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Well, here you go you pro-hatchery salmonid fans!
You will see some problems with hatchery fish but don't feel surprised, it has been overwhelming for many years.

I skimmed through the report and highlighted some of the interesting points.

This is very scientific and reinforces the numerous scientific reports on hatchery/wild fish.

I felt the need to post this because some fishermen including an ifisher that suggested we let hatchery summer steelhead go above North Resevoir.

This new report reinforces the decision that was made in '99 to halt the upper Clackamas River summer steelhead program.


Naturally Spawning Hatchery Steelhead Contribute to Smolt
Production but Experience Low Reproductive Success

Oregon Department of Fish and Wildlife,
2501 Southwest First Avenue,
Portland, Oregon 97207, USA

Washington Department of Fish and Wildlife,
600 Capitol Way North,
Olympia, Washington 98501, USA

Abstract.—We used genetic mixture analyses to show that hatchery summer-run steelhead Oncorhynchus
mykiss, an introduced life history in the Clackamas basin of Oregon, where only winterrun steelhead are native, contributed to the naturally produced smolts out-migrating from the basin.
Hatchery-produced summer steelhead smolts were released starting in 1971, and returning adults were passed above a dam into the upper Clackamas River until 1999. In the 2 years of our study, summer steelhead adults, mostly hatchery fish, made up 60% to 82% of the natural spawners in the river.
Genetic results provided evidence that interbreeding between hatchery summer and wild winter steelhead was likely minor. Hatchery summer steelhead reproductive success was relatively poor. We estimated that they produced only about one-third the number of smolts per parent that wild winter steelhead produced.
However, the proportions of summer natural smolts were large
(36–53% of the total naturally produced smolts in the basin) because hatchery adults predominated on the spawning grounds during our study. Very few natural-origin summer adults were observed, suggesting high mortality of the naturally produced smolts following emigration.

Counts at the dam demonstrated that hatchery summer steelhead predominated on natural spawning grounds throughout the 24-year hatchery program.
Our data support a conclusion that hatchery summer steelhead adults and their offspring contribute to wild winter steelhead population declines through competition for spawning and rearing habitats.

Genetic risks to wild fish populations caused by
interbreeding with hatchery fish have been frequently
addressed in research and have been of
great concern to managers for at least the last several
(Reisenbichler and McIntyre 1977;
Hindar et al. 1991; Waples 1991; Reisenbichler
and Rubin 1999; Lynch and O’Hely 2001). Most
management efforts to decrease the risks of hatchery
programs to wild populations have focused on
decreasing interbreeding between hatchery and
wild fish (Lindsay et al. 2001). Low apparent
breeding success by the hatchery fish has often
been assumed to indicate low risk to the wild fish
(ODFW 1992b).

For many years, this premise guided a large
hatchery program
by the Oregon Department of
Fish and Wildlife (ODFW) to produce summer-run
steelhead Oncorhynchus mykiss for the Clackamas
River, which enters the lower Willamette River in

The Willamette River enters the lower
Columbia River at river kilometer (rkm) 160, as
measured from the mouth of the Columbia River.
Winter-run steelhead are native to the Clackamas
River, but summer steelhead were not historically
present. The Skamania stock summer steelhead at
the South Santiam Hatchery (henceforth, ‘‘hatchery
summer’’ stock) were introduced into the basin
in 1971 to provide a sport fishery.
On average,
160,000 marked hatchery summer steelhead
smolts were released into the basin annually. An
average of 2.4% of them survived to adulthood,
based on annual smolt releases and adult returns
to North Fork Dam fish ladder at rkm 48 on the
main-stem Clackamas River (ODFW, unpublished
data). Substantial numbers of hatchery summer
adults were passed above the dam into natural
spawning grounds starting in 1975. Very few unmarked
summer steelhead were ever observed in
the Clackamas River, either at the dam or in the
fishery, indicating poor reproduction by or survival
of the hatchery fish passed upstream. It was
therefore assumed that these fish did not spawn
It was also assumed that life history
differences, such as those described by Leider et
al. (1984), precluded interbreeding between summer
and winter runs. Risks to wild winter steelhead
from the hatchery summer steelhead program were
assumed to be very low.

A decline in Clackamas River wild winter steelhead
abundance occurred in the 1990s (Chilcote
1998) and caused a more careful consideration of
factors affecting the population, including the
hatchery summer steelhead program.
We hypothesized
that hatchery summer steelhead were successfully
spawning and producing juvenile offspring
that largely died before reaching adulthood.

If this were so, hatchery summer adults and their
offspring could have been occupying substantial
amounts of winter steelhead spawning and rearing
habitat and contributing to wild winter steelhead
declines through competition.

Although summer
and winter steelhead show distinct differences in
adult life histories, their juvenile life histories and
habitat requirements are thought to be similar,
which would maximize competitive interactions
between them (Fraser 1969; McMichael et al.
2000; Keeley 2001). Leider et al. (1984) demonstrated
that hatchery summer steelhead spawned
significantly earlier than wild winter steelhead.
Thus, summer steelhead may be expected to
emerge earlier and occupy choice feeding territories
before wild winter steelhead, which may
place winter steelhead at a particular disadvantage.

To evaluate potential effects of the hatchery
summer steelhead program on wild winter steelhead,
we had to address two issues: (1) whether
hatchery summer steelhead were spawning naturally
and producing smolts and (2) whether the
summer steelhead produced had any effects on the
productivity of wild winter steelhead. This paper
addresses the first issue by investigating the contribution
by hatchery summer steelhead to naturally
produced smolts out-migrating from the
Clackamas River. The second issue will be addressed
in a subsequent paper.

General approach.—Adult fish passing upstream
to natural spawning grounds in the Clackamas
basin and juvenile out-migrants produced in
the upper basin have been enumerated annually at
North Fork Dam fish passage facilities since 1958.
The ODFW has estimated that about 80% of winter
steelhead spawning and rearing habitat in the
Clackamas basin is above North Fork Dam
(ODFW 1992a). We planned to compare the allelic
composition of all steelhead populations that
might be breeding in the upper Clackamas with
that of naturally produced smolts captured at the
dam and use genetic methods for mixture analyses
to determine the contributions of the various stocks
to natural smolt production.

