Fig. 4.

Schematic eukaryotic phylogeny displaying, per lineage, the coevolution of the mitochondrial genetic code with the codon-specific RFs. The red circle indicates the unique primary endosymbiosis event that originated the mitochondrion. The green algae stop-codon reinvention hypothesis is detailed in the gray “zoom-in” area. Species relationships were assembled from two studies: the main tree is based on the consensus tree depicting the six main eukaryotic groups from Simpson and Roger (2004) and the green algae lineage is based on the 18S rRNA gene tree published by Worden et al. (2009). Branching order is meaningful, but not branch length. Red font highlights the exceptions to the coevolution discussed in the text. The star marks the “TGA-stop reinvention” with pRF2 relocalization hypothesis in the green lineage. Question marks are used for uncertain data, and two asterisks indicate no mitochondrial genome available. (See supplementary methods, Supplementary Materials online for details about the species used in making this figure).