Mitochondrial DNA Variation in Chinook (Oncorhynchus tshawytscha) and Chum Salmon (O.keta) Detected by Restriction Enzyme Analysis of Polymerase Chain Reaction (PCR) Products

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Abstract
We analyzed intraspecific mitochondrial DNA variation in chinook salmon (Oncorhynchus tshawytscha) from drainages in the Yukon River (Alaska and Yukon Territory), the Kenai River (Alaska), and Oregon and California rivers; and chum salmon (O. keta) from the Yukon River and Vancouver Island, and Washington rivers. For each species, three different portions of the mtDNA molecule were amplified separately using the polymerase chain reaction and then digested with at least 19 restriction enzymes. Intraspecific sequence divergences between haplotypes were less than 0.01 base substitution per nucleotide. Nine chum salmon haplotypes were identified. Yukon River chum salmon stocks displayed more haplotypes (eight) than the stocks of Vancouver Island and Washington (two). The most common chum salmon haplotype occurred in all areas. Seven chinook salmon haplotypes were identified. Four haplotypes occurred in the Yukon and Kenai rivers and four occurred in Oregon/California, with only one haplotype shared between the regions. Sample sizes were too small to quantify the degree of stock separation among drainages, but the patterns of variation that we observed suggest utility of the technique in genetic stock identification.