Maximum likelihood phylogeny derived from analysis of the AP3 nucleotide dataset. Bootstrap percentages (above 50) are placed at the nodes. The name of each taxon is in parentheses following the locus name. The node corresponding to the euAP3/TM6 duplication is indicated with a star while the branch associated with the subsequent euAP3-specific frameshift event is indicated with an arrow. Colored vertical bars on the right are used to indicate the paralog lineage membership of the adjacent loci: the purple bars represent the euAP3 lineage; the green bar, the TM6 lineage; and the blue bars, the ancestral paleoAP3 lineage. The phylogenetic positions of the associated taxa are denoted as Core Eudicot, Basal Eudicot, Magnoliid, Monocot or ANITA (See Additional file 1,  and ). Colored branches are used to indicate the "frameshift potential" of each locus: black branches mean that a single nucleotide frameshift in the paleoAP3 or euAP3 motif would recover 0–3 amino acids of the other motif; orange branches, 4–6 amino acids; and red branches, seven or more amino acids. For instance, as shown in Fig. 3A, the first reading frame of PloAP3-1 encodes a perfect paleoAP3 motif but the second reading frame would produce a motif with seven out of the ten euAP3 motif residues, and, therefore, the PloAP3-1 branch is red. In contrast, the second reading frame of the AreAP3 paleoAP3 motif would have only two amino acids similar to the euAP3 motif, which is indicated by a black branch for AreAP3. Additionally, some paleoAP3 cDNAs would encode a positionally correct stop codon for a euAP3 motif in their second frame. These loci are denoted with red asterisks.