Projects
Students in the REU program will be members of at least one research theme: Evolution, Ecology or Systematics. On the application, students are required to rank up to three projects that interest them. Possible projects for 2013 are:
Modeling
Modeling projects are ideal for both biology and mathematics students.
Dr. Mark Holder, Accuracy of phylogenetic tree reconstruction
The accuracy and efficiency of competing methods for inferring evolutionary trees has been thoroughly studied using computer simulations under very simple models of sequence evolution. However, we still have a very limited understanding of the robustness of tree inference methods to violations of their assumptions. We can now simulate sequences under models of protein sequence evolution that explicitly incorporate constraints imposed by the requirement of the protein to fold into a given 3D-conformation. Simulating data on model phylogenies and then testing the accuracy of phylogenetic estimation procedures at reconstructing trees would provide an ideal project for REU students. Conducting the research would train students in the basic techniques of bioinformatics (e.g. cluster computing using the Holder lab's 200-core linux cluster, developing simple data pipelines, and conducting phylogenetic analyses). The results will be publishable as a novel contribution to our understanding of the behavior of tree estimation methods. Interested students will be able to extend this framework to studying the effects of multiple sequence alignment on tree inference, and will even be able to develop new inference techniques using the framework of Approximate Bayesian Computation (which allows simulation tools to serve as the basis for Bayesian inference).
Dr. John Kelly, Models of evolution
An REU student will work with Dr. Kelly on an evolutionary theory project. This will likely involve developing a mathematical model, and then exploring this model with analytical and computer based methods. Potential research topics include but are not limited to the evolution of behavior, disease resistance, life history, and molecular evolution.
Dr. Maria Orive, Models of host-endosymbiont associations
The undergraduate researcher would participate in a collaborative research project (involving scientists at the University of Kansas, Harvard University, Northeastern University, 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. The increasing availability of genetic data for both hosts and symbionts brings with it a need for new theoretical models allowing interpretation and analysis of such data. Specific activities include numerical analyses of our models using analytical software such at Mathematica (Wolfram), using computer programming to develop simulations for model testing, and statistical analyses of SNP 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.
Evolution
Evolution projects are primarily lab based
Dr. Justin Blumenstiel, Evolutionary dynamics of genome defense by RNA silencing.
We are particularly interested in the dynamics of coevolution between genomic parasites and the piRNA defense machinery. Our work is highly integrative employing methods that range from molecular genetics to genomics and theoretical biology. Specific summer projects include: Using DNA sequencing and population genetic analysis to test the hypothesis that the genome defense machinery evolves fastest under increasing transposable element burden, using gene expression analysis to determine whether increasing TE burden can drive higher levels of expression in the piRNA machinery and testing whether population level variation in transposable element activity can be explained by patterns of epigenetic inheritance of piRNAs.
Dr. Daniel J. Crawford, Evolution of plant reproductive biology.
I have long been interested in and published on the origin and evolution of flowering plants on oceanic islands. Recent studies have centered on how plants cope following their dispersal to distant, isolated, oceanic islands. I am now focused on the reproductive biology of the genus Tolpis (relative of lettuce and dandelions) in the Macaronesian Islands (Canary Islands, Madeira, Azores, and Cape Verde Islands). Several students have been involved in this project and two of them have been authors on two publications. There are now more than 1,000 plants of island Tolpis growing in the greenhouse and potential projects for future students include determining the breeding systems (whether a plant can self-fertilize) of plants from different islands and archipelagos, whether there can be selection for lower-higher levels of self-fertility, and whether self-fertility varies among flowers on the same plants. The results are important in the interpretation of a long-debated issue in plant island biology, the value of self-fertility (reproductive assurance) versus self-incompatibility (genetic diversity) in the origin and diversification of island plants.
Dr. Jennifer Gleason, Evolution of behavior
The Gleason lab focuses on the evolutionary behavioral genetics of courtship traits that contribute to speciation in Drosophila species. REU projects in the lab will concentrate on two areas: 1. determining the sensory modalities important to reproductive success in single or closely related species of Drosophila or 2. phylogenetic analysis of courtship behaviors across a clade. Although Drosophila are a model system for genetics, very little is known about the reproductive behaviors of individual species and how they are evolving, thus there is great potential for a student to make a substantial contribution to the field.
