Figure 2

Phylogeny of selected teleost MHCI U lineage alpha 1 domains. Phylogenetic tree based on handmade alignment (shown in Additional file 6: Text S3) of selected alpha 1 domain amino acid sequences. The tree is made using Neighbor-joining P-distance and pairwise deletions. 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 from1000 trials are shown. The various U lineage alpha 1 domain lineages [13,57] are shown as shaded boxes with Roman numbers outside each lineage cluster. Sequence GenBank references are as follows: Atlantic salmon (Salmo salar): UBA*0101 AAN75113, UBA*0201 AF504023, UBA*0701 AAN75109, UBA*0801 AAN75115, UBA*0901 AAN75119, UBA*1001 AAN75118, UBA*1401 AAN75110, UBA*4001 AEW27162, UGA ACX35601. Rainbow trout (Oncorhynchus mykiss): UBA*101 AF287483, UBA*401 AF287487, UBA*0501 AAG02508, UBA*0901 AAG02512, UBA*4501 AY278451, UBA*4701 AY278449, UBA*4801 AF318188, UBA*4901 AF318190. Brown trout (Salmo trutta): UBA*0101 AF296374, UBA*0701 AF296380, UBA*0801 AF296381, UBA*0901 AAG02528, UBA*1001 AF296383. Sockeye salmon (Oncorhynchus nerka, unpublished data): UBA*0101 KM085986, UBA*0201 KM085987, UBA*0310 KM085988 and UBA*0401 KM085989. Medaka (Oryzias latipes): UAA*0202 AB450991, UBA*0201 BAB83850.2. Paddlefish (Polyodon spathula): UBA*01 ACV87421, UBA*03 ACV87423 and sturgeon (Acipencer sinensis) ACV87437 [60]. Human: HLA-A2 AAA76608.2. Stickleback (GA; Gasterosteus aculeatus), tetraodon (TN; Tetraodon nigroviridis), fugu (TR; Takifugu rubripes), cavefish (AM; Astyanax mexicanus) and tilapia (ON20; Oreochromis niloticus) references are shown in Additional file 4: Text S2. Zebrafish (Danio rerio), carp (Cyprinus carpio), catfish (Ictalurus punctatus), cod (GM; Gadus morhua), tilapia lineage III, Wuchang bream (Megalobrama amblycephala), guppy (Poecilia reticulata), snakehead murray (Channa striata), eel (Anguilla japonica) and shark (Squalus acanthias) sequence references are shown in parenthesis in the figure. Alpha 1 domain phylogenies with more teleost sequences in addition to alpha 2 and alpha 3 domain phylogenies can be found in Additional file 6: Text S3.