Evolution of Cell Types in Tunicate Blood

Abstract

Major evolutionary innovations have occurred at the level of cell types, from the emergence of neurons in early metazoans to the specialization of adaptive immune cells in vertebrates. To study the developmental and genetic mechanisms driving cell type diversification, we rely on comparative analyses of present-day organisms. Single cell genomics have revolutionized the field, enabling quantitative comparisons of diverse species with little prior knowledge required. With this detailed molecular view of cell states, it remains unclear which species and tissues will be fruitful to study. Species-of-focus should ideally have enough divergence that there is variation to study, while also having enough similarities that we can identify homologous components. Innate immunity is a promising system, with highly conserved molecular pathways alongside constant diversification driven by rapidly evolving pathogens. We chose to study immune cells in tunicates, a group of chordate invertebrates. Tunicates are our closest relatives lacking adaptive immunity, placing them at a key position in the evolution of immune systems. Their blood cells are comprised primarily of innate immune cells, though these cells have been poorly characterized at a molecular level. In this thesis, I present modernized characterizations of tunicate blood and demonstrate its potential as a system for studying cell type evolution. Chapter 2 documents a technical problem for working with marine organisms and introduces a solution to overcome it. In Chapter 3, this solution lets us generate a high-quality blood cell atlas from the well studied tunicate species, Ciona robusta. By using this atlas to make quantitative comparisons to vertebrate blood cells, we find that tunicate and vertebrate immune cells have diverged significantly. This divergence suggests that immune systems might be highly variable across Metazoa, but it is difficult to learn how diversity arises at such large distances. In Chapter 4, we instead look within tunicates, and single-cell RNA sequencing data from eleven species reveals a mix of highly conserved and rapidly diverging blood cell states. We use this data to study how gene regulatory relationships change at varying evolutionary distance. Altogether, this work reveals the enormous diversity of cell types even within chordates, and it establishes tunicate blood as a promising system for studying cell type evolution.