We assumed that three genetically distinct parental
populations potentially spawned in the basin:
(1) the hatchery summer steelhead stock, (2)
a hatchery winter steelhead stock that was released
into the lower Clackamas basin but that could stray
into upstream areas, and (3) the wild Clackamas
winter steelhead population. The hatchery summer
steelhead stock originated from Skamania stock,
which was founded in the 1950s from wild summer
steelhead populations in the Klickitat and Washougal
rivers of southwest Washington (Reisenbichler
et al. 1992).
This stock had been transferred
to ODFW South Santiam Hatchery in the mid-
Willamette basin and had been reared without further
stock mixing or importation since the 1970s.
The winter steelhead hatchery stock, released at
the U.S. Fish and Wildlife Service Eagle Creek
National Hatchery in the lower Clackamas basin,
was originally derived from steelhead in Big
Creek, an Oregon tributary to the lower Columbia
River (rkm 43).
The third population, unmarked
winter steelhead returning to the Clackamas River,
was assumed to represent the wild native gene

Field sampling.—We sampled the three stocks
to form our genetic baseline data set. We sampled
68 unmarked winter-run adult steelhead over 3
years (25 in 1995, 16 in 1996, and 27 in 1997) at
North Fork Dam in April and May, their peak runtime.

We sampled juvenile hatchery summer steelhead
(N 5 51) at South Santiam Hatchery in 1995
and juvenile hatchery winter steelhead (N 5 50)
at Eagle Creek Hatchery in 1996. We collected
out-migrating smolts, identified as naturally produced
based on lack of adipose fin clip marks,
the North Fork Dam downstream migrant trap during
the peak of steelhead out-migration from 12
to 15 May 1995 (N 5 50) and 29 April to 5 May
1996 (N 5 42).

All samples were delivered frozen
on dry ice to the Washington Department of Fish
and Wildlife (WDFW) Genetics Laboratory in
Olympia Washington, where they were stored at
2808C until dissection. Approximately 1 cm3 each
of skeletal muscle, heart, liver, and retina was extracted
from each fish and put in individually labeled
plastic culture tubes (12 3 17 mm). Tissues
were kept frozen on dry ice during dissection and
subsequently were stored at 2808C until analysis.
We used annual adult and juvenile counts at

North Fork Dam to estimate the sizes of parent,
smolt, and adult offspring populations so that we
could calculate the relative production of offspring
by our three parent populations. Lower Columbia
steelhead populations largely produce 2-year-old
smolts and 4-year-old adults (Busby et al. 1996).
Therefore, the 1995 smolt sample corresponded to
the 1993 parent year and the 1997 adult offspring
return year, and the 1996 smolt sample corresponded
to the 1994 parent year and the 1998 adult offspring
return year. The count of summer steelhead
parents included both natural and hatchery summer
steelhead passed above North Fork Dam,
which was reduced by 15% to adjust for mortality
during the long prespawning holding period.

Hatchery and wild winter steelhead parents were
the counts of marked and unmarked winter steelhead,
respectively, passed above the dam. Smolt
offspring were the counts of unmarked smolts
passed below the dam. Adult offspring were the
counts of unmarked winter and summer steelhead
at the dam plus the estimated number of fish harvested
before reaching the dam (from Chilcote

Electrophoresis.—All allozyme analyses for this
study were conducted at WDFW Genetics Laboratory.
We used horizontal starch-gel electrophoresis
following the general methods of Aebersold
et al. (1987) to assay genetic variation at 60
enzyme-coding loci in steelhead (Table 1). Locus
and allele nomenclature followed Shaklee et al.
(1990a). Additional description of laboratory
methods can be found in Phelps et al. (1994a). We
reported allele mobilities in accordance with the
coastwide genetic stock identification consortium,
a group of west coast agencies and universities
that has coordinated and standardized allozyme
methodologies for Oncorhynchus species. We used
computer-based quality control procedures for genotype
scoring as described in Phelps et al.
(1994b). This protocol served as a check for field
sampling errors and gel loading errors and provided
multiple independent scores for many loci,
as recommended by Shaklee and Phelps (1990).

Genetic data analyses.—We used the computer
program BIOSYS-1 (Swofford and Selander 1989)
for calculating allele frequencies, average heterozygosities,
percentages of polymorphic loci, average
number of alleles per locus, Hardy–Weinberg
(HW) genotypic equilibrium tests per sample, and
pairwise genetic distances. We used chi-square
goodness-of-fit tests to compare observed genotype
proportions with those expected under HW
equilibrium conditions in each parent baseline and
smolt sample. For baseline sample tests, we included
only loci that had at least five variant individuals,
and when more than two alleles were
observed at a locus, we pooled genotypes into
three classes (homozygotes for the most common
allele, heterozygotes for the most common allele
and one of the other alleles, and all other genotypes)
because chi-square values can be inflated
when expected frequencies of some classes are low
(Sokal and Rohlf 1981). We tested for allele frequency
homogeneity between samples with a loglikelihood
ratio test and G-statistic (Sokal and
Rohlf 1981). To evaluate relationships among samples,
we used Cavalli-Sforza and Edwards (1967)
chord genetic distances and the NTSYS-pc computer
program (Rohlf 1994) to conduct multidimensional
scaling analyses (Lessa 1990).

