The rise of complex life: Tracing the origins of the eukaryotic cell

Compared with prokaryotes, eukaryotic cells are tremendously complex. Eukaryotic cells are larger, contain more genetic material, have an elaborate endomembrane system and operate a dynamic cytoskeleton. The last eukaryotic common ancestor (LECA) very likely already had this typical eukaryotic organisation. The large gap between prokaryotic and eukaryotic complexity because of the lack of evolutionary intermediates makes the emergence of eukaryotes from prokaryotes (eukaryogenesis) one of the greatest evolutionary enigmas and the topic of a lively scientific debate. Many scenarios have been proposed on the order of events during this transition but empirical data supporting a specific scenario are scarce. The research described in this thesis contributes various novel data. I have reconstructed proto-eukaryotic genetic innovations to illuminate the intermediate stages that resulted in the first complex, eukaryotic cells. To perform these reconstructions, I applied both large-scale phylogenomic and small-scale phylogenetic methods to a diverse set of eukaryotes and prokaryotes. Firstly, I focus on the gene duplications that occurred during the transition. We reconstructed and characterised these proto-eukaryotic duplications. Genes that were inherited form the archaeal ancestor were duplicated frequently while relatively few duplications occurred in endosymbiont-derived and metabolic genes. By analysing the branch lengths in phylogenetic trees, we obtained relative time estimates for the duplication events, mitochondrial endosymbiosis and horizontal gene transfers from other prokaryotes. Proteins that build the complex eukaryotic cell, such as the endomembrane system and cytoskeleton, resulted from early duplications, in contrast with the late duplication of regulatory proteins. According to our time estimates, mitochondrial endosymbiosis probably took place between the two duplication waves. Subsequently, the abovementioned duplication data have been combined with the inferred presence of shared intron positions between paralogs to trace the spread of introns through the proto-eukaryotic genome. We detected many intron positions that were shared between proto-eukaryotic paralogs. We argued that most of these shared introns originated from intron insertions before the duplication event. This implies that introns had spread early in eukaryogenesis. Introns are removed from pre-mRNA molecules by the spliceosome, one of the most complex molecular machines that originated during eukaryogenesis. We inferred the evolutionary histories of the different spliceosomal proteins in LECA using phylogenetic trees and intron analyses. Both the introns and the core of the spliceosomal machinery originated from self-splicing group II introns. Proteins that were added to this spliceosomal core primarily had a ribosome-related function. Numerous gene duplications shaped the spliceosome into a highly complex machinery in LECA. The many shared introns between spliceosomal paralogs indicate that introns were widespread through the proto-eukaryotic genome before most spliceosomal complexity originated. Finally, I discuss the implications of our findings on the distinct scenarios for the origin of eukaryotic complexity. I point to potential directions for future research and highlight promising development that may affect our views on eukaryogenesis