Mitochondrial genomics of the Ray-finned fishes

Dr. Richard Broughton's laboratory at the Oklahoma Biological Survey and the OU Department of Zoology is examining diversification among genes, genomes, and organisms.  His research uses molecular characters to understand evolution at several levels including molecular evolution at the genetic or genomic level, divergence of populations and species, and phylogenetic patterns among species and higher taxa.

The ray-finned fishes (class Actinopterygii) exhibit extreme diversity with more extant described species than all other vertebrate groups combined and are of major ecological and economic importance. Despite extensive morphological study, phylogenetic relationships among many actinopterygian lineages remain unclear.

Dr. Broughton is currently compiling a data set of complete mitochondrial genomes from 73 species of ray-finned fishes, including representatives of 32 (of 42) orders and extensive sampling from the largest orders, Cypriniformes and Perciformes. Mitochondrial genomes and nuclear gene sequences are being used to generate a robust hypothesis of phylogenetic relationships among the most important lineages of ray-finned fishes. This will reveal diversification patterns and provide insights on the evolution of early vertebrates. Of particular interest is the placement and timing of a whole-genome duplication that occurred early in the radiation of teleosts. The duplication means that fishes, including the important model systems zebrafish and pufferfish, have two copies of genes found in only one copy in tetrapods. Multiple gene copies provide a powerful approach for determining gene function not available in other vertebrate systems and are useful for assessing gene function in human, mouse, and other mammalian systems.

The mitochondrial data are also being used to investigate nucleotide sampling properties in phylogenetic analysis. The influence of several important evolutionary parameters on phylogenetic accuracy will be investigated. These parameters include a) the frequency of variable nucleotide sites in the sample; b) the evolutionary divergence among taxa; c) the evolutionary rate variation among included lineages; and d) the extent and distribution of nucleotide compositional bias among sampled taxa. Patterns of natural selection acting on specific genes and mechanisms of DNA strand-specific mutational bias are also under study. The results will provide a deeper understanding of the behavior of nucleotide data in phylogenetic analysis and improve the efficiency and accuracy of molecular phylogenetic and comparative genomic studies.