Phylogenetic tree of MHC class II α1 domain sequences. The sequences which possess αW43 are labeled with the orange letter “W”. The bootstrap consensus tree was inferred from 500 replicates using the Neighbor-Joining method . The tree is drawn to scale, with branch lengths representing the number of amino acid substitutions per site (see scale bar). Numbers behind names relate to references listed in Additional file 10: Text S4. Sequences that are also depicted in Figure 2 have their names with colored shapes indicative for the species: black square for spotted gar, red circle for Atlantic salmon, green circle for zebrafish, purple square for medaka, violet triangle for stickleback, gray diamond for Tetraodon, teal triangle for Fugu, blue diamond for Nile tilapia. Identical shapes, but white, are used for other reported sequences of those species. DM sequences are shown with the yellow background color. Tetrapod classical (-related) sequences are shown with the orange background color. The other background colors distinguish DA, DB and DE sequences, and within the DA group also cyprinid, salmonid and neoteleost sequences are distinguished. The dashed blue line divides the DA/DB lineage from the other class II sequences. S1, S2 and S3 indications plus dashed lines refer to products of genes situated in the respective synteny regions (Figure 2). Spotted gar 501A1 shows some interesting similarity with MHC class II of other classes of vertebrates (see also Additional file 10: Text S4 and Additional file 3: Figure S3B), but this single sequence does not provide sufficient information for valid discussion.