The generation of MHC class II gene polymorphism in the genus Mus

Nucleotide sequences of exon 2 from 46 alleles of the murine MHC class II Aβ gene derived from 12 rodent species were determined using the polymerase chain reaction (PCR). This exon (273 bp) exhibited extensive nucleotide sequence diversity that did not follow predicted phylogenetic relationships. The nucleotide sequence diversity of exon 2 was focussed predominantly in five discrete sub‐domains which contained polymorphic sequence motifs. These sub‐domains each encode a segment of the antigen binding site of MHC class II molecule. The alleles in each sub‐domain were organized into homogeneous lineages by parsimony analysis. The alleles in these lineages were very stable over long evolutionary periods. Some alleles derived from mice and rats have the same sequence motifs, indicating that they have been retained as polymorphisms since prior to the separation of the genus Mus and Rattus (10 Myr). Our findings indicate that polymorphism of MHC class II genes are generated by a combination of two processes. The steady accumulation of point mutations has produced highly divergent polymorphic sequence motifs in each sub‐domain. This diversity is extensively amplified by repeated intra‐exonic recombinations that shuffle these polymorphic sequence motifs into many, novel, allelic combinations. These intra‐exonic recombinational events do not seem to occur at a extraordinary rate, or at specific sites within the exon. The protein sequences encoded by the polymorphic sequence motifs differed on average in 39.3% of amino acids and 67.3% of these substitutions were non‐conservative. These findings indicate that they encode protein segments in the antigen binding site with distinct chemical properties. Codons for the antigen binding site have accumulated more non‐synonymous (amino acid replacement) substitutions than synonymous (silent) substitutions, whereas the opposite is true for the non‐antigen binding site codons in exon 2. All these results suggest that diversity is selectively maintained within the antigen binding sites. We propose that a special mechanism (termed divergent allele advantage), together with overdominant selection, accounts for the maintenance of a large number of highly divergent alleles in natural mouse populations. The extraordinary conservation of sequence motifs suggest that purifying selection may operate on MHC genes to selectively maintain certain sequence motifs and possibly combinations of specific motifs.