Research Output per year
I use phylogenetic and molecular methods to look at the early evolution of life, including resolving issues regarding the structure and rooting of the tree of life and the major domains, and methods for inferring ancestral genome size and content in order to reconstruct ancestral metabolism and mode of life.
I am currently working on a project where I attempt to root the tree of Bacteria. A rooted tree of Bacteria is essential to infer the gene content and reconstruct the metabolism of the last bacterial common ancestor (LBCA). Knowledge of the LBCA’s metabolism has implications for reconstructing the metabolism of the last universal common ancestor (LUCA) and testing hypotheses about the early evolution of life on Earth. Many current ideas pertaining to the nature of the earliest life are informed by hypotheses of prokaryotic phylogeny. However, rooting the tree of bacteria has proven difficult, with conventional rooting using outgroups leading to many differing root positions. Recent discoveries of a huge diversity of new uncultured phyla, in particular the Candidate Phyla Radiation (CPR), have further complicated matters, and the relationships between the major bacterial phyla still have little resolution. I am rooting the tree using probabilistic gene tree-species tree reconciliation methods. These are hierarchical models in which HGTs, gene duplications and losses are integrated into an overall model of genome evolution using amalgamated likelihood estimation (ALE), and in which patterns of gene family evolution contain information about the root of the tree.
A rooted tree of Bacteria can be used to reconstruct the metabolism of the ancestral bacterium, and the results may be compared to those obtained from the use of these methods on Archaea, which allows us to infer information on the nature of LUCA. ALE may also be used to investigate the rate of bacterial HGT over time, to evaluate how HGT has affected vertical phylogenetic signal and the evolution of early cells.
Research output: Contribution to journal › Article (Academic Journal)