Putative amino acid sequence alignment.

<p>The alignment starts at the 2nd amino acid position encoded by the exon 2 in MHCIIB. Sequences of chicken (<i>Gaga</i>_BLB1-haplB19 and <i>Gaga</i>_BLB2-haplB19, GenBank accession no. AB426151), barn owl (<i>Tyal</i>_DAB1-allele02, EU442602) and little spotted kiwi (<i>Apow</i>_DAB*allele08, HQ639687) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069135#pone.0069135-Miller4" target="_blank">[90]</a> are shown for comparison. Dots represent identity to the sequence on top. Asterisks (*) indicate the amino acid positions under positive selection (based on CodeML analysis, model M8, posterior probability >0.95). Plus signs (+) mark the antigen-binding sites (ABS) in humans <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069135#pone.0069135-Brown1" target="_blank">[64]</a>. Tracts 1–7 depict codons contained in conversion tracts as given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069135#pone-0069135-t003" target="_blank">Table 3</a>. Black triangles represent the placement of two recombination breakpoints as detected by GARD.