Fig. 4

Phylogenetic distribution of known non-canonical genetic codes in nuclear genes of eukaryotes. The schematic phylogenetic tree was drawn on the basis of phylogenetic and phylogenomic analyses for eukaryotes as a whole [60, 71, 72] (our own Fig. 1 and Additional file 2: Figure S1) and for the relevant subgroups with non-canonical codes [12, 13, 73–77]. Multifurcations indicate uncertain or controversial branching order, dashed branches indicate different positions of Metamonada within eukaryotes suggested by different studies, branches drawn as double lines indicate paraphyletic groupings. The types and occurrences of the different non-canonical codes are based on this study (the rhizarian exLh and Iotanema) and the following previous reports: fungi [14, 15]; Amoeboaphelidium [13]; oxymonads [11]; Blastocrithidia [18]; ulvophytes [12]; ciliates [7, 9, 16, 17]. Note that, for simplicity, code variants with a context-dependent dual meaning of UAR or UGA codons as sense or termination ones (UAR in Blastocrithidia and Condylostoma, UGA in Parduczia and Condylostoma) are not distinguished from those with a “complete” reassignment. We also omitted some ciliate species with their putative non-canonical codes supported by little data that are specifically related to and possibly sharing the same code with better studied species. Changes in the genetic code are mapped onto the tree primarily (black circles) using Dollo parsimony (no reversions are allowed). An alternative maximum parsimony scenario with reversions weighted the same as other changes is indicated by the respective code numbers in white circles. An alternative branching order to the one indicated in the figure was supported by some studies for some of the ciliate lineages, but the alternative topology does not decrease the minimal number of codon reassignments required to explain the distribution of non-standard genetic codes