The Denver lab’s interests in evolutionary genetics and genomics are diverse.  Our main research activities investigate the relative roles of mutation and natural selection in shaping nematode genome evolution using long-term sets of Caenorhabditis elegans and Caenorhabditis briggsae mutation-accumulation (MA) lines.  The MA lines were propagated across hundreds of generations as single randomly selected hermaphrodite worms, resulting in an effective population size equal to one for each MA line.  This treatment severely reduced the efficiency of natural selection and ensured that mutations accumulated over time in an essentially neutral fashion.  By comparing molecular mutation spectra in the MA lines to patterns of genomic variation in Caenorhabditis natural isolates using DNA sequencing and tiling microarray approaches, we have been able to gain new and unexpected insights into the relative roles of mutation and natural selection in shaping animal genome evolution.  We are also developing experimental evolution approaches using various DNA repair-deficient C. elegans strains to investigate the evolutionary plasticity of the mutation rate.

Our interests have recently expanded beyond the Caenorhabditis paradigm to nematodes in the Panagrolaimus genus.  Nematodes in this genus are free-living, can be easily cultured and cryogenically preserved under the same conditions as C. elegans, and provide a powerful system for investigating a myriad of evolutionary questions.  Panagrolaimus is closely related to the Strongyloides and Halicephalobus groups of animal parasites, offering a system for comparative approaches to studying the evolution of parasitic lifestyles.  Nematodes in this genus can also endure extreme environmental conditions as they have been collected from Antarctica and can survive in anhydrobiosis for many years.  Multiple examples of gonochoristic, hermaphroditic, and parthenogenetic reproductive modes have all been reported in Panagrolaimus, providing an excellent framework for examining the evolutionary origins, causes, and consequences of shifts in reproductive mode.  We are presently applying molecular phylogenetic approaches to this system and will initiate experimental evolution studies in the future.

In addition to nematode-oriented research, we also study the evolution of DNA repair genes and pathways throughout eukaryotic phylogeny using phylogenomic approaches.  Previous work focused on DNA glycosylases involved in base excision repair – all of the major DNA repair pathways will be targeted for similar studies in the future.  Collaborations are also ongoing with Stephen Giovannoni’s lab at OSU to investigate molecular evolutionary processes in the ubiquitous Pelagibacter (SAR11) bacterioplankton group, and with David Lambert’s group at the Allan Wilson Centre for Molecular Ecology and Evolution in New Zealand where we are exploring metagenomic approaches to studying ancient DNA samples from Adélie penguin subfossil bones.