Fig. 2. (A) Unrooted phylogenetic tree of paired-like homeobox genes from the PRD class, constructed from the homeodomain only. Bf, Branchiostoma floridae (amphioxus); Ce, Caenorhabditis elegans; Ci, Ciona intestinalis (ascidian); Dm, Drosophila melanogaster; Hv, Hydra vulgaris; Mm, Mus musculus; Sm, Schistosoma mansoni. Q50 and K50 denote the amino acid of homeodomain position 50. (B) Molecular phylogenetic tree of Dmbx family proteins. This tree is constructed from the entire amino acid sequences (after removal of unalignable regions) and is rooted by H. vulgaris manacle protein. Both trees are constructed by the neighbour-joining method. Branch lengths are proportional to evolutionary distance corrected for multiple substitutions. Scale bar: 0.1 underlying amino acid substitutions per site. Figures on branches indicate robustness of each node, estimated from 1000 bootstrap replicates.