Fig. 4. OTR-VTR gene family trees.

a, Tree topology inferred with the phylogenetic maximum likelihood method on an exon nucleotide alignment (MAFFT), with 1,000 non-parametric bootstrap replicates. Bootstrap values are shown as percentages at the branch points (values <50% were considered less informative). The tree is rooted with the three VTR genes we found in amphioxus. The gene names of the current accessions (see Table 1 and Supplementary Tables 4a–e for full list of synonyms) were written over according to our revised synteny-based orthology. Scale bar, phylogenetic distance of 0.78 substitutions. b, Tree topology inferred with the phylogenetic TreeFam method on an amino acid alignment generated via the Ensembl ‘gene tree’ tool (gene tree identifier: ENSGT00760000119156). Left, red boxes denote inferred gene duplication node; blue boxes denote inferred speciation events; and turquoise boxes denote ambiguous nodes. Right, green bars denote multiple amino acid alignment made with MUSCLE; white areas denote gaps in the alignment; and dark green bars denote consensus alignments. Gene names are revised according to our synteny-based orthology; Extended Data Fig. 8 shows a tree with the current nomenclature in Ensembl.