Panel of experts: Dr. Ruth Withler (chair), Dr. Craig
Busack, Mr. Richard Carmichael, Dr. Kenneth Currens, Prof. Tony
Gharrett, Prof. Michael Gilpin, Dr. Stewart Grant (rapporteur),
Prof. Michael Lynch, Prof. Thomas Quinn, Prof. Nils Ryman, Prof.
Dolph Schluter, Prof. Eric Taylor
A panel of biologists with expertise in population genetics and
related fields met on the second day of the workshop to summarize
the information presented by the speakers, and to evaluate, as
best they could in a day, the genetic effects of the straying
of hatchery fish into natural populations. Panelists agreed firstly
that one-way gene flow from genetically distinct, non-native fish
into a set of local populations decreases the levels of diversity
among populations. Secondly, such one-way gene flow also accelerates
the loss of both neutral and selectively advantageous genetic
diversity within populations. The loss of diversity within populations
results in the potential for decreased fitness and, hence, reduced
productivity in a short time frame (50 years and less), whereas
the loss of diversity among populations decreases the flexibility
to adapt to changing environmental conditions and, hence, decreases
productivity of local populations in a longer time frame (50+
years). It is relatively easy to identify the demographic parameters
affecting genetic diversity and fitness, and to determine the
general direction of impact from straying as the parameter values
change (Table 1 [below]). However, it is difficult to predict the magnitude
of the overall impact because of our limited ability to quantify
the effects of gene flow, natural selection, and other processes
on natural salmon populations.
Forces that bring about genetic change in populations are mutation,
migration, natural selection, and random genetic drift. Most
of the panel's discussion focused on the relative importance of
genetic drift and natural selection on the fate of genetic variation
introduced by mutation or migration under a variety of population
structures. Particular consideration was given to the effects
of drift and natural selection on adaptive genetic variation in
small populations. Many of the assumptions made in population
genetic models, such as constant population size and discrete
generations, are not met in salmonid populations, and the panel
attempted to outline the consequences that violation of these
assumptions would have on predicting the effects of non-native
straying. Before specific questions about straying are addressed,
the following brief descriptions of processes bringing about genetic
change and demographic factors influencing the type and extent
of change in salmonid populations are outlined.
Table 1. Parameters that influence the genetic effects
that straying of non-native fish has on natural populations.
Values on the right generally result in larger effects on natural
populations.
| Parameter | Values of interest |
| Genetic distance between hatchery and natural populations | Small --------> Large |
| Life-history traits in hatchery and natural populations | Similar --------> Dissimilar |
| Natural selection | Weak ---------> Strong |
| Magnitude of straying | Low -----------> High |
| Duration of straying | Short ----------> Long |
| (1 generation) -- (25 generations) | |
| Natural migration rates | High -----------> Low |
| Natural population size | Large ---------> Small |
| (1,000s) ------ (10s) | |
| Reproductive success of hatchery strays | Low ---------> High |
| Number of populations affected by straying | Few --------> Many |
Natural selection
The strength of natural selection for or against a trait (phenotype)
is measured by the selection coefficient, s, which is the
difference in fitness between the phenotype in question and an
alternative form. Estimates of s for adaptive traits are
between 0.0 and 0.5. However, reported values are most likely
higher than the average value in nature, because the effects of
small selection coefficients are difficult to detect. Moreover,
for traits influenced by many genes, the quantity that affects
the maintenance or loss of alleles at each locus is the strength
of selection on a locus, not the strength of selection on the
expressed trait.
Random genetic drift
Even in the absence of natural selection, not all spawners contribute
equally to the next generation. Moreover, for any given spawner,
both alleles at each locus may not be equally represented in the
next generation, because of the chance segregation of alleles
into gametes and because of the chance union of some gametes over
others. Genetic drift is the random change in allele frequencies
that occurs in finite populations due to the sampling of gametes
between generations. The loss of alleles by genetic drift is
unpredictable, but may be substantial in small populations, in
which even beneficial alleles may be lost due to the effects of
drift. A theoretical measure of the genetically effective population
size is Ne, the size of a hypothetical population of equal
sexes and random variation in family size that experiences the
same amount of random drift as a natural population with census
size N. In salmon, Ne for a population is the effective
number of spawners each year times the generation length (in years).
