Sequence variation in a 216 bp portion of the major histocompatibility comp
lex (MHC) II B1 domain was examined in 74 individual lake trout (Salvelinos
namaycush) from different locations in Lake Superior, Forty-three alleles
were obtained which encoded 71-72 amino acids of the mature protein. These
sequences were compared with previous data obtained from five Pacific salmo
n species and Atlantic salmon using the same primers. Although all of the l
ake trout alleles clustered together in the neighbor-joining analysis of am
ino acid sequences, one amino acid allelic lineage was shared with Atlantic
salmon (Salmo salar), a species in another genus which probably diverged f
rom Salvelinus more than 10-20 million years ago. As shown previously in ot
her salmonids, the level of nonsynonymous nucleotide ;substitution (d(N)) e
xceeded the level of synonymous substitution (d(S)), The level of nucleotid
e diversity at the MHC class II B1 locus was considerably higher in lake tr
out than in the Pacific salmon (genus Oncorhynchus), These results are cons
istent with the hypothesis that lake trout colonized Lake Superior from mor
e than one refuge following the Wisconsin glaciation, Recent population bot
tlenecks may have reduced nucleotide diversity in Pacific salmon population
s.