Transposable Elements -
Most research in our lab revolves around transposable elements (TEs). These DNA sequences have the ability to move around and/or make copies of themselves within the genomes they occupy. For example, around 10 percent of the human genome is made up of copies of an ~300bp sequence called Alu. Most eukaryotic genomes harbor these elements and we consider it our job to investigate what impact these elements have had on those genomes (not to mention the inverse - the impact genomic conditions have had on the evolution of the TEs) We're also interested in using transposable elements to elucidate evolutionary patterns and processes. As part of our efforts, we participate actively in multiple large-scale genome projects including Bat1K, Genome 10K, and the Broad Institute’s 200 mammals project.
Crocodilian Genomics -
Crocodilians are an ancient group of reptiles of tremendous ecological, social, and evolutionary importance. As one of the major extant reptilian clades, a basic grasp of the structure and function of their genomes is essential to understanding amniote evolution as well as protecting reptile diversity. We have sequenced and assembled the genomes of three crocodilians with the help of colleagues at universities around the world. We are continuing our research into crocodilian evolution by working with the Genome 10K initiative and the Vertebrate Genomes Project to sequence and assemble high quality drafts of every crocodilian species. More information on our work is here.
Bat Evolutionary Genomics -
Our laboratory was fortunate to be the first to find evidence of unprecedented transposable element activity in a particular family of bats and this field has developed as one of our major research efforts. Briefly, all mammals studied to date appear to be the nearly exclusive playground of one class of TEs, the retrotransposons. Other researchers had determined that the second class of elements, DNA transposons, had not had a significant impact on mammalian genomes for the last 40 million years or so. Myotis lucifugus (the little brown bat) however, has exhibited the opposite trend. For the past 35-40 million years, retrotransposon activity has decreased and DNA transposons have experienced a dramatic resurgence in activity. We are interested in several questions related to this activity including why the taxonomic limits of the activity and the impacts of this activity on genomic function and taxonomic diversity of these bats.
Since then, we’ve expanded our efforts to investigate how bat genomes evolve more generally. As part of that effort, David Ray is a co-director of the Bat1K initative. This effort seeks to generate high-quality genome assemblies for all ~1300 species of bat. Our lab will lead the TE-based analyses for the effort.
Butterfly Evolutionary Genomics -
Heliconiine butterflies have undergone a substantial adaptive radiation in the New World tropics. We think that much of that radiation can be explained through the impact of transposable elements impacting gene regulation and genome structure in the ~40 species that occupy Central and South America. We recently identify substantial differences in the genome structure of heliconiine subclades that is driven by differential TE dynamics.
Mammalian Conservation Genomics -
We partner with agencies in Texas, Louisiana, and at the federal level (USDA) to investigate the population dynamics of rodents and bats. Current investigations center on the conservation status of the Texas kangaroo rat (Dipodomys elator), all Texas pocket gophers, and Myotis and Eptesicus bats in Louisiana. Our efforts will inform the responsible agencies as to how best to proceed with conservation decisions on these important species.