• class II;
  • divergent allele advantage;
  • MHC;
  • Pema EB;
  • Peromyscus;
  • symmetric balancing selection


We studied population polymorphism at a major histocompatibility complex (MHC) class II beta gene in the deer mouse (Peromyscusmaniculatus). We found that: (i) a single population of Pmaniculatus has significantly higher levels of DNA and protein sequence diversity than worldwide samples from homologous genes in other taxa, including humans and mice; and (ii) the genealogy of allelic sequences in Pmaniculatus deviates significantly from theoretical expectation under a model of symmetric balancing selection, in that alleles are relatively more divergent than expected. We suggest that the observation of high levels of pairwise allelic sequence divergence and deviation of the genealogy from theoretical expectation in Pmaniculatus together provide support for a divergent allele advantage model for the maintenance of MHC polymorphism.