Gametic phase (linkage) disequilibrium may be
present in populations where recent introgression
or hybridization has occurred (see Campton 1987)
or in samples containing a mixture of individuals
from noninterbreeding, well-differentiated gene
pools. We evaluated gametic disequilibrium in the
two wild smolt samples and in a sample formed
by combining the 1995 wild winter adult sample
and the hatchery summer stock sample. We assumed
this combined sample would act as a simple
mixture of individuals from the two populations
with no hybrids present and would provide an estimate
of gametic disequilibrium expected in such
a sample. Using only polymorphic loci with variant
alleles present at rates of 5% or higher, we
calculated Burrows composite gametic disequilibrium
coefficients (Weir 1979) with a computer program
supplied by Jon Brodziak (National Marine
Fisheries Service, Woods Hole, Massachusetts)
and modified by Craig Busack (WDFW).
We used two models to evaluate genetic contributors
to smolt production. Our first approach
assumed smolts were a genetic admixture produced
by all possible matings of the parent stocks.
We used methods described by Long (1991) and
his computer program (ADMIX). This program
uses a weighted least-squares estimation method
to calculate contributions from parental sources to
an introgressed or hybridized population. Both
sampling error and genetic drift are accounted for
in computing standard errors (Long 1991). Given
program input data requirements, we used frequencies
for the common allele ( *100 or *a) at 17
loci (Table 1). We tested each smolt sample separately.
The second model assumed that smolts resulted
largely from assortative mating, in which the three

TABLE 1.—Allele frequencies at 37 allozyme loci for
samples of Clackamas River steelhead smolts and baseline
samples of wild Clackamas River winter-run (CRW),
hatchery summer-run (HS), and hatchery winter-run (HW)
steelhead populations; N 5 number of fish successfully
scored per locus. The following 23 loci had a frequency
of 1.000 for the *a ( *100) allele in all samples: sAAT-3 *,
mAH-1,2 *a, mAH-4 *, CK-A1 *, CK-A2 *, CK-C1 *, FH*,
IDDH-1 *, mIDHP-1 *, LDH-A1 *, LDH-A2 *, LDH-B1 *,
ME*, mMEP-1 *, MPI *, PEP-LT *, PGM-1 *, PGM-1r *,
mSOD *, TPI-1 *, TPI-2 *, and TIP-4 *.
Locus, N,
allele code
and statistic
smolts CRW HS HW

a These isolocus pairs represent two loci with common alleles having
the same electrophoretic mobility and in which variant alleles
cannot be assigned to either locus. Frequencies are for both loci
combined (4 alleles/isolocus).
b Locus used for admixture analysis.
c Locus used for maximum likelihood estimates of mixture composition.)
parent stocks bred only within their own group
and did not hybridize. This may be a more realistic
model for summer and winter steelhead, based on
the findings of Leider et al. (1984). We also had
to assume that hatchery winter steelhead were reproductively
isolated from both wild winter steelhead
and the summer steelhead. Using maximum
likelihood estimation (MLE) methods for mixedstock
analysis, we estimated contributions from
each parent stock to each smolt sample.

This methodology
has been used to estimate stock composition
in salmon fishery harvests (Shaklee et al.
1990b) and in out-migrating juvenile chinook
salmon (Marshall et al. 2000). We used the MLE
computer program of Milner et al. (1983) as modified
by Millar (1987). Input data were allele frequencies
at 22 loci that were polymorphic in at
least one parent stock (Table 1) and the 22-locus
genotypes for individual smolts. The MLE program
would identify impossible genotypes in the
smolts based on allele presence and absence in
parent stocks. These genotypes may indicate a hybrid
if baseline data are accurate. Hybrid genotypes
could lack such distinguishing allelic combinations
but might increase estimate variances.

Genetic analyses.—Allele frequencies for 37
variable loci in smolt and parent baseline samples
are presented in Table 1. A variety of loci appeared
informative for mixture analyses (e.g., sAH*, ADA-
2*, ALAT*, GAPDH-3*, LDH-B2*, PGK-2*). Some
alleles were observed in smolt samples but not in
baseline samples (e.g., sMDH-B1,2*83, PEPD-
1*87, TPI-3*102; Table 1).

Genetic variability per sample differed slightly
among parent baseline samples (Table 2). Wild
winter steelhead had higher average alleles per locus
and higher percentages of polymorphic loci,
but sample size was also larger. Both smolt samples
had a relatively high percentages of loci polymorphic
at the 1% criterion level. Differences between
observed and expected mean heterozygosities
were not significant in any sample.
found significant deviations from expected HW
proportions in baseline samples at the following
loci among the number of tested loci (N): hatchery
summer stock at ALAT* (12), wild winter stock at
GAPDH-3* (15), and hatchery winter stock at
sIDHP-2* (12). These proportions of significant
tests per sample were close to those expected by
chance (0.05). In the 1995 smolt sample we found
significant HW test results for three loci (ADA-2*,
bGLUA*, and PEPD-1*), all due to heterozygote
deficiencies. At bGLUA* we observed only a homozygote
for a variant allele (*c/c). Note that
bGLUA*c allele frequencies were too low in baseline
samples to expect homozygous genotypes (Table
1). We did not detect any significant deviations
from HW equilibria in the 1996 smolt sample.
Overall allele frequencies were significantly different
(P , 0.001) in all possible pairwise comparisons
among the three parent samples and between
each parent sample and the smolt samples.

TABLE 2.—Measures of genetic variability, based on 56 loci, in baseline samples of wild steelhead smolts and parent
stocks. Standard deviations are shown in parentheses.
Group or stock
sample size
per locus
of alleles
per locus
Percentage of loci
polymorphica at
.5% .1%
Mean heterozygosity
Actual Expected
1995 smolts
1996 smolts
South Santiam Hatchery
Skamania summer run

Eagle Creek Hatchery
Big Creek winter run
Wild Clackamas winter run

a The two levels of polymprohism indicate the frequency of alleles other than the *a allele.
FIGURE 1.—Three-dimensional scaling plot of Cavalli-
Sforza and Edwards (1967) chord genetic distances
among potential parent stocks and smolt samples for
wild winter and hatchery steelhead in the Clackamas

Allele frequencies of the two smolt samples were
significantly different from each other (P 5 0.03).
Tests included 20–22 loci, depending on sample
variability. Genetic distances (22 loci) among all
samples plotted in three-dimensional space (Figure
1) showed both smolt samples to be nearly equally
distant from hatchery summer and wild winter
steelhead samples and most divergent from the
hatchery winter steelhead sample. Genetic distance
between wild winter steelhead and each
hatchery stock was nearly equal.
In our test sample for gametic disequilibrium
(wild winter and hatchery summer samples combined),
we found significant (P , 0.05) disequilibrium
between two locus pairs (ALAT* and PGK-
2*; and LDH-B2* and PGK-2*). Some of the largest
allele frequency differences between wild winter
and hatchery summer samples occurred at
LDH-B2* and PGK-2* (Table 1). In the 1995 smolt
sample we found significant gametic disequilibrium
between two locus pairs (ADA-2* and NTP*;
and LDHB-2* and NTP*). In the 1996 smolt sample
we found significant disequilibrium between
three locus pairs (ADA-2* and sAH*; ADA-2* and
sSOD-1*; and sMEP-1* and sSOD-1*).
Mixture analyses of smolts.—

Estimated contributions
of potential parent stocks to each smolt
sample using each model are shown in Table 3. In
general, we found high contributions from the
hatchery summer stock using either model, particularly
in the 1995 smolt sample.

