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Geographic variation at an Mhc class I A1 exon was surveyed in 14 populations of coho salmon (Oncorhynchus kisutch) and 15 populations of chinook salmon (O. tshawytscha) inhabiting rivers of British Columbia, Canada. A total of 2,504 fish were sampled using denaturing gradient gel electrophoresis (DGGE), which distinguished 17 alleles in coho salmon and 20 alleles in chinook salmon. Heterozygosity at the A1 locus was moderately high for both coho (0.7) and chinook (0.6) salmon, but sequence divergence was low, with mean inter- and intraspecific nucleotide similarities of approximately 0.96. In a maximum parsimony tree, all of the observed alleles clustered into two trans-specific lineages. Within each lineage, coho and chinook alleles tended to fall into species-specific subclusters. Much of the intraspecific allelic variation within each lineage could be accounted for by nonsynonymous point mutation, indicative of balancing selection. The FST values for both coho (0.11) and chinook (0.13) salmon indicated that much of the allelic diversity was partitioned among populations. Neighbor-joining analyses of A1 allelic frequencies among coho and chinook salmon populations showed strong patterns of geographic differentiation similar to those based on neutral genetic markers such as microsatellite loci. Both natural selection and the salmonid zoogeographic history of frequent population bottlenecks have shaped the patterns of diversity observed at this and other Mhc exons in Pacific salmonids.

Polymorphism of the nucleotide sequences encoding 149 amino acids of linked major histocompatibility complex (Mhc) class II B1 and B2 peptides, and of the intervening intron (548-773 base pairs), was examined within and among seven Pacific salmon (Oncorhynchus) species. Levels of nucleotide diversity were higher for the B1 sequence than for B2 or the intron in comparisons both within and between species. For the codons of the peptide binding region of the B1 sequence, the level of nonsynonymous nucleotide substitution (dN) exceeded the level of synonymous substitution (dS) by a factor of ten for within-species comparisons, and by a factor of four for between-species comparisons. The excess of dN indicates that balancing selection maintains diversity at this salmonid Mhc class II locus, as is common for Mhc loci in other vertebrates. Levels of nucleotide diversity for both the exon and intron sequences were greater among than within species, and there were numerous species-specific nucleotides present in both the coding and noncoding regions. Thus, neighbor-joining analysis of both the intron and exon regions provided phylogenies in which the sequences clustered strongly by species. There was little evidence of shared ancestral (trans-species) polymorphism in the exon phylogeny, and the intron phylogeny depicted standard relationships among the Pacific salmon species. The lack of shared allelic B1 lineages in these closely related species may result from severe bottlenecks that occurred during speciation or during the ice ages that glaciated the rim of the north Pacific Ocean approximately every 100000 years in the Pleistocene.