A phylogenomic exploration of early bacterial evolution

Abstract

There are many challenges associated with the reconstruction of early evolutionary history. This is particularly true in the case of Bacteria. Despite being one of the two primary domains of life, and therefore crucial to our understanding of the early history of life, there is little consensus regarding the deepest evolutionary relationships within the bacterial tree. Due to the large spans of time that have elapsed since the origin of the domain, there are many difficulties in modelling their evolution, with bacterial phylogenies frequently affected by artefacts in the analyses. There are therefore a number of questions still unresolved regarding the relationships between major phyla, the root of the tree, and indeed whether the abundant horizontal gene transfer known to characterise prokaryotic evolution has not obscured vertical signal to the point of rendering a tree analogy moot. Recent discoveries of a huge diversity of new uncultured phyla provide new data, but are often difficult to resolve within the bacterial tree, with the relationships between the major bacterial lineages still showing little resolution. Bacteria also represent the most genetically and metabolically diverse organisms on the planet, and as such there are many questions pertaining to the evolution of diverse physiologies and metabolism through time. In this thesis, we attempt to address these issues by using innovative genomic approaches while incorporating much of the previously unknown bacterial diversity. We produce a rooted tree of Bacteria, demonstrate the inadequacies of outgroup rooting, and quantify the contributions of both vertical and horizontal signal to bacterial evolution. We additionally infer the order of events in early bacterial evolution, and reconstruct ancestral metabolisms for the earliest bacterial lineages. Taken together, these results can be integrated to produce a model of early bacterial evolution which contributes to our understanding of the earliest phase of life on Earth.

Date of Award	26 Nov 2020
Original language	English
Awarding Institution	The University of Bristol
Supervisor	Rich D Pancost (Supervisor) & Tom Williams (Supervisor)