Tracing the evolutionary history of cellular life

Abstract

The diversity of life on Earth is immense, with organisms colonizing even some of the most extreme habitats on the planet. Remarkably, despite such immense diversity within the biosphere, all living things are united by a set of commonalities that hint to a single shared ancestry of all life. That is, all cellular life on Earth as we know it descended from a single primordial entity known as the last universal common ancestor (LUCA). A central approach to understanding this evolutionary descent from LUCA and the diversification of life is to visualize the known biosphere within a schema that provides insight into evolutionary relationships. These connections can be organized into a tree-like network known as the “tree of life” (TOL), a radiating diagram assembled from branches and nodes that represent life’s evolutionary history from our microbial ancestors to now, with LUCA sitting at the root of this tree. The TOL can provide a foundation for asking pertinent questions about different periods in cellular history and the characteristics of major ancestors at turning points along this evolutionary road from the earliest stages of life to now, a journey that spans nearly 4.5 billion years. Modern versions of the TOL are constructed by analyzing changes in the DNA sequences of genes, and in recent decades, the quality and quantity of genomic data sampled from the environment has provided a valuable source of information that has uncovered new branches in the TOL representing newly discovered lineages. Retracing the major events in life’s evolution is challenging and requires careful and methodical inquiry. This thesis addresses unresolved key questions regarding deep cellular evolution from the earliest node in the tree of life representing LUCA, to the divergence and radiation of Archaea and Bacteria, endosymbioses contributing to eukaryogenesis, and the structure of the TOL. To this end, I applied diverse bioinformatics approaches including phylogenetics (single genes, sets of genes, all genes on a genome), gene tree-species tree reconciliations, molecular dating, and metabolic and ancestral reconstructions. In this thesis, I examine the shape of the tree of the primary domains of life and their evolutionary distance (Chapter 2), the timing of cellular evolution and the history of the ATP synthase (Chapter 3), and the nature of the last bacterial common ancestor (Chapter 4). Chapter 5 is a literature review on current perspectives on the TOL including the evolutionary impact of the enigmatic Virosphere. The final chapter (Chapter 6) discusses the diversity and global impact of the Archaea. In all, this work provides a greater understanding of past evolutionary events and presents new tools that can be applied to address evolutionary inquiries and unresolved questions regarding evolution of cellular life.