Phylogenetic reconstruction of runt domain evolution. Top left: unrooted tree of RD proteins based on the runt domain; X1, X2 and X3 denote the RUNX clades, BfRUNT, FrRUNT, TnRUNT, CiRUNT, OdRUNT, SpRUNT and CeRNT1 represent RUNT proteins from amphioxus, fugu, Tetraodon, Ciona, Oikopleura dioica, sea urchin and C. elegans, respectively, while taxa named Dm- represent D. melanogaster RD proteins. Top right: unrooted tree of first exons of human and fugu runt domain genes. Bottom: expanded species trees for the three RUNX orthologous groups. For all trees, numbers indicate percent bootstrap support; the horizontal bars indicate 10% divergence along each branch. White and gray backgrounds indicate comparisons at the nucleotide and amino acid level, respectively. The dashed branch in the RUNX2 panel represents the position of zebrafish (A) prior to AsaturA analysis. The arrows indicate the change effected by this correction.