Evaluating the Phylogenetic Utility of Genes: A Search for Genes Informative About Deep Divergences among Vertebrates

Abstract

Genes widely used in systematic studies have proven valuable for the resolution of relatively shallow (300 MY A) divergences, but genes useful for moderately deep divergences have been lacking. Computerized data bases of gene sequences are growing at a rapid pace and provide a rich resource of genes likely to contain phylogenetic information about many levels of divergence. Despite the fact that the chosen gene must be appropriately matched to the phylogenetic divergence(s) of interest, little attention has been given to the estimation and/or evaluation of the likely phylogenetic utility of genes. Knowledge of the phylogenetic relationships and divergence times among organisms for which gene sequences are commonly available provides a powerful tool for estimating this utility. I conducted a survey with the goal of identifying the most promising genes for investigating divergences ranging from approximately 50 to 200 MYA in an amphibian clade. Nine nuclear protein genes were identified. These genes may be useful to systematists working on taxa with similar divergence times, and the general approach may serve as an example of how other such surveys could be conducted.