Phylogenomic approaches to understanding the phylogeny and early evolution of eukaryotes

In the last few decades, computational analysis of genes and genomes have shown that the most familiar biological `kingdoms' animals, fungi and plants represent only a tiny corner of the diversity of Life. The deepest evolutionary divergences in the living world are between Bacteria, Archaea and `eukaryotes'. Eukaryotes includes all the nucleus-containing complex-celled organisms: animals, plants, fungi and a huge number of equally important `kingdoms' that are mostly microbes. Still, fundamental gaps remain in our understanding of early eukaryote evolution remain. Many new super-kingdom-level groups ('supergroups') of microbial eukaryotes (protists) continue to be discovered. The placement of these lineages and the fundamental divisions within the eukaryote tree of life remain unclear. As a result, we still lack a clear picture of the common ancestor of all eukaryotic cells and how it first evolved. Over the five years of the proposed research, trainees, collaborators and I will use high-throughput DNA sequencing technology, comparative genomics methods and sophisticated statistical modeling approaches to address these fundamental questions about the tree of life. First, in collaboration with Alastair Simpson's group, we will place newly discovered single-celled microbes in eukaryote tree of Life, using large numbers of gene sequences we will obtain from the expressed portions of their genomes. By comparing gene sequence data from these new organisms to gene sequences with the same functions from many better characterized lineages including simple cellular life (Bacteria and Archaea), we will delineate the deepest branches in the eukaryote tree of Life. We will then characterize the full genome sequences of novel protist organisms and representatives of other poorly-studied supergroups. Sophisticated computational analyses of these data will allow us to infer the genetic innovations occurred in the common ancestors of supergroups and help clarify the genetic makeup of the common ancestor of all eukaryotes. In so doing, we will shed light on how and when some of the major 'transitions' in evolutionary history of life took place on the ancient Earth. Finally, we will invest considerable effort in improving the actual computational/statistical evolutionary methods used to estimate evolutionary trees from genetic sequence data and make these new methods available in publicly-available software tools. This will improve our abilities to resolve the deep tree of life, but will also be useful for other basic and applied science, including applications such as tracing viral spread and diversification in populations. The interdisciplinary nature of this research will furnish the trainees with important transferable skills in molecular biology, genomics, bioinformatics and statistics, as well as critical thinking, mentoring, presentation and technical writing. All of these skills are broadly useful for careers in the biological or biomedical sciences.