Figure 1

Phylogenies of seven Fugu co-orthologs. Fugu (fr) co-ortholog protein sequences are highlighted by red boxes and named according to scaffold number they were located on (for example, frS86 = scaffold_86). Zebrafish (dr) or stickleback (ga) sequences are highlighted by green boxes and uncharacterized proteins named after the SwissProt ID or the chromosome they are located on. Bootstrap values are indicated at each node. Other tetrapod sequences included: human (hs), mouse (mm), rat (rn), dog (cf) and chicken (gg). Invertebrate outgroups are shaded orange and contain sequences from the following species: Ciona intestinalis (ci), Drosophila melanogaster (dm) and Caenhoribditis elegans (ce). Trees: (a) BCL11A using the closest paralog BCL11B as a comparator. (b) EBF1 using the closest paralog EBF3 as a comparator. (c) FIGN using the closest paralog FIGN1L as a comparator. (d) PAX2 using one of its two closest paralogs PAX5 as a comparator. (e) SOX1 using its closest paralog SOX3 as a comparator. (f) UNC4.1 has no known closely related paralogs. (g) ZNF503 using its closest paralog ZNF703 as a comparator.