The wild winter
stock was the other major contributor. Contributions
to smolts from the hatchery winter stock were
minor and imprecise according to both models.
Admixture analysis, which assumed interbreeding
among stocks, indicated that hatchery summer
steelhead made the largest contribution to 1995
smolts, followed by wild winter steelhead (Table

Admixture analysis also indicated that hatchery
winter steelhead made a moderate contribution to
1995 smolts, but this estimate was quite imprecise.
The mixed-stock MLE analysis, which assumed
noninterbreeding, showed large proportions of
wild winter and hatchery summer steelhead progeny
among the 1995 smolts and only a very small
proportion due to hatchery winter steelhead. The
MLE program also found two 1995 smolts with
impossible genotypes given parent baseline data,
and these were excluded from stock composition

Wild winter steelhead were the major contributors
to 1996 smolts in ADMIX results, and hatchery
summer steelhead contributions were substantial
(Table 3). Initial admixture analysis of 1996
smolts gave a negative contribution estimate for
TABLE 3.—Parent stock contribution estimates from admixture analysis and composition estimates from mixed stock
maximum likelihood (MLE) analysis for 1995 and 1996 Clackamas steelhead smolt samples and composition of 1993–
1994 parents and 1997–1998 adult offspring. All values are percent; SDs are given in parentheses.
Parent stock
1995 Smolts
of smolts
(N 5 48)a
1997 adult
1996 Smolts
of smolts
(N 5 42)
(N 5 42)
1998 adult
Wild Clackamas winter run
South Santiam Hatchery
Sakamania Stock summer run
Eagle Creek Hatchery
Big Creek Stock winter run

a Two fish were removed from the original sample of 50 because they had genotypes that could not be allocated to a parent stock given
parent baseline allele frequencies.
b All unmarked winter steelhead were presumed to be wild.
TABLE 4.—Estimates of naturally produced smolt and
adult offspring per parent produced by wild winter and
introduced summer steelhead in the Clackamas River.
Smolts per parenta
Wild winter Summer
Adults per parent
Wild winter Summer

a The range of results reflects the differences between the results
of the admixture and maximum likelihood analyses.)
the hatchery winter stock, so we removed it from
the baseline for a final estimate. Mixed-stock MLE
analysis found that 1996 smolts contained a majority
of wild winter steelhead progeny, a large
proportion of hatchery summer steelhead progeny,
and a small component of hatchery winter steelhead.
Overall, we found that stock contribution estimates
varied more widely between years in admixture
analyses than in mixed-stock analyses.
However, it was apparent from both models that
hatchery summer steelhead contributed at relatively
high levels to natural production of smolts
in both years.

One of the excluded genotypes in the 1995 smolt
sample may indicate the presence of hatcheryorigin
rainbow trout O. mykiss because of variant
alleles at …

We based this interpretation
on Roaring River hatchery stock rainbow trout allele
frequencies (WDFW, unpublished data), a
stock that has been planted in North Fork Reservoir.
The other impossible genotype may indicate
a hybrid between summer and winter stocks, based
on alleles at sAH*, GPI-A*, and sIDHP-1*. Also,
two smolts in each year possessed an allele that
was absent in parent baselines, but had multilocus
genotypes acceptable in MLE analyses when the
single locus genotype was excluded.

Relative production of offspring by summer and
wild winter steelhead.—The 1993 parents of 1995
smolts included 82% summer steelhead and 15%
wild winter steelhead (Table 3). The 1994 parents
of 1996 smolts included 60% summer steelhead
and 37% wild winter steelhead. The 1997 adult
offspring included 87% winter steelhead and 13%
summer steelhead, and 1998 adult offspring included
82% winter steelhead and 18% summer
steelhead. Winter steelhead adult offspring were
believed to be primarily the progeny of the wild
winter steelhead because (1) few hatchery winter
parents passed the dam in 1993 and 1994 and (2)
estimated hatchery winter stock contributions to
1995 and 1996 smolts were very small.

The hatchery summer stock predominated
among the parents in both brood years of our study,
based on numbers passing above the dam, but they
produced half or less of the smolts and only a small
proportion of the naturally produced adult offspring.
The relatively poor reproductive success
of summer steelhead is evident in the number of
smolts and adult offspring produced per parent by
the two brood years (Table 4).
Summer steelhead
produced only 18–37% of the smolts per parent
that were produced by wild winter steelhead and
only 4–13% of the adult offspring per parent that
were produced by wild winter steelhead.

We found that hatchery summer steelhead contributed
substantially to natural smolt production
according to both of our models of stock interbreeding.
The previous assumption that hatchery
summer steelhead did not spawn successfully had
to be dismissed, which required us to evaluate
which model most appropriately described the behavior
of Clackamas steelhead populations.
lower Columbia basin tributaries that have native
populations of both life histories, summer and winter
steelhead maintain reproductive isolation
through run and spawn-timing differences and seasonal
migration barriers within a drainage. There
are no physical barriers in the upper Clackamas
and any overlap in spawn timing and location
could promote interbreeding between hatchery
summer and wild winter steelhead. Our genetic
data provided evidence about the potential levels
of interbreeding.

