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.