High levels of MHC class II allelic diversity in lake trout from Lake Superior

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.