Fig. 1. Sequence analysis of amphioxus and lamprey AP-2 proteins. (A) Clustal alignment of amphioxus AP-2, lamprey AP-2 and mouse AP-2. Identical residues are shaded black, biochemically similar residues are boxed. Underlined regions of mouse AP-2 represent the proline-rich transactivation domain (N-terminal) and the DNA-binding/dimerization domain (C-terminal). The regions of highest homology between the three sequences are within these functionally important domains. (B) Neighbor-joining phylogenetic tree of vertebrate and amphioxus AP-2 protein sequences. Drosophila serves as an outgroup. Numbers at branch points are confidence values derived from 1000 bootstrap resamplings of the alignment data. Sequence distance is indicated to the bottom left as substitutions per base. Lamprey AP-2 (Pm) is an outgroup to the gnathostome AP-2s and has no affinity for any one AP-2 family member, consistent with there being a single lamprey AP-2 gene. Amphioxus AP-2 (Bf) falls outside the vertebrate clade. The divergent mouse AP-2 groups with amphioxus AP-2 at low bootstrap values, and its phylogenetic relationship to the other vertebrate AP-2 family members is unclear. Dm, Drosophila melanogaster; Bf, Branchiostoma floridae; Pm, Petromyzon marinus; Hs, Homo sapiens; Mm, Mus Musculus; Gg, Gallus gallus; Xl, Xenopus laevis.