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Fishery Bulletin 102(1) 



haplotypes (A and B) and their sequences are presented 

 in Figure 1; the chinook salmon individuals were from the 

 Upper Columbia River summer and fall ESU (Methow 

 River, WA). A second intraspecific polymorphism in chi- 

 nook salmon was observed at position 341 between our 

 ND3 sequence and the published sequence (Domanico 

 and Phillips, 1995) (Fig.l). Sufficient nucleotide varia- 

 tion exists in the d-loop (Shedlock et al., 1992) and in the 

 COIII/ND3 region ( Fig. 1 ) to distinguish among the salmon 

 species by sequencing; both regions were used for bone 

 identification. 



Six restriction enzymes were selected from the COIII/ 

 ND3 sequence that appeared to distinguish among all the 

 species (Dpn II, Sau 961, Fok I, Ase I, Apo I, and Bst NI) 

 (Fig. 1). The Dpn II and Bst NI cut patterns are redundant 

 in that only one of these enzymes is required for species 

 identification when used in conjunction with the other four 

 enzymes (however, only Dpn II exhibits the intraspecific 

 chinook polymorphism, see below). Haplotype patterns for 

 all species are listed in Table 3. The haplotypes were scored 

 with a simple alphabetic system: "A" was uncut (368 base- 

 pair (bp) band) and "B" was cut (the size differed depending 



on enzyme). A few of the enzymes had an alternative cut 

 site, and the resulting haplotype we labeled "C." The "B" 

 haplotype produced by Apo I occurs in steelhead and the 

 bands migrate at 300 and 68 bp, whereas the bands of the 

 "C" haplotype in sockeye, chum, and pink salmon migrate 

 at 250 and 118 bp. The enzyme Bst NI also has two cut pat- 

 terns: the sockeye salmon "B" haplotype bands migrate at 

 282 and 87 bp and the "C" haplotype bands in pink salmon 

 migrate at 271 and 98 bp. The Dpn II "B" haplotype in 

 chinook salmon creates two fragments, 290 and 80 bp; the 

 "C" haplotype in pink salmon creates three fragments, 292, 

 53, and 24 bp. 



To confirm that the restriction enzyme polymorphisms 

 were diagnostic within each species, we surveyed all seven 

 Pacific salmon species representing multiple populations 

 spanning a large geographic range (Table II. No intra- 

 specific polymorphisms were detected among populations 

 with the exception of chinook salmon (Tables 1 and 3). A 

 single intraspecific polymorphism was found with the Dpn 

 II enzyme in chinook salmon lineages in the Columbia 

 and Snake River basins (Tables 1 and 3). Chinook salmon 

 from the Snake River spring-summer run (Lookingglass 



