532 
Fishery Bulletin 99(4) 
Table 2 
Number and variability of restriction sites observed in each of the seven mtDNA regions we examined using 12 restriction endo- 
nucleases in our preliminary survey. 
Region 
Fragment 
size 
Mean 
number 
of sites 
Mean 
number of 
nucleotides 
% 
coverage 
Number of 
variable 
sites 
Number 
of 
haplotypes 
Haplotype 
diversity 
USE) 
Nucleotide 
diversity 
(per 1000) 
12S/16S 
2402 
53.5 
226.7 
9.44 
3 
4 
0.485 ±0.042 
2.15 
ND1/ND2 
2689 
41.5 
184.7 
6.87 
3 
4 
0.485 ±0.042 
2.65 
COI/COII 
2471 
39.7 
168 
6.8 
3 
3 
0.057 ±0.038 
0.25 
A8/COIII 
2115 
29 
126.7 
5.99 
0 
1 
0 
0 
ND3/ND4 
2331 
31 
130 
5.58 
0 
1 
0 
0 
ND5/ND6 
2470 
36.5 
157.2 
6.36 
5 
4 
0.470 ±0.040 
5.99 
Cytb/D-loop 
2659 
57 
248.7 
9.35 
2 
3 
0.670 ±0.014 
1.87 
Total 
16,642 
291.28 
1254.8 
7.54 
16 
11 
0.803 ±0.024 
1.70 
Table 3 
Observed numbers of each mtDNA haplotype, haplotype diversity, and nucleotide diversity (substitutions per 1000 bp) within col- 
lections of coho salmon examined in a preliminary survey of North Pacific Ocean coho salmon (Nei and Tajima, 1983; Nei ,1987). 
Standard errors are in parentheses. Homogeneity of haplotype frequencies ( P MC < 10~ 4 ) was tested with using Monte-Carlo simula- 
tion based on 10,000 resampling iterations to estimate probability (Roff and Bentzen, 1989). 
Collection 
n 
A-D cluster 
Haplotype 
E-H cluster 
Haplotype 
Haplotype 
diversity 
Nucleotide 
diversity 
A 
A' 
B 
C 
C' 
D 
E 
E' 
F 
G 
H 
Hugh Smith River 
10 
3 
0 
0 
4 
1 
0 
2 
0 
0 
0 
0 
0.78 
1.31 
Fish Creek (Taku River) 
10 
7 
1 
0 
0 
0 
1 
0 
0 
1 
0 
0 
0.53 
0.88 
Ford Arm River 
10 
2 
0 
4 
1 
0 
0 
2 
0 
0 
1 
0 
0.82 
1.65 
Crooked Creek 
10 
5 
0 
0 
4 
0 
0 
1 
0 
0 
0 
0 
0.64 
0.78 
Eek River 
10 
0 
0 
0 
4 
0 
0 
4 
0 
0 
0 
2 
0.71 
1.87 
Delta Clearwater River 
10 
0 
0 
0 
0 
0 
0 
0 
0 
0 
0 
10 
0.00 
0.00 
Kamchatka River 
10 
5 
0 
0 
4 
0 
0 
0 
1 
0 
0 
0 
0.06 
0.94 
Total 
70 
22 
1 
4 
17 
1 
1 
9 
1 
1 
1 
12 
0.80 
1.70 
(±0.024) 
(±0.000) 
Average 
0.59 
1.06 
(±0.11) 
(±0.24) 
collections from individual drainages ranged from 0.00 to 
0.82 and nucleotide diversities ranged from 0.00 to 1.87 
substitutions per 1000 bp. The distribution of haplotypes 
among collections was highly heterogeneous, which is note- 
worthy given the small sample sizes (n=10) (Table 3). 
Phylogenetically, there were two clusters of haplotypes 
(haplotypes A-D and haplotypes E-H) (Fig. 3). Haplotypes 
of the two clusters differed by five or more restriction sites, 
and the average nucleotide divergence between individual 
haplotypes in the two clusters averaged 2.72 nucleotide 
substitutions per 1000 nucleotides, as compared to an av- 
erage nucleotide diversity within each cluster of 0.87. The 
cluster of A-D accounted for the majority of fish, but hap- 
lotypes of both clusters were observed in collections from 
all drainages, except for fish from the Delta Clearwater 
River, which had only haplotype H. Bootstrap estimates 
of nucleotide divergence between clusters and average nu- 
cleotide diversity within clusters, estimated from the en- 
tire sample of 70 fish, were 2.98 ±0.06 and 0.35 ±0.05 (sub- 
stitutions per 1000 nucleotides), respectively. 
Expanded coho mtDNA survey based on 
variable sites 
We increased the number of populations surveyed to 13 
and increased sample sizes to 20, except for the Kam- 
