Dee Denver
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Assistant Professor, Zoology |
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Education
Ph.D. 2002, University of Missouri, Kansas CityResearch
The Denver lab’s main focus is in understanding the extent and causes of natural mutational variation in animal genomes. We integrate diverse evolutionary, population-genetic, molecular, genomic and mathematical perspectives and methodologies to study this fundamental issue in biology.
Nematodes are our main study system – we investigate mutation and molecular evolutionary phenomena in Caenorhabditis, Panagrolaimus and other roundworm lineages. In collaboration with Charles Baer at the University of Florida, we are using a long-term set of C. elegans and C. briggsae mutation-accumulation (MA) lines as a unique resource for understanding baseline mutational phenomena. The MA lines evolved in the lab for 250 generations as single, randomly-selected hermaphrodite animals. This treatment resulted in an effective population size equal to one in the MA lines across generations, allowing for all but the most deleterious mutations to accumulate in the genome in an essentially neutral fashion. To investigate genome-wide mutation processes in the MA lines, we are applying both novel “next generation” DNA sequencing technologies and comparative genomic hybridization to full-genome tiling array methodologies. To effectively apply these cutting-edge approaches to understand the mutation process, we are also developing a growing range of analytical software applications that are openly available to the scientific community. For example, TileQC provides a front-end system for evaluating quality and managing data deriving from Illumina 1G high-throughput DNA sequence data. We also collaborate with Suzanne Estes at Portland State University to investigate the genetic trajectories of compensatory mutations in C. elegans.
We are developing C. briggsae as a powerful new model for understanding within-species mutational variation. We recently discovered the presence of naturally occurring mitochondrial genome deletions that are hypothesized to play central roles in driving elevated mutation rates in particular C. briggsae lineages. We are also optimistic that C. briggsae will grow into a powerful general model for evolutionary analysis given the recent discovery of new closely-related sister species and genetically diverse natural isolates.
Outside of Caenorhabditis, we are developing Panagrolaimus nematodes as a new model for understanding the mutational and evolutionary consequences of transitions to asexuality. We have identified the evolutionary transition from sexual to parthenogenetic reproductive model in this group, and are planning future studies aimed at understanding mutation processes in sexual and asexual Panagrolaimus lineages.
We also study the evolution of DNA repair proteins and pathways throughout eukaryotic phylogeny using phylogenomic and other bioinformatic approaches. We are finding substantial among-genome variation in DNA repair gene repertoires, and evidence that nematodes encode substantially fewer DNA repair activities than other major animal groups.
Recently, we have also taken an interest in studying mitochondrial genome evolution in Plethodon salamander species native to Oregon.
If you find the things that we do to be interesting, drop one of us an email! The Denver lab is always looking to recruit or collaborate with individuals at all levels who share our values in understanding the mutation process and other big, basic questions in evolutionary biology.