Fig. 2

Golden pheasant IA (most of the α1 and α2 domains) amino acid alignment. Numbers above the alignment refer to residue positions. Locus-specific residues belonging to the IA1 gene are indicated by open boxes. PBR sites predicted from consensus positions of chicken class I molecules [49, 50] are marked with a “+” symbol. The positively selected sites (PSSs) for IA1 and IA2 are indicated above and below the alignments, respectively. A filled asterisk represents PSS identified using the M8 site model, while a filled or open prism marks a PSS detected by REL or FEL, respectively. Interlocus recombination events determined by the RDP program produced 9 daughter recombinants, with their respective recombined regions indicated by grey shading; IA2-E2*14 as the major parent is denoted with an open triangle and IA1-E2*13 as the minor parent is denoted with a filled triangle