Stray rate and gene flow
From the perspective of natural populations, the key parameter
for measuring gene flow is the proportion of non-native fish actually
spawning in the receiving local population(s). Only strays (immigrants)
that actually reproduce in a locality result in gene flow into
a local population. The observed number of strays in a local
population is often used to calculate the proportion of immigrants,
m, but stray fish may not reproduce, or may have reduced
reproductive successes relative to local fish. Thus, m
is the genetically effective rate of straying that represents
actual gene flow into a population. The observed proportion of
strays in a local population theoretically provides an upper limit
for estimating m, assuming that strays have, at best, reproductive
success equal to wild fish.
Just as the observed proportion of strays may overestimate the
genetically effective proportion of strays, the census size, N,
of a population typically overestimates the effective population
size, Ne, that determines the genetic consequences of gene
flow into a population. Studies of other organisms indicate that
Ne is usually much less than N, so that Ne/N
is often between 0.33 and 0.10. Since natural gene flow may increase
the effective size of local populations, spawner counts alone
may underestimate the effective sizes of geographically or temporally
defined stocks. Such stocks represent partially isolated local
subpopulations of a much larger metapopulation, and the much larger
Ne of the metapopulation determines the impact of gene
flow on the total population. However, when the Ne of
the immigrant population is small, gene flow can reduce the Ne
of a local population.
Mutation
Mutational rates differ from one part of the genome to another,
and individual mutations vary in their effect on the organism
in which they occur. In large populations, natural selection
will effectively limit the frequency of deleterious alleles through
the elimination of individuals homozygous for them. However,
the impact of individual mutations on an organism are often low,
so that in small populations genetic drift may lead to an accumulation
of deleterious alleles in spite of selection against them.
Heterosis or hybrid vigor
Heterosis is an increase in fitness, primarily in the first (F1) generation after hybridization, that results after mating between individuals from genetically different populations. It can be caused by the masking of deleterious recessive genes in inbred populations, and by balancing selection (heterozygote advantage) at some loci.
Outbreeding and outbreeding depression
Outbreeding is the mating of individuals from genetically divergent
populations. If the genetic differences are great enough, the
result can be a reduction in fitness, termed outbreeding depression.
Two types of outbreeding depression may occur.
Type 1: Reduced hybrid fitness. Mating with individuals possessing
traits that are maladaptive in the local environment will result
in the production of hybrid progeny with reduced fitness in that
environment. This effect will occur in the first (F1) generation
after hybridization and in subsequent generations if any of the
hybrid progeny survive to spawn. However, a reduction in fitness
from Type 1 outbreeding depression may be masked by an increase
in fitness from heterosis, particularly in the F1 generation.
Type 2: Breakup of coadapted gene complexes. Some combinations
of alleles at different loci within a population may function
as a unit, or a coadapted gene complex, to confer a selective
advantage upon individuals. Matings between local and non-native
individuals can lead to the disruption of these gene complexes
and produce a reduction in fitness. Because F1 hybrid progeny
receive one complete set of chromosomes from each parent, gene
complexes generally remain intact until chromosome reassortment
and recombination occurs during reproduction. Thus, Type 2 outbreeding
depression will typically not be apparent until F2 or later generations.
Estimates of effective population size and gene flow can be used
to predict the rate of loss of neutral genetic diversity within
and among populations and, to a lesser degree, the loss in fitness
within populations that can result from particular levels of one-way
gene flow (straying) into these populations. For populations
in which the selection coefficient, s, is less than the
effective stray rate, m, the time in generations for which
the proportion, P, of native genes remains in a local population
is
| tp = lnP/m. | (1) |
For example, the time to a 50% loss of local, neutral genes (P
= 0.5) is
| t0.5 = 0.69/m. | (2) |
With high levels of gene flow, the loss of 50% of alleles can
occur fairly rapidly:
69 generations for m = 0.01 (1.0% gene flow)
25 generations for m = 0.025 (1.5% gene flow)
12 generations for m = 0.05 (5.0% gene flow).
Two important consequences follow from Equation (1): First, as
m increases, the fraction of alleles lost also increases,
and alleles are lost more rapidly. As the fraction of locally
beneficial alleles that can be maintained in the population is
reduced, the frequencies of nonlocal deleterious alleles will
increase. The loss of alleles of adaptive importance at high
values of m leads to reduced average fitness within the
local populations in the short term, if the strays have lower
fitness. Second, the proportion