Dr. Lena Hileman, Genetics of plant morphological evolution
The evolution of plants has resulted in staggering morphological diversity – ultimately due to differences in underlying genetic programs specifying developmental trajectories. However, specific genetic changes responsible for morphological divergence are largely unknown. My research focuses on understanding how developmental programs have been modified during flowering plant evolution, leading to differences in plant form. The primary way I involve undergraduates in research is to introduce them to a discrete hypothesis for how changes in a genetic pathway may correlate with differences in flower morphology (e.g., evolutionary shifts between insect- and wind-pollination syndromes). I then outline from inception to completion how to test the hypothesis. This generally involves PCR-based candidate gene isolation, estimation of gene phylogenies, qPCR or in situ studies of gene expression, and reverse-genetic studies of protein function. REU students will undertake one or more of these specific objectives after a period of training with me, a postdoc, or graduate student. During their tenure in the lab, they will continue to be mentored individually and through lab group interactions to ensure that their research objectives are achieved and they gain an appreciation for how their project fits with broader objectives of the lab and the field of plant developmental evolution.
Ecology
Some ecology projects will involve fieldwork
Dr. Bryan Foster, Grassland community ecology
REU students in my lab will work directly with me and my graduate students to develop a project suitable for the summer time frame. The project can involve a field and/or laboratory component to investigate linkages between plant functional traits, phylogenetic relatedness of species and the dynamics of grassland community assembly. Within this broad theme students can choose from several alternative avenues of investigation tailored to their own interests and curiosity. For example, students more interested in evolutionary relationships can focus more attention on phylogenetic analysis. Students more interested in the ecological dimension could focus more on questions about plant traits and community structure.
Dr. Joy Ward, Global climate change
My research focuses on understanding how changes in atmospheric carbon dioxide concentration ([CO2]) affect the evolution of plants between the last glacial period, the present, and into the future. During the last glacial period, [CO2] was among the lowest levels that occurred during the evolution of land plants. In addition, [CO2] is expected to continue rising into the next century, with expectations of considerable global warming. In my laboratory, REU students will have the opportunity to study a broad range of plant responses to this continuum in [CO2] change. There would be a wide range of projects to choose from that could be completed during the limited REU summer period. These projects can range from conducting stable isotope analyses on glacial plants (to understand their physiology when they were alive) to conducting flowering time studies with molecular techniques in future [CO2] environments.
Systematics
Systematics projects involve molecular techniques applied to diverse species groups
Dr. Jenny Archibald, Diversification of camas lilies
Lineages of organisms can diverge from each other in many different ways, including changes seen in DNA, morphology, ecology, and multiple types of reproductive isolation. The Archibald lab is currently studying diversification in each of these categories within camas lilies in North America, using the results to aid understanding of processes of evolution as well as species delimitation. Students will understand the work integrated across the various level of divergence, while participating in focused projects either in a molecular phylogenetics lab or at field populations in Kansas.
Dr. Mark Mort, Evolution of oceanic flora
Oceanic islands have long been recognized as natural laboratories for the study of evolution. The Mort lab uses molecular data to infer phylogenetic relationships and levels of genetic diversity among flowering plants from the Canary Islands, especially stonecrops (Crassulaceae) and the sunflower genus Tolpis. These data are supplemented with studies of breeding system physiology and morphology to understand better the patterns and process of the radiation of this flora. REU students will design independent projects that reflect their interests, such as 1) phylogenetic studies, 2) estimating population level genetic diversity and conservation status or 3) assessing breeding system for focal taxa. Many phylogenies of insular plants have been published, but few studies integrate analyses of molecular and biosystematic data to study both the pattern and process of the radiation of these remarkable floras.
Dr. Andrew Short, Evolution of aquatic beetles
Aquatic beetles are a diverse group of insects found worldwide and contain more species than all birds and mammals combined. Recent fieldwork in northern South America has yielded a large number of species new to science. With my guidance, the student will select a well-circumscribed project to examine the evolution of a group of aquatic beetles. The student will use both morphological and molecular methods to 1) study existing species and contribute to naming and description of at least one new species, and 2) place the species in an evolutionary context using phylogenetic methods. The student will be exposed to modern molecular methods in systematics, cutting edge digital imaging technology and electron microscopy, bioinformatics, and work in residence within KU's extensive museum collections.