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.  Possible projects for 2016 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 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. Jorge Soberón, Modeling the Mammalian Species Numbers in North America since the last Interglacial Period

Background paper. Generally speaking, we will be using available GBIF databases to extract a table of reported species occurrences of mammals of North America, clean and debug the database, and then use R scripts to model the potential distribution of all the species. These will then be “stacked” to get predictions of species numbers. This is a project for the quantitative-minded individual. We will be using databases, the R environment, Geographical Information System methods, cellular automata, and simulations. This also requires some amount of mathematical reasoning. I expect to write a scientific paper out of this work, in collaboration with a former student of mine, Andrés Lira. If a math student is interested, we can emphasize the conceptual aspects and the theory. If a computer scientist is interested, then we can work on a numerically challenging simulation.

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.

Evolution

Evolution projects are primarily lab based


Dr. Jim Bever: see below under Ecology.

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, 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. Lena Hileman, Genetics of plant morphological evolution

Background Paper. In my lab we study evolutionary changes in flower form with special interest in how flowers have diversified through changes in their underlying genetic programs. REU students in my lab will work on projects that advance our understanding of how flowers adapted to hummingbirds as pollinators evolve from flowers adapted to bees as pollinators. Students will work in our model genus, Penstemon. This is an exciting genus for studying floral evolution in response to changing pollinators since species with hummingbird-adapted flowers have evolved many times from an ancestral condition bee-adapted flowers. Adaptation to hummingbird pollinators includes changes in flower color, flower shape, and nectar production. REU projects will focus on either the trait changes directly using morphometric, microscopy, or enzymatic assays, or on the genetic basis of these trait changes using quantitative genetic or gene expression tools. Prerequisite: A course in genetics is recommended.

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

Background PaperThe 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.

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. 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.

Systematics

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


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.

Dr. Leo Smith, Fish Systematics

Background PaperThe 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. 


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