Outside the well-studied mammalian models of human and mouse, the chicken has one of the best-understood immune systems, largely due to the interests and investment of the commercial poultry industry. The chicken Major Histocompatibility Complex (MHC) has been particularly well-studied, since variation at the chicken MHC is strongly associated with resistance and susceptibility to disease, particularly infectious pathogens. Furthermore, its 'minimal essential' gene content and organisation makes the chicken MHC a useful model for immunologists.

The vast majority of work on the chicken MHC has used highly inbred experimental lines, derived from commercial flocks, which contain a few standard MHC haplotypes. This thesis aims to understand the extent to which insights developed in these lines can be applied to other populations, species and broader taxonomic groups. The examination of features of the adaptive immune systems in non-model populations and species also provides insights into the fundamental evolutionary flexibility of this system, and could help to inform zoonotic disease surveillance, rural poultry development initiatives, conservation and commercial poultry breeding strategies.

First, diversity in the classical MHC class I and II genes in 'fancy' breeds and free-range local, or 'village', chickens was compared to that previously observed in commercial flocks. The expanded database of chicken MHC diversity resulting from examination of these populations is a valuable resource for both the scienti c and agricultural communities and describes a largely untapped pool of potentially useful genetic diversity.

Second, three defining features of the chicken MHC were examined in three passerine bird species. The results show deviation from the 'chicken-type' MHC in all three species, as well as variation between the passerine species themselves, highlighting substantial evolutionary flexibility in the system.

Finally, a family of peptide editing genes, of which one, TAPBPL, is notably absent in placental mammals, was investigated using genomic databases to assess phylogenetic distribution and biochemical methods to investigate function and regulation.

At all scales, significant variation in antigen processing and presentation is reported, challenging some of the assumptions made in models of both chicken and mammalian MHC evolution. While the need to apply insights with care across lineages is highlighted, a better understanding of the similarities and differences present at different scales can also help appropriate insights to be applied with confidence in important inter-disciplinary contexts.