Major histocompatibility complex differentiation in Sacramento River chinook salmon

The chinook salmon of the Sacramento River, California, have been reduced t o a fraction of their former abundance because of human impact and use of t he river system. Here we examine the genetic variation at a major histocomp atibility complex class II exon in the four Sacramento chinook salmon runs. Examination of the alleles found in these and other chinook salmon reveale d nucleotide patterns consistent with selection for amino acid replacement at the putative antigen-binding sites. We found a significant amount of var iation in each of the runs, including the federally endangered winter run. All of the samples were in Hardy-Weinberg proportions. A significant amount of genetic differentiation between runs was revealed by several measures o f differentiation. Winter run was the most genetically divergent, while the spring, late-fall, and fall runs were less differentiated.