Baseline allele frequency data for the three
Clackamas steelhead stocks demonstrated that
adults classified phenotypically as wild winter
steelhead were genetically divergent from both introduced
summer and winter hatchery stocks.Wild
winter steelhead genetic differentiation indicated
that this population has not been homogenized by
interbreeding with hatchery stocks. These data
support the hypothesis that among-stock reproductive
isolation is relatively high.
However, interbreeding
is not completely precluded by these
results because population genetic data before the
hatchery programs are not available for comparisons.
Also, we would not have detected summer–
winter interbreeding if such hybrids had a summer
run-time phenotype.

Genetic data for smolts provided evidence that
the samples contained fish from separate source
Heterozygote deficiencies and significant
gametic disequilibria in the 1995 smolt sample
indicated that it contained individuals from genetically
divergent populations. Although we
found no significant HW disequilibria in the 1996
sample, significant gametic disequilibria results indicated
that individuals originated from separate,
divergent sources.
In general, estimation of gametic
disequilibrium between loci is a more powerful
test for nonrandom mating than single-locus
HW tests (Campton 1987).
Allelic variants seen in smolts but not in baseline
samples likely reflect sampling error for baselines
and nonnative rainbow trout presence. Baseline
sample sizes and inclusion of only one brood
year from hatchery populations may underestimate
variability, given steelhead allelic diversity
(Phelps et al. 1994a). However, not only was one
hatchery rainbow trout likely present in our smolt
samples, but other genotypes with sMDH-B1,2*83
alleles may indicate gene flow between nonnative
hatchery rainbow trout and native steelhead
(Phelps 1991).

The admixture analysis of 1995 smolts, which
assumes interbreeding among parent stocks, indicated
higher contributions by both the summer
and winter hatchery stocks and, therefore, higher
hatchery fish reproductive success than the mixedstock
MLE analysis, which assumes assortative
mating. However, we believe that hatchery winter
stock contributions were overestimated and very
imprecise for 1995 smolts because of analytical
limits of the ADMIX program. These limitations
also prevented an estimate of hatchery winter stock
contributions to 1996 smolts, even though sAH*c
allele frequencies (Table 1) implied a contribution.

Because ADMIX used only the frequency of one
allele (usually the most frequent) at loci that met
variability criteria, the program ignored information
provided by multiple alleles per locus and
low-frequency alleles exclusive to one, or not present
in any, parent source. Given the low proportion
of hatchery winter adults (Table 3), we doubt
that hatchery winter stock contributions to 1995
smolts were as large as the ADMIX point estimate
suggests. We also think wild winter steelhead contributions
may have been misallocated to the
hatchery winter stock because of restricted data

Estimate accuracy was likely enhanced by the
analytical advantages of the MLE program. All
alleles at all variable loci were used as parent
source data, which maximized differentiation
among stocks. Input of multilocus genotypes of
smolts allowed identification of individuals not attributable
to baseline data. The very small contributions
from the hatchery winter stock matched
its low proportions in potential parents (Table 3).
Also, all but two smolt genotypes from the 1995
and 1996 smolt samples were allocated to parent
stock sources, which supports the intrastock breeding

This successful allocation of most smolts to a
single parent source by mixed-stock MLE analysis
gave us confidence that interbreeding among winter
and summer steelhead was at very low levels.

We recognize, however, that given the many alleles
shared among stocks, interbreeding could produce
genotypes more closely resembling those of a parent
stock rather than a hybrid. Genotypic ambiguity
may be a source of the relatively large MLE
standard deviations, but this is difficult to evaluate
because small sample size was likely the major
contributor to large error values.
Whatever interbreeding may have occurred be-
FIGURE 2.—Panel (A) shows the number of steelhead
adults that passed into natural spawning areas above
North Fork Dam on the Clackamas River from 1958 to
1999. The gray area shows the wild winter steelhead
adults, while the line shows the total number of adults.
The difference between total and wild winter adults was
primarily hatchery summer steelhead, although small
numbers of hatchery winter steelhead and naturally produced
summer steelhead were also passed in some years.
Panel (B) shows the number of naturally produced steelhead
smolts out-migrating past North Fork Dam from
1960 to 2001. The gray area shows the estimated number
of wild winter steelhead smolts, while the line shows
the total number of smolts observed. The difference between
total and the estimated wild winter smolts is estimated
summer steelhead smolts, assuming that summer
steelhead production over the duration of the hatchery
program was similar to that in our 2 study years.)
tween hatchery and wild fish, it has not diminished
the genetic and biological distinctiveness of the
wild winter steelhead population, and we do not
believe it has had an effect on the productivity of
the wild population. The decline in wild winter
steelhead abundance was not likely due to diminished
reproductive success of a greatly hybridized

Hatchery summer steelhead were able to produce
smolt offspring, but they did so with much
less success than wild winter steelhead. In the 2
years of this study hatchery summer steelhead produced
about a third or less as many smolts per
parent and about a tenth or less as many adult
offspring per parent as wild winter steelhead did.

Theoretical work by Lynch and O’Hely (2001) predicted
that hatchery stocks like the nonnative,
mixed-origin South Santiam Hatchery summer
stock, which has been in artificial production for
many generations, should have substantially depressed
fitness in a stream environment compared
with the local wild population. Our results are consistent
with Chilcote et al. (1986) and Leider et al.
(1990; but see also Campton et al. 1991), who
demonstrated poor reproductive success in Kalama
River, Washington, of Skamania Hatchery summer
steelhead, the progenitor of the South Santiam

Relatively poor reproductive success by hatchery
summer steelhead did not preclude these fish
from producing one-third to one-half of the wild
(natural origin) smolts in the Clackamas basin in
the 2 years of our study. This most likely occurred
because hatchery summer steelhead formed the
largest proportions of spawners that produced our
study smolts (Table 3). Hatchery summer steelhead
also predominated in the natural spawning
population in most other years of the hatchery program.

