Protein evolution and the early history of life

Abstract

Throughout human history philosophers have tried to understand the inter-relatedness of the vast array of organisms found on Earth. The study of phylogenetics has provided a window into which we can understand how life has evolved on this planet, and analyses have shown that life is composed of two primary domains, Archaea and Bacteria. Traditional phylogenomic analyses have found the evolutionary distance between Archaea and Bacteria to be a significant one. However, a recent analysis suggests that perhaps they were much more closely related than previously thought. Here, I examine an inferred set of universal marker genes suggesting a closer evolutionary distance between the two primary domains. I compare this set of markers with those of previous analyses, and examine the verticality and evolutionary history of the component genes. I also infer a novel set of markers based on these results to infer a new tree of life. I find the distance between Archaea and Bacteria is a great one; however, I find it is susceptible to substitutional saturation and the use of inappropriate models of molecular evolution. I also examine the molecular evolution of multiple proteins found in eukaryotes: a zinc-finger protein involved in blood-cell differentiation, a protein complex involved in protein recycling, and a motor protein which transports cellular cargo. As a whole this work demonstrates how we can use phylogenetic analysis to answer questions about ancient and more recent branches in the tree of life.

Date of Award	21 Jun 2022
Original language	English
Awarding Institution	University of Bristol
Supervisor	Dek N Woolfson (Supervisor) & Tom Williams (Supervisor)