Small et al. : Population and stock indentification of Oncorhynchus kisutch 
851 
baseline by sampling randomly, with replacement, 
thus simulating the randomness present in data col- 
lection. For each simulated mixed-stock fishery, stock 
contributions were estimated in 50 independent simu- 
lations, and means and standard deviations for the es- 
timated contributions of each population were obtained. 
Results 
Allele frequencies and heterozygosity 
Observed heterozygosity was high in all populations 
at OfslOl, ranging from 0.72 for Nitinat River to 0.97 
for Waukwaas River (Table 1). Heterozygosity was 
slightly lower at Ots3, ranging from 0.70 for Zolzap 
River to 0.82 for Cluxewe River (Table 1). At Ots 103, 
observed heterozygosity varied widely among re- 
gions, ranging from 0.25 in the Thompson River (TR) 
to 0.89 in North Coast Vancouver Island populations 
(NCVI) (Table 2). For Thompson River populations, 
the apparently low heterozygosity values were due 
to high frequencies of the null allele. Of the 22 popu- 
lations with data for multiple year classes, Atnarko 
was the only one for which allele frequencies differed 
significantly among year classes at all loci. Allele fre- 
quencies differed significantly among year classes in 
the Kitimat, Sustut, and Toboggan populations at 
Ots3, in the Kitimat River and Pallant Creek popu- 
lations at OfslOl, and in the Quinsam and Tobog- 
gan populations at Ots 103. Year-class variation in 
the Fraser and Thompson River populations are re- 
ported in Small et al. (1998). Multiple samples from 
individual populations clustered together in NJ 
analyses (except for three lower Fraser River popu- 
lations as noted in Small et al., 1998), indicating that 
allele frequency differences among year classes were 
less than those among populations. Thus, all fish 
collected from the same location in different years 
were pooled and treated as a single population in 
subsequent analyses. 
Hardy-Weinberg equilibrium 
The degree of deviation from HWE varied substan- 
tially among the 3 loci (Table 1). After correction for 
multiple tests (P<0.0015), three populations 
(Atnarko, Deadman and Upper Pitt) deviated from 
HWE at Ots 101, and three populations (Kitimat, Big 
Qualicum, and Sustut) were out of HWE at Ots3 
(Table 1). In most populations, observed heterozy- 
gosity was lower than expected heterozygosity (Table 
1), and this lower heterozygosity was reflected in 
single-locus F [s values of 0.0435 (SD 0.009) for Ots 101 
and 0.0617 (SD 0.008) for Ots3 (both P<0.005). HWE 
was rejected for Ots 103 in 25 out of 34 populations 
(Table 2), reflecting the presence of the null allele. 
The single locus F is value was 0.2738 (SD 0.008). Fish 
homozygous for the null allele were scored in most 
populations and corrected Ots 103 allele frequencies 
were generated for all populations (Table 2). 
Population differences 
In pairwise tests, all populations had significantly 
different allele frequencies at one or more loci, with 
the exception of two geographically proximate popu- 
lations in the Thompson River (Lemieux River and 
Dunn Creek), and two sets of populations from the 
adjacent Skeena and Nass River systems: (Cedar 
River [Skeena)]and Zolzap River [Nass]; and Sustut 
River [Skeena] and Meziadin River [Nass]). The 
single- and multilocus F gt values indicated signifi- 
cant differentiation among populations with values 
of 0.040 (SD 0.006) for OfslOl, 0.054 (SD 0.009) for 
Ots3, 0.059 (SD 0.009) for Otsl03 (all P<0.005) and 
a multilocus value of 0.051 (SD 0.006, P<0.005). 
Allele frequencies 
With the exception of Ots 101 allele 96, found only in 
the Robertson Creek population, all alleles were 
present in more than one population and region. 
Thus, population- or region-specific alleles were gen- 
erally nonexistent, but allele frequencies varied 
among populations and regions. At OfslOl, lower 
Fraser River populations had high frequencies of 
smaller alleles (74% shorter than 143 bp in length) 
and relatively low frequencies of large alleles, 
whereas Thompson River populations had low fre- 
quencies of small alleles (64% longer than 161 bp). 
In the Thompson River populations, Ots 3 allele 66 
was absent and allele 94 was more common than in 
populations from other regions. Ots3 alleles 104 and 
106 were found only in the Skeena and Nass River 
populations. The most striking differentiation pro- 
vided by Ots 103 was the high frequency (0.44) of the 
null allele in Thompson River populations. This was 
three times the next highest frequency (0.15) that 
occurred in the north and west coast Vancouver Is- 
land populations. 
Population structure 
The unrooted consensus NJ dendrogram possessed 
three major branches that provided regional defini- 
tion among coho salmon populations of British Co- 
lumbia (Fig. 2). The best defined branch contained 
the Thompson River (and Bridge River of the upper 
Fraser drainage) populations, that occurred together 
