Abstract 1 1.1 Introduction 2 1.2 The Ribosomal RNA Paradigm and the Archezoa Hypothesis 2 1.3 From SSUrDNA Trees to Protein-Coding Gene Trees 3

1.3.1 Availability of Molecular Phylogenetic Markers and the Advent of Genomics 5

1.3.2 Phylogenetic Methodologies 6 1.4 Eukaryote Diversity and Phylogeny 8

1.4.1 Eukaryote Molecular Phylogeny 9 1.4.2 Rooting of the Eukaryotic Tree 9

1.5 Organelles of Endosymbiotic Origins, Their Genomes and Proteomes 10 1.5.1 Mitochondria and Their Alpha-Protebacterial Origins 11 1.5.2 Plastids 11

1.6 Eukaryote Origins 12 1.6.1 The Serial Endosymbiosis Theory and Related Hypotheses 13 1.6.2 The Hydrogen Hypothesis 14 1.6.3 Other Theories of Eukaryogenesis 15

1.7 The Cell – A Final Comment 16 Acknowledgments 17 References 17

Eukaryotic organismal diversity is underpinned by an extraordinary organizational diversity at the cellular and molecular levels. Comparative cell and molecular biological studies on a broad range of eukaryotes are yielding a large number of surprising results. This chapter presents an overview of some of these results and illustrates how some of this diversity is now appreciated within an evolutionary framework. It discusses some of the most interesting

*DSH: david.horner@unimi.it; RPH: rch@nhm.ac.uk

new hypotheses on eukaryote evolution and the methodological advances needed to rigorously test them, and in so doing highlights the significance of the other chapters making up this book. It focuses on the impact of studies of microbial eukaryotes and organelles of endosymbiotic origin on our current understanding of both the origin and the evolution of eukaryotes. We speculate that comparative biology (not restricted to comparative genomics) of a broad diversity of microbial eukaryotes will be critical to the development of biological science in the 21st century.