Class I MHC polymorphism and evolution in endangered California Chinook and other Pacific salmon

Twelve MHC class 1 exon 2 sequences were uncovered in a sample from the end angered Sacramento River winter-ran Chinook salmon in the central valley of California. Phylogenetic analysis of the 12 sequences indicates that the a lleles descend from two of six major allelic lineages found among four Paci fic salmon species. Nine of the 12 alleles belong to an allelic lineage tha t began diversifying 8 million years ago, just prior to the estimated time of Chinook speciation. The most recent common ancestor of all 12 winter-run alleles is estimated to be 15 million years ago, approximately 5 million y ears before the radiation of the Pacific salmon species. The average nonsyn onymous distance among the peptide binding-region codons, of exon 2 for the 12 alleles is significantly higher than the average synonymous distance in these codons. We estimate the symmetrical overdominant selection coefficie nt against homozygotes for this exon to be 0.038. Thus, strong positive and balancing selection has maintained functional diversity in the peptide-bin ding region of the exon over millions of years and this variation has not y et been substantially eliminated by increased genetic drift due to the rece nt dramatic decline in abundance of this Chinook salmon population.