9515

• UCREFRP Catalog Number: 9515
• Author: Waples, R. S., G. A. Winans, F. M. Utter and C. Mahnken
• Title: Genetic Approaches to the Management of Pacific Salmon
• USFW Year: 1990
• USFW - Doc Type: Fisheries
• Copyright Material: YES

and Ryman 1987). However, there has never been a com-
prehensive attempt to measure the levels of inbreeding
actually occurring in hatcheries or to determine whether
measures that have been adopted to increase effective
population size have been adequate. In the only salmon
study that measured all the parameters necessary to calculate
effective population size, Simon et a1. (1986) showed that
a dangerously low N~ may have occurred in some years in
a coho salmon hatchery regularly returning thousands of
adults each year.
We describe here several approaches that can be used to
evaluate the extent of genetic changes. They can easily be
incorporated into a program to monitor the effectiveness
of hatchery operations.

Levels of Genetic Variability

One of the most serious problems faced by wild and
hatchery populations is the permanent loss of genetic
material. Not only can such losses affect the immediate
performance of a stock (see Allendorf and Ryman 1987),
but they also limit its flexibility to respond to changing
conditions in the future. A useful measure of the amount
of genetic variability in a population is the percentage of
heterozygous individuals averaged over many gene loci
(H). Interpretation of heterozygosity values is not always
simple, however. The wide range of H values found in
different organisms (0 to over 50%; Nevo et al. 1984) means
that any particular value by itself gives little indication of
the genetic health of a population. Even within Pacific
salmon species, H may vary naturally by a factor of 4 or
more among wild populations from different geographic
areas (Utter et al. 1989) and by 50% among populations
within a drainage (Winans 1989), with little if any apparent
effect on fitness.
The important goal in managing Pacific salmon popula-
tions, therefore, is not to achieve a particular level of
heterozygosity, but to ensure that existing levels of genetic
variability are not compromised by management practices.
One evaluation strategy is to monitor changes in hetero-
zygosity levels over time in all hatchery stocks. However,
because H is most strongly affected by changes in the
frequency of common alleles, serious losses of rarer alleles
can occur before significant decreases in heterozygosity are
apparent (Fig. 2). An effective monitoring program needs
a more sensitive indicator of problems posed by inbreeding
before they cause serious, perhaps irreversible, damage.

Change in Allele Frequency

An early indication of small population size can be
obtained by monitoring changes in allele frequency over
time. Genetic changes in Pacific salmon populations have
been difficult to interpret because most existing models of
such changes were derived for organisms with simpler life
history strategies. Recent approaches using computer sim-
ulations to model the complex pattern of one-time repro-
duction with overlapping year classes found in these species
have provided a context for the interpretation of observed
genetic changes (Waples and Tee11990; Waples, in pressl).
Results of these simulations have been used to show that
allele frequency changes observed in a group of nine chinook
salmon populations from coastal hatcheries in Oregon (Fig.

22

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3) most likely reflect a limited effective number of breeders.
In contrast, temporal changes in nine Oregon wild stocks
and three California hatchery stocks were relatively small
and can be explained by a model involving small amounts
of genetic drift in relatively large populations (Waples and
TeeI1990).
The magnitude of allele frequency change has been used
to estimate N, in organisms with discret.? generations (Krim-
bas and Tsakas 1971; Nei and Tajima 1981; Waples 1989),
and a similar approach can be used to estimate N~ in Pacific
salmon (Waples, in press2). Estimates of N~ provide an
indication of the degree of inbreeding occurring in a pop-
ulation and, therefore, a means of evaluating the success

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Figure 2. Loss of genetic variation over time due to genetic drift
in Pacific salmon populations. Results are from simulations (Wa-
ples, in press!) using an age structure typical of many chinook
salmon populations (average age at reproduction = 4 years). If
the effective number of breeders each year (N~) is small, large
numbers of alleles at low initial frequency (P.) can be lost before
there is any detectable decline in heterozygosity. Monitoring allele
frequency change provides a much more sensitive indication than
heterozygosity of potential problems related to inbreeding.

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Figure 3. Genetic changes over 2-4 years in samples (N "= 100
individuals) from nine wild and nine hatchery populations of
chinook salmon from Oregon. For each population, chi square
tests of equality of allele frequencies in temporally-spaced samples
were performed for an average of 10 gene loci; the percentage of
single-locus tests yielding a significant (P < 0.05) result is indicated
by the height of the columns. A small effective population size
appears to be the most likely explanation for the relatively large
differences found in most of these hatchery stocks (Waples and
TeeI1990).

Fisheries, Vol. 15, No.5