder lab are:
- Building improved models and methods for incorporating extinct species into phylogenetic estimation procedures which rely on probabilistic statistical models.
- Developing methods for studying associations between host/parasite genealogies. In particular we are interested in disentangling the effects biogeographic processes from those co-evolution and host-range limitations.
- Summarizing the state of phylogenetic knowledge as a part of the Open Tree of Life project.
Dr. Maria Orive, Modeling Evolutionary Genetics
Background Paper. The undergraduate researcher will benefit from a research experience that closely integrates evolutionary biology and mathematics. The student would choose one of two different research projects. The first is a collaborative project (involving scientists at KU, Harvard, Northeastern, and the New England Aquarium) investigating patterns of host-endosymbiont associations. Symbioses between multi-cellular hosts and their endosymbionts are widespread throughout marine and many terrestrial systems. We focus on the well-known example of corals and their photosynthetic dinoflagellates and on developing new theoretical models allowing interpretation and analysis of genetic data for both hosts and symbionts. The second project will investigate the 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). Developing models that describe how genetic and life history structure affect the rate of evolution is crucial for understanding and predicting patterns of evolution and extinction under changing selective conditions.
Specific activities may include numerical analyses of our models using analytical software such at Mathematica (Wolfram), using computer programming to develop simulations for model testing and parameter exploration, and statistical analyses of genetic data collected by collaborators. The undergraduate researcher will gain hands-on experience in the application of mathematics, numerical analyses, and statistics to questions in biology, and gain an understanding of how theory and data can be linked.
Prerequisite: A course in genetics OR computer programming
Dr. Jamie Walters, Molecular evolution and genome biology of butterflies
Background Paper. The 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.
Evolution projects are primarily lab based
Dr. Justin Blumenstiel, Evolutionary Epigenetics and RNA Silencing
Background Paper. RNA silencing is a critical mechanism of genome defense against transposable elements. However, germ line defense by small RNAs can often have off-target effects that lead to gene silencing. Because small RNAs are transmitted through the female germ line, and not the male germ line, there is a strong maternal effect on gene silencing by these mechanisms. This project will focus on assessing how small RNA silencing shapes maternal effects on gene expression across generations. This will be achieved by generating high-throughput RNA sequencing data from different populations of Drosophila. The project will be most suitable for a student with a genetics background and interest in genomics and epigenetics.
Dr. Jennifer Gleason and Paula Roy, Visual signals in Drosophila
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 signals in different groups of Drosophila. The proposed project would explore the different senses used in courtship of the Drosophila suzukii and Drosophila takahashii groups, with a focus on visual signals. The student will be involved in observing courtship behavior to identify which signals significantly affect courtship success across the groups. Some use of video and auditory recording equipment may be necessary, depending on senses that the student wishes to explore. There is great flexibility in the project that may be directed by student interest.
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. Lena Hileman, Genetics of plant morphological evolution
Background Paper. In my lab we study the evolution of flowering plants with special interest in how flowers have diversified through changes in developmental programs. REU students in my lab will work on one of the following two research projects: 1) We are studying the evolution of hummingbird pollinated flowers from insect pollinated flowers in the genus Penstemon. Hummingbird pollinated flowers have evolved multiple times in this lineage and we are studying where, on the phylogeny, these transitions occurred, and how these transitions occurred at the molecular genetic level. 2) We are studying the evolution of flower symmetry across the flowering plants. Previous work from our lab, and from other labs has demonstrated that similar genes are involved in the many transitions from radial flower symmetry to bilateral flower symmetry that have occurred during the diversification of flowering plants. To better understand how these same types of genes could be independently recruited to program bilateral flower symmetry, we are studying how these genes function in species with radially symmetrical flowers (e.g., poppies, carnations, morning glories).
Prerequisite: A course in genetics is recommended
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). How do solitary bees, wasps, and their nest parasites respond to habitat modification in tallgrass prairie ecosystems? In this study, we are assessing species richness, abundance, and rates of parasitism among twig and wood nesting bees in tallgrass prairies, using trap nests. We examine species richness, species abundance, parasitism rate and resource use of these bees in surviving patches of original prairie (remnant prairie) and restored prairies. 2) Social spider biogeography. 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. In the past 15 years C. citricola has expanded its range dramatically. To understand range expansion, students participating in this project will sequence mtDNA of one spider from each collection site in Israel, align and compare sequences with other publicly available C. citricola sequences, and plot the geographic distribution of mtDNA variation.
Some ecology projects will involve fieldwork
Dr. Ben Sikes, Ecology of Soil Microbes
Background Paper. Research 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.
Systematics projects involving molecular and/or morphological techniques applied to diverse species groups
Dr. Leo Smith, Fish Systematics
Background Paper. The Smith lab explores the history and diversification of fishes. We use a combination of phylogenetic trees, field collections, and focused anatomical, morphometric, and genomic analyses to understand the evolution and diversification of freshwater or marine fishes. Research in the lab is currently emphasizing deep-sea and bioluminescent species. The lab is currently working on both molecular and molecular approaches to studying the evolution of deep-sea fishes. REU students will help design their own project that matches their interests, examples could include: 1) evolution of body shape or discrete structures in a group of fishes (e.g., body shape variation in deep-sea hatchetfishes [Sternoptychidae]); phylogenetic studies (e.g., relationships among dragonfishes [Stomiidae] or lanternfishes [Myctophidae]); comparative morphology of light organs or lures in bioluminescent fishes.