Changing ideas about eukaryotic origins

Abstract

The origin of eukaryotic cells is one of the most fascinating challenges in biology, and has inspired decades of controversy and debate. Recent work has led to major upheavals in our understanding of eukaryotic origins and has catalysed new debates about the roles of endosymbiosis and gene flow across the tree of life. Improved methods of phylogenetic analysis support scenarios in which the host cell for the mitochondrial endosymbiont was a member of the Archaea, and new technologies for sampling the genomes of environmental prokaryotes have allowed investigators to home in on closer relatives of founding symbiotic partners. The inference and interpretation of phylogenetic trees from genomic data remains at the centre of many of these debates, and there is increasing recognition that trees built using inadequate methods can prove misleading, whether describing the relationship of eukaryotes to other cells or the root of the universal tree. New statistical approaches show promise for addressing these questions but they come with their own computational challenges. The papers in this theme issue discuss recent progress on the origin of eukaryotic cells and genomes, highlight some of the ongoing debates, and suggest possible routes to future progress.

Keywords: eukaryotes; evolution; phylogenetics.

Figure 1.

Competing hypotheses for the origin of eukaryotes. (a) In the textbook ‘three domains’ tree, the eukaryotes and Archaea are monophyletic sister groups, with each lineage as old as the other. (b) The ‘two domains’ view, supported by improved phylogenetic methods and taxonomic sampling. In this scenario, Bacteria and Archaea comprise the two primary cellular lineages, with eukaryotes formed in a symbiosis between them. Both trees are shown rooted on the branch leading to the Bacteria although, as discussed in §5, the analyses on which this root position is based must be interpreted with caution.