Research
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For a brief description of some of the major burning questions we address, read on or contact me:
The impact of transposable element (TE) movement within and between genomes
Discovered over 50 years ago, the full significance of impact of mobile DNA on genome structure and function has only recently begun to come to light. The wealth of publicly-available data and the tremendous advances in sequencing technology now make it possible to understand the landscape and dynamics of the genome in ways never before possible. We now know, for example, that the majority of most eukaryotic genomes is comprised of mobile DNA and its carcasses. We do not, however, know the origin of such DNA or its full impact. Research in the lab has focused on the horizontal transfer of TEs (HTT) among different species, calculating rates of TE movement within a given lineage, and exploring the consequences of germline versus somatic TE activity. In addition to these projects, we are also involved with analyzing TEs in several whole genome sequencing projects and comparative genomic analyses. These projects are being conducted with collaborators at many institutions, including the University of Lyon, the University of Poitiers, Kansas State University, and Indiana University.
Rates and patterns of mutation in the evolutionary and ecological genetics model, Daphnia pulex
Previous work focused on the influence of sex (recombination) on the proliferation of TEs in Daphnia pulex, a cyclically parthenogenetic organism (capable of reproducing with and without sex). Their reproductive system, as well as their rich history as a model organism in population biology, community ecology, and ecotoxicology, make Daphnia a great system for exploring the impact of mutation on a range of biological processes. In our lab, we use Daphnia to experimentally estimate mutation parameters, factors influencing the evolution of the mutation rate, and the effects of mutation on other important traits, such as competitive ability or niche width. Current and ongoing projects are aimed at quantifying the rates and phenotypic effects of spontaneous mutation in a variety of isolates, populations, and species. We also conduct experiments and assays in a range of environmental conditions to explore the properties of mutations and the variation visible to selection. Recent student projects have focused, for example, on the effects of mutation on salt tolerance and metabolism. Using Daphnia as a model allows us to combine fieldwork, benchwork, and bioinformatic analyses to explore the genotypic and phenotypic consequences of mutation in a tractable, but ecologically relevant, system. This work is, in part, collaborative and includes colleagues working on Daphnia at the University of Basel, and Universite of Québec, and Indiana University.
Contrasting patterns of genome evolution among nuclear and
organellar genomes Although they exist within the same cellular and population-genetic environment, the architecture and dynamics of nuclear and organellar genomes differ tremendously. We are interested in understanding the mutation process across genomes within the a cell, especially in light of the fact that certain key fitness traits (e.g., body size) depend on the compatibility of protein subunits encoded in multiple genomes with different evolutionary dynamics.
Various projects in the lab address the congruence and incongruence observed when comparing evolutionary genomic patterns between the nucleus and organelles. In addition to lab work, we are involved in a collaborative project looking at Speckled Rattlesnake populations. In addition to comparative analyses, exploring the genetic basis for the evolution of dwarves and giants on desert islands in the Sea of Cortés (see map at right), a whole genome sequencing project for this species, Crotalus mitchelli, is currently underway. This project is long term and involves a number of collaborators from Tarleton State University and the University of Texas at Arlington.
Genomics and Transcriptomics Projects in East Africa:
During the 2013-14 academic year, I was doing research and teaching in East Africa. My teaching is centered around a series of workshops that are aimed at introducing young East African scientists to bioinformatics and genomics. DNA sequence data forms the basis of a great deal of the current research in biology-- and it is freely available on the internet. Further, many of the tools to analyze sequence data are free-- developed by biologists to solve their own research problems, but then available for others to use and modify in order to answer new questions or old questions in new systems. My goal with the workshops is to help young biologists
exploit bioinformatic data and tools so that they can pursue their research interests in ways that are quick and cost-effective, and utilize methods that rely less on refrigeration, reagents, and consumables than molecular biology techniques. Workshops were held at the University of Nairobi, Makerere University, the Nelson Mandela African Institute of Science and Technology, and at the Biosciences East and Central Africa Hub of ILRI.I am also coordinating a large, collaborative genome consortium sequencing the whole genome and multiple transcriptomes of Busseola fusca-- a lepidopteran crop pest that devastates up to 1/3 of the maize crop in East Africa every year. My interest in the species stem from cases of horizontal transfer we identified when we scanned the whole genome of the parastoid wasp, Cotesia sesamiae (which is used for biocontrol of B. fusca and was sequenced several years ago). There are many partners in the project, ranging from entomologists interested in the biology and physiology of this stemborer, to genomicists interested in crop improvements and food security, to students interested in learning the basics of whole genome sequencing, assembly, and annotation. It is a joint effort between scientists and students at ILRI, ICIPE, and the University of Nairobi (pictured here: Gladys Bichanga [PhD student] isolating DNA for the project).
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