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*
Departments of Structural Biology and Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305;
Department of Medicine and Epidemiology, University of California School of Veterinary Medicine, Davis, CA 95616;
Department of Natural Resources, Colorado Division of Wildlife, Montrose, CO 81401;
Department of Animal Sciences, Cell Biology and Immunology Group, Wageningen University, Wageningen, The Netherlands; and
¶ Department of Zoology, University of Aberdeen, Aberdeen, United Kingdom
Rainbow trout (Oncorhynchus mykiss) and brown trout
(Salmo trutta) represent two salmonid genera separated
for 15–20 million years. cDNA sequences were determined for the
classical MHC class I heavy chain gene UBA and the MHC
class II 
-chain gene DAB from 15 rainbow and 10 brown
trout. Both genes are highly polymorphic in both species and diploid in
expression. The MHC class I alleles comprise several highly divergent
lineages that are represented in both species and predate genera
separation. The class II alleles are less divergent, highly species
specific, and probably arose after genera separation. The striking
difference in salmonid MHC class I and class II evolution contrasts
with the situation in primates, where lineages of class II alleles have
been sustained over longer periods of time relative to class I
lineages. The difference may arise because salmonid MHC class I and II
genes are not linked, whereas in mammals they are closely linked. A
prevalent mechanism for evolving new MHC class I alleles in salmonids
is recombination in intron II that shuffles 
1 and 2 domains into
different combinations.
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