Defining eukaryotes to dissect eukaryogenesis

The origin of eukaryotes is among the most contentious of debates in evolutionary biology, attracting multiple seemingly incompatible theories seeking to explain the sequence in which eukaryote characteristics were acquired. Much of the controversy arises from differing views on the defining characteristics of eukaryotes. We argue that eukaryotes should be defined phylogenetically and this clarifies where competing hypotheses of eukaryogenesis agree and how we may test among aspects of disagreement. Some hypotheses make predictions about the phylogenetic origins of eukaryotic genes and are distinguishable on that basis. However, other hypotheses differ only in the order of key evolutionary steps, like mitochondrial endosymbiosis and nuclear assembly, which are not currently phylogenetically identifiable. Stages within eukaryogenesis may be made identifiable through the absolute dating of gene duplicates that map to eukaryote apomorphies, such as in genes of host or mitochondrial origin that duplicated and diverged functionally prior to LECA. In this way, it may finally be possible to distinguish heat from light in debate over eukaryogenesis.