MHC class I variation among wild, domestic and insular populations of the zebra finch (Taeniopygia guttata)

The zebra finch (Taeniopygia guttata) is a passerine bird native to Australia and the Lesser Sunda Islands, with domesticated populations derived from each of these localities. The Lesser Sundas and domesticated zebra finches have undergone historic bottlenecks and previous analyses using neutral markers have reported striking genetic differences among these populations. However, comparisons utilizing functional loci are lacking. Immune genes are thought to strongly rely on genetic variation to convey a greater resistance to pathogens. Genes of the major histocompatibility complex (MHC), a component of the vertebrate adaptive immune response involved in antigen presentation, have received considerable attention as a classic example of balancing selection. Here, we characterize the third exon of the highly variable MHC class I [alpha] chain, which encodes the [alpha]2 domain of the peptide binding region (PBR). Despite natural and human-mediated population bottlenecks, we find that high MHC polymorphism persists across all populations. We report higher levels of nucleotide diversity when compared with neutral loci and strong evidence of positive selection acting on important residues forming the PBR. Clear population differentiation is also evident and this may be due to adaptation to captivity and life on islands. Due to its importance in pathogen recognition, selection seems to have maintained variability of the MHC class I [alpha]2 domain, even in the presence of a genetic bottleneck