Phylogeny of alpha 1 domain sequences from all five MHCI lineages. Phylogenetic tree of selected alpha 1 domain amino acid sequences from the five defined lineages. The tree is base on hand-made alignment shown in Additional file 11: Text S8a and rooted using the human, shark and chimaera sequences. The tree is drawn to scale, with branch lengths representing the number of amino acid substitutions per site (see scale bar). Bootstrap values in percentage based on 1000 trials are shown on each node. GenBank sequence references not found in Additional file 4: Text S1 or Additional file 3: Text S2 are as follows: [S lineage] ayu (Plecoglossus altivelis) is JP747954, catfish (Ictalurus punctatus) is JT320438; [P lineage] seabass (Morone saxatilis) is GBAA01146398; [Z lineage] carp (Cyprinus carpio) ZB1 is L10420, lungfish (Protopterus aethiopicus) is AAF15304.1; [U lineage] zebrafish (Danio rerio) UBA is AAH74095.1, medaka (Oryzias latipes) UAA is AB450991and UBA is BAB83850.2, salmon (Salmo salar) UBA is AAN75116.1, paddlefish (Polyodon spatula) UBA*01 is ACV87421 and UBA*03 is ACV87423 while sturgeon (Acipencer sinensis) is ACV87437. The remaining sequence references are: spiny dogfish (Squalus acanthias) is AAN77874, elephant shark (Callorhinchus milii) is AFM85876.1, human (Homo sapiens) HLA-G is EAX03236.1, HLA-A2 is AAA76608.2, and HLA-B27 is CAA83876.1. The five lineages are shown on the right of each colored box. Alternative locus designations and the atypical Z lineage definitions Z2 and Z3 are shown in parenthesis behind the sequence names.