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Highly polymorphic genes with central roles in lymphocyte mediated immune surveillance are grouped together in the major histocompatibility complex (MHC) in higher vertebrates. Generally, across vertebrate species the class II MHC  DRA  gene is highly conserved with only limited allelic variation. Here however, we provide evidence of trans-species polymorphism at the  DRA  locus in domestic sheep ( Ovis aries ). We describe variation at the  Ovar-DRA  locus that is far in excess of anything described in other vertebrate species. The divergent  DRA  allele ( Ovar-DRA*0201 ) differs from the sheep reference sequences by 20 nucleotides, 12 of which appear non-synonymous. Furthermore,  DRA*0201  is paired with an equally divergent  DRB1  allele ( Ovar-DRB1*0901 ), which is consistent with an independent evolutionary history for the  DR  sub-region within this MHC haplotype. No recombination was observed between the divergent  DRA  and  B  genes in a range of breeds and typical levels of MHC class II DR protein expression were detected at the surface of leukocyte populations obtained from animals homozygous for the  DRA*0201 ,  DRB1*0901  haplotype. Bayesian phylogenetic analysis groups  Ovar-DRA*0201  with  DRA  sequences derived from species within the Oryx and Alcelaphus genera rather than clustering with other ovine and caprine  DRA  alleles. Tests for Darwinian selection identified 10 positively selected sites on the branch leading to  Ovar-DRA*0201 , three of which are predicted to be associated with the binding of peptide antigen. As the Ovis, Oryx and Alcelaphus genera have not shared a common ancestor for over 30 million years, the  DRA*0201  and  DRB1*0901  allelic pair is likely to be of ancient origin and present in the founding population from which all contemporary domestic sheep breeds are derived. The conservation of the integrity of this unusual  DR  allelic pair suggests some selective advantage which is likely to be associated with the presentation of pathogen antigen to T-cells and the induction of protective immunity.

Trans-Species Polymorphism and Selection in the MHC Class II DRA Genes of Domestic Sheep