From 1975 through 1999, they made up 30–
88% of the steelhead passed above North Fork
Dam, according to dam counts (Figure 2a). If we
assume their contributions to wild smolts in other
years were similar to those estimated for 1995 and
1996, we can show that annual wild winter steelhead
smolt production appears to have declined
over the 24-year period (Figure 2b). This apparent
decline was masked by the presence of summer
steelhead smolts in the total smolt counts at the

We conclude that even though naturally spawning
hatchery steelhead may experience poor reproductive
success, they and their juvenile progeny
may be abundant enough to occupy substantial
portions of spawning and rearing habitat to the
detriment of wild fish populations. The capacity
of the Clackamas basin to produce steelhead
smolts is expected to be finite (Allen 1969). Therefore,
the large numbers of introduced summer
steelhead would have competed heavily with wild
winter steelhead for habitat resources, and this
may have contributed to their decline.
We will investigate
potential ecological effects of the summer
steelhead on the productivity of the wild winter
steelhead population in a second paper.

In the Clackamas basin, smolt offspring of
hatchery fish appear to have wasted the production
from natural habitat because very few survived to
return as adults.
The summer steelhead hatchery
program was not intended to produce a natural
spawning population, but the adult offspring, at
least, could have contributed to fisheries. However,
second-generation production failure also could be
a potential risk for hatchery supplementation programs
that seek to produce adult returns from naturally
spawning hatchery fish and thereby boost
wild population size. We caution managers about
concluding that natural spawning and smolt production
by hatchery fish is evidence for the success
of supplementation programs. Evidence for success
must also include returning adult offspring
and no depression of wild fish productivity. Potential
competition between hatchery and wild fish
for habitat is pertinent to supplementation programs
where natural reproductive success by
hatchery fish is the major goal. Supplementation
programs should be attuned to basin carrying capacities
so that they do not reduce wild fish productivity
through competition for resources.

Funding for this study was provided by Portland
General Electric (PGE). Doug Cramer, PGE, and
Sharon Vendshus of ODFW provided field and
sampling support. Genetic analysis was conducted
at the Washington Department of Fish andWildlife
Genetics Laboratory, with special thanks to intern
David Cierebiej. Also thanks to Robin Waples,
Mark Chilcote, and an anonymous reviewer for
valuable reviews, comments, and discussions.

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and F. M. Utter. 1987. Manual for starch gel electrophoresis:
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Allen, K. R. 1969. Limitations on production in salmonid
populations in streams. Pages 3–18 in T. G.
Northcote, editor. Symposium on salmon and trout
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Busby, P. J., T. C. Wainwright, G. J. Bryant, L. J. Lierheimer,
R. S. Waples, F. W. Waknitz, and I. V. Lagomarsino.
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space competition by juvenile steelhead trout. Ecology
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Spawning characteristics of sympatric populations
of steelhead trout (Salmo gairdneri): evidence for
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Leider, S. A., P. L. Hulett, J. J. Loch, and M.W. Chilcote.
1990. Electrophoretic comparison of the reproductive
success of naturally spawning transplanted and
wild steelhead trout through the returning adult
stage. Aquaculture 88:239–252.
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genetic structure. Systematic Zoology 39:
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2001. Reducing Impacts of Hatchery Steelhead
Programs. Oregon Department of Fish andWildlife,
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the genetic fitness of natural populations. Conservation
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Marshall, A. R., H. L. Blankenship, and W. P. Connor.
2000. Genetic characterization of naturally
spawned Snake River fall-run chinook salmon.
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McMichael, G. A., T. N. Pearsons, and S. A. Leider.
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juvenile steelhead trout on wild salmonids
in a Yakima basin watershed. Pages 365–380 in E.
E. Knudsen, C. R. Steward, D. D. MacDonald, J.
E. Willams and D. W. Reiser, editors. Sustainable
fisheries management: Pacific salmon. Lewis Publishers,
New York.
Millar, R. B. 1987. Maximum likelihood estimation of
mixed stock fishery composition. Canadian Journal
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Milner, G. B., D. J. Teel, and F. M. Utter. 1983. Genetic
stock identification study. National Marine Fisheries
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Portland, Oregon.
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plan. Oregon Department of Fish andWildlife,
Phelps, S. R. 1991. Genetic analysis of Yakima River
steelhead: initial analysis of within-basin genetic
diversity and comparison to hatchery steelhead and
rainbow trout. 1991 Annual Progress Report of the
Washington Department of Fisheries to the Bonneville
Power Administration, Contract DE-B179-
89BP00102, Portland, Oregon.
Phelps, S. R., B. M. Baker, P. L. Hulett, and S. A. Leider.
1994a. Genetic analysis of Washington steelhead:
initial electrophoretic analysis of wild and hatchery
steelhead and rainbow trout. Washington Department
of Fish and Wildlife, Report 94-9, Olympia.
Phelps, S. R., L. L. LeClair, S. Young, and H. L. Blankenship.
1994b. Genetic diversity patterns of chum
salmon in the Pacific Northwest. Canadian Journal
of Fisheries and Aquatic Sciences 51(Supplement
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differences in growth and survival of juvenile
hatchery and wild steelhead trout, Salmo gairdneri.
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S. W. Landino. 1992. Genetic variation in steelhead
of Oregon and Northern California. Transactions of
the American Fisheries Society 121:158–169.
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changes from artificial propagation of Pacific salmon
affect the productivity and viability of supplemented
populations. ICES Journal of Marine Science
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S. Whitt. 1990a. Gene nomenclature for proteincoding
loci in fish. Transactions of the American
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S. R. Phelps. 1990b. The electrophoretic analysis
of mixed-stock fisheries of Pacific salmon. Pages
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and medicine. Progress in Clinical and Biological
Research, volume 344. Wiley, New York.
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large-scale, multi-agency program for genetic stock
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Biometrics 35:235–254.

[ 02-16-2004, 03:57 PM: Message edited by: Born to be Wild ]

4,224 Posts
Captain Dano,

Nice report... Sounds liek the methods didn't really supprt the results since they where so different than expected.

Too bad in genetics there is so much room for error in the results. For sure hatchery summers are contributing to a wild population which is kewl, however bad.

It would be nice to see the study in a river w/ out roaring river rainbow, and not summers verses winters, just wild winters verse hatchery winters. That could be very interersting, there are just too many variable and too small of sample for this to be a conclusinve study.

Make sure u all relize that the sample sizes where too small to make many conclutions other than there is alot of genetic diversity in all three populations plus the roaring river rainbows contributing too makes things very interesting.

