Resolving the deep branches in the Tree of Life with complex and highly parameterized Bayesian models of molecular evolution
Collecting DNA sequence data is no longer a rate-limiting step in molecular phylogenetics. Yet for all its promise, genome-scale phylogenetics is currently limited to unrealistically simple evolutionary models due to computational constraints. My work would leverage the massive CPU/GPU resources on Blue Waters and newly developed statistical models to explore codon-based Bayesian methods for resolving deep (inter-ordinal) branches in the amphibian phylogeny with hundreds of genes. This research stands to make significant and impactful contributions to our understanding of tetrapod relationships. But more broadly, the methods proposed here have the potential to fundamentally change the ways that phylogeneticists analyze multi-gene data sets.