Using 28S and COI Coding Sequences to Measure the Rate of Mitochondrial Gene Evolution in Octocorals
Mentor:Catherine McFadden, Vivian and D. Kenneth Baker Professor of Biology and Incumbent Department Chair, Harvey Mudd College
Mitochondria in the cells of all eukaryotic organisms retain their own genome, a vestige from their origins as free-living bacteria. In most animals, mitochondrial DNA evolves 5-10X faster than nuclear DNA. In coral and sea anemones, however, mitochondria genes evolve 10-100X more slowly than nuclear DNA. One hypothesis proposed to explain the slow rate of mitochondrial gene evolution in one group of corals, octocorals, is the presence in their mitochondrial genome of the protein-coding gene, mtMutS. The mtMutS gene, formerly known as MSH1, has been hypothesized to be involved in repairing mismatched DNA in the mitochondrial genomes of octocorals. However, we suspect the efficiency of the mechanism behind this repair function to vary between taxa. Using nuclear 28S rDNA sequences along with mitochondrial cytochrome oxidase subunit I (COI) DNA sequences, we compared the rate of gene evolution in some members of the genera Leptophyton and Alcyonium to three different taxa of octocorals that evince typical evolutionary rates in the presence of the mtMutS gene. Pairwise distances and maximum likelihood phylogenies were calculated and constructed using Tamura 3-parameter model of substitution with gamma-distributed rates among sites and complete gap deletion treatment in MEGA 5.2.2. Bootstrap analysis was conducted to ensure the accuracy in variance estimation. Statistical analysis of the pairwise distances was performed in Stata12. We determined that this clade of Leptophyton exhibits high rates of mitochondrial gene evolution, suggesting either impaired efficiency or complete inactivity of the mtMutS repair gene.