Putative nucleotide sequences for DQB exon 2 alleles of the major histocompatibility complex (MHC) were amplified and determined in the 16 cetacean species using the PCR technique. The 172 bp sequences amplified showed no multiple alleles more than two in each of the examined individuals. The sequences of the 31 cetacean DQB alleles detected were monophyletic with the HLA-DQB1, and were separated from the lineages of HLA- DQB2 and DQB3. These results suggest that the locus is the homolog to the human DQB1 gene. The observed frequency of nonsynonymous substitutions in the cetacean DQB sequences was significantly higher than that of synonymous substitutions. The amino acid variation at the putative peptide binding region (PBR) was considerably high. These results imply that positive selection has promoted its variability at the cetacean DQB gene as other mammalian MHC. The DQB gene tree showed that four Mysticeti alleles branched off from the clade consisted of Mysticeti alleles only and were included in the clade consisted of Odontoceti alleles. This suggests trans-species polymorphism in the cetacean MHC gene.

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