The biggest conclutions of this paper are that summers are naturally reproducing and producing smolts that are directly competing with wild fish. Stands to reason why they stopped letting summers above the falls on the Siletz for the same reason and it has made a big difference.

[ 02-11-2004, 12:24 AM: Message edited by: Ty ]

1,334 Posts
Been digging up some of the more recent work by UW graduate students and their studies on steelhead.

I was directed towards the Environmental Biology of Fishes and 2 specific articles by McLean and Seamons.

If you get the chance, check out the site and read their papers. Well worth your time. Also, check their references, as that is also a huge wealth of articles.

Environmental Biology of Fishes

Click on the "Forthcoming Papers" link, and read the papers about steelhead.

Got some more tidbits for you, a compilation of stuffs from the UW studies:

•The biggest fish dont necessarily produce more juvenile offspring. The biggest females produce larger young of the year and yearling offspring but that effect gets washed out by age 2 (smolts).

•Bigger females also tend to produce more YOY but not yearling or smolt offspring.

•There is a much stronger effect of arrival date on female reproductive success in that the females that arrived early (about 2 weeks before the median return date) had twice the
number of smolt offspring of later arriving females.

•There was an unexpectedly high and consistent contribution by mature male parr of around 40%, meaning that young males that had not yet even gone to the ocean were the dads of about 40% of the offspring (YOY, yearling and smolts) consistently across 4 brood years!

•As far as the anadromous adult males go, there is some very anecdotal evidence that the earliest arriving (which are typically large) males have the highest number of YOY, yearling or smolt offspring.

•Size at age has a small but significant genetic component. This means that size potential is heritable.

•Growth rate has a significant genetic component, again meaning that size potential is heritable. Size issues get confounded (heavily) by environmental effects in that the conditions of both the freshwater and marine environments play a large part in determining adult size.

•Wild steelhead have a very variable life history. They may emigrate to the ocean as 1, 2 or 3 year olds and may spend 1, 2 or 3 years at sea. A fish that spent 1 year in freshwater and 3 years at sea will be significantly larger (maybe 2-4 inches) than fish that spend 2 years in freshwater and 2 years at sea even though they are the same age and were born in the same year. The decisions of how much time to spend in fresh water or salt are somewhat determined by environmental and genetic conditions.

•Translation: its difficult to say with any certainty that large parents will produce large returning offspring.

•Repeat spawning is not very common in steelhead (~10% at the study site and 95% of those are females). The largest fish you catch might be repeat spawners, but I think its way more likely they are just fish that spent an extra year at sea before returning to spawn the first time.

3,268 Posts
By the basis of the article, with the hatchery summers removed, the wild winters should do better. But better may only be a few hundred more fish, and never produce a fishery. Time will tell though. And it is good that these changes are being made in places like the Clack and Molalla, so that case studies are avialable as we move into the future. It's too early for me anyhow to embrace a region-wide shift of such proportion. At the present time, we have a net loss of a summer steelhead fishery and a lot of hope for the winter fish. If the winters don't dramatically increase in numbers over a few generations, then what?

1,154 Posts
Not having the time to read all of the above...does either report conclude that keeping hatchery adults away from spawing wild fish is MORE or LESS critical to survival of wild fish than smolt competition?

This would theoretically create a possible strong argument to keep all hatchery adults away from spawning wild fish...(ie- by trapping, etc)

Isn't this the new protocol for the upper Sandy river?

[ 02-11-2004, 01:32 PM: Message edited by: half canuck ]

1,154 Posts
Its interesting to note the variation in wild fish in the amount of time spent in rivers as juveniles and time at sea. Mother nature provides this variation so disasters (floods, droughts) do not wipe out a run.

My thoughts are that we've all heard the talk about the genetics and how hatchery vs. wild are often genetically quite similar. This point ignores the fact that hatchery fish are not as successful at spawning....therefore a hatchery fish spawning w/ a wild fish dilutes the chance of a successful spawn. So, the best plan should be to insure wild fish spawn w/ wild fish. The best solution it seems to me is to use all means necessary to guarantee wild fish spawn with other wild fish in the best and most protected environment possible.


[ 02-11-2004, 01:31 PM: Message edited by: half canuck ]

1,386 Posts
That's some exciting reading! Not quite like Stephen King, is it?
Good info but no recommendations. Can you imagine what that paper cost us to get written?

6,139 Posts
Yawn -

Now for the REST OF THE STORY - that paper that Dan posted is way OLD information that is no longer relevant to the Clackamas hatchery program(s).

1) They no longer allow hatchery fish (summers or winters) above North Fork Dam. Everything above North Fork dam is now a wild fish only spawning sanctuary. 2) The former Big Creek winter stock is gone and has been changed to 2 different Clackamas river conservation broodstock strains. 3) The steelhead program on the Clackamas river is now modeled on the Hood River conservation broodstock program study, which you can read by clicking the following link.



1. Fish from old hatchery stock consistently have very low fitness (usually less than 50% that of wild fish) when breeding in the wild. The fact that H(old stock) x W crosses consistently produce fewer offspring than W x W crosses (Table 4) suggests that having H(old stock) breeders in a system might lower the fitness of the wild population. Whether the surviving wildborn offspring of such crosses re-establish “wild” levels of fitness after one full generation of selection in nature remains to be tested.

2. Fish from new, conservation hatchery stock have fitness that is about equal to that of wild fish (less than wild in two years, greater than in the third year). The same pattern is apparent whether one examines the relative fitness of individual parents or that of pairs that left at least one offspring. The similar fitnesses H(new stock) x W and W x W pairs, suggests that having H(new stock) fish in the system is probably not obviously dragging down the fitness of the wild population for genetic reasons (as might have been expected under some models; e.g. Lynch and O’Hely, 2001). Thus, the conservation hatchery program appears to have added a demographic boost to the population without having obvious negative genetic consequences - at least in regards the effects of domestication selection and mutation accumulation that should occur in the hatchery. We have not yet conducted a formal analysis of the effect of the hatchery program on the effective size of the wild population (e.g. Ryman et al., 1995), but the high levels of microsatellite diversity we still observe in both runs suggest that reduced effective size is not a problem.

