Rachel Lockridge Mueller
Assistant Professor
Department of Biology
Colorado State University
Fort Collins, CO 80523
rlm@colostate.edu
(970) 491-6717
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E v o l u t i o n o f G e n e s a n d G e n o m e s
Molecular Mechanisms of Gene Rearrangement—Genome evolution is shaped, in part, by the rearrangement of individual genes or genomic regions. My research has examined the molecular mechanisms of such rearrangement using mitochondrial genome sequences. I have identified extensive reorganization in plethodontid salamander mitochondrial genomes (Mueller and Boore, Mol. Biol. Evol. 2005). My analyses of pseudogenes and near-identical copies of genes and regulatory regions demonstrate that rearrangement resulted from duplication of a portion of the genome. I am continuing to add sequence data within rearranged lineages and their close relatives to (1) measure pseudogene decay/excision rates, (2) characterize sequences that facilitate duplication, and (3) evaluate these rearrangements as phylogenetic characters. I also plan to use a comparative approach including other taxa with highly rearranged genomes to investigate organismal-, cellular-, and genomic-level properties linked to mitochondrial genome instability.
Dynamics of Nucleotide Substitution—The evolution of any gene results from the interaction of many factors. My research has used mitochondrial genome sequences and both Bayesian and maximum likelihood statistical techniques to compare nucleotide substitution dynamics among functional categories of genes (Mueller, Syst. Biol., 2006). I have estimated absolute rates of evolution and rate heterogeneity for each mitochondrial gene using a molecular clock-independent approach and multiple fossil calibrations. Using these estimates, I have explored the effects of amino acid composition, base composition, and functional constraints on sequence evolution.
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