3. The surprisingly large number of missing parents, and the fact that most missing parents are fathers (Fig. 3), suggests that precocious parr or resident trout are obtaining matings that produce anadromous offspring. Alternate explanations for offspring that lack both parents include a large number of unclipped hatchery fish or wild strays entering the system.


4,840 Posts
Thanks for that link UG, interesting stuff.

37,111 Posts
It is nice to see that we can learn from a study, change techniques, and significantly improve results.

Good information.

3,904 Posts
Discussion Starter #12
Yawn -

Now for the REST OF THE STORY - that paper that Dan posted is way OLD information that is no longer relevant to the Clackamas hatchery program(s).

1) They no longer allow hatchery fish (summers or winters) above North Fork Dam. Everything above North Fork dam is now a wild fish only spawning sanctuary. 2) The former Big Creek winter stock is gone and has been changed to 2 different Clackamas river conservation broodstock strains. 3) The steelhead program on the Clackamas river is now modeled on the Hood River conservation broodstock program study, which you can read by clicking the following link.
<font size="2" face="verdana,arial,helvetica">Brad, that report that I posted is not old but new!
It came out and was published last fall or winter.
That you consider way old info?
I would consider it relevant because it explains that the beloved hatchery summer’s in the Clack apparently screwed up the native Clack winter’s!
It also explains and justifies why we no longer allow the non-native hatchery summer’s above North Fork Resavoir.

I wasn’t aware that they are no longer allowing hatchery winter’s above the dam but applaud them for that.
Reports like the one I posted help prevent fish managers from making the same mistakes and correct mistakes like the Clack and many other rivers.

Now I don’t know what is going on with some new brood’s or whatever on the Clack, but I doubt that they are spending millions on the program like the Hood River program that produces a small amount of hatchery fish at a very high cost!

Regardless, they are still hatchery fish.
And for the “rest of the story” Brad, you might read the other new report that I posted the abstract and a small portion at the end of this post.

You never answered my question on the “other thread” on how much those Hood brood’s cost.
$500.00 per adult? $1000.00 per adult?
I guess it just tax payers money.

Thanks for the URL’s Shad Boy and Parker.
I will check them out soon.

Nice report... Sounds liek the methods didn't really supprt the results since they where so different than expected.

Too bad in genetics there is so much room for error in the results. For sure hatchery summers are contributing to a wild population which is kewl, however bad.

It would be nice to see the study in a river w/ out roaring river rainbow, and not summers verses winters, just wild winters verse hatchery winters. That could be very interersting, there are just too many variable and too small of sample for this to be a conclusinve study.
<font size="2" face="verdana,arial,helvetica">Here is another new report out on wild and hatchery steelhead.
I will email it to you so you have the entire report.
And there are many more!

Relationship between natural productivity and
the frequency of wild fish in mixed spawning
populations of wild and hatchery steelhead
{Oncorhynchus mykiss}

Mark W. Chilcote

Abstract: The proportion of wild fish in 12 mixed populations of hatchery and wild steelhead {Oncorhynchus mykiss}
was evaluated for its relationship to mean and intrinsic measures of population productivity. The population mean of
ln{recruits/spawner} was used to represent mean productivity. Intrinsic productivity was represented by values for the
Ricker a parameter as estimated from fits of spawner and recruit data. Significant regressions {p < 0.001} were found
between both measures of productivity and the proportion of wild fish in the spawning population {Pw}. The slopes of
the two regressions were not significantly different {p = 0.55} and defined a relationship suggesting that a spawning
population comprised of equal numbers of hatchery and wild fish would produce 63% fewer recruits per spawner than
one comprised entirely of wild fish. Study findings were not sensitive to likely levels of data error or confounded by
extraneous habitat correlation with Pw. Population status assessments and conservation monitoring efforts should include
Pw as a critical variable. For natural populations, removal rather than addition of hatchery fish may be the most
effective strategy to improve productivity and resilience.

“The primary finding of this study was the apparent relationship
between productivity and the proportion of wild fish
in the spawning population. It is possible that this relationship
was an outcome of naturally spawning hatchery fish
having lower reproductive success than wild fish. Presumably,
if hatchery fish had lower reproductive success, they
would produce fewer recruits per spawner than wild fish.
Therefore, adding hatchery fish to a natural spawning population
would be expected to cause overall productivity, as defined
in this study, to decline.
Lower reproductive success
for naturally spawning hatchery steelhead has been documented
in several other studies {Chilcote et al. 1986; Leider
et al. 1990; Reisenbichler and Rubin 1999}. However, it is
also possible that this study’s primary finding was the product
of adverse ecological interactions between hatchery and
wild fish and not differential reproductive success. Hatchery
programs, in some unknown manner, may have been ecologically
detrimental to the survival and recruitment of wild
fish. This would have had a depressing effect on overall population
productivity. It was beyond the scope of this study,
partially because of the retrospective nature of its analytical
design, to resolve the question of ecological versus reproductive
mechanisms with respect to the observed relationship
between productivity and Pw. However, this question is
clearly a topic that seems a fruitful direction for future empirical

It appears, at least for these populations, that among population
differences in productivity were influenced by
the relative mixture of wild and hatchery fish in the spawning
population. If one were to infer that this relationship
holds for all salmonids, then the possible management implications
are fourfold.

First, in conducting conservation status
assessments, interpretation of past recruitment performance
must incorporate the depressing effect of naturally spawning
hatchery fish.

Second, it is critical that fish conservation
monitoring and evaluation efforts track the relative frequency
of wild and hatchery fish in natural spawning populations.

Third, strategies that use hatchery fish to rebuild depressed
wild populations may be counterproductive because they are
likely to cause a loss in overall population productivity and
thereby cancel the recruitment benefit from adding hatchery
spawners to the population.

Fourth, an effective method to
increase the productivity of natural populations and associated
conservation benefits may be to minimize the frequency
of hatchery fish in natural spawning populations”.

[ 02-16-2004, 06:44 PM: Message edited by: Born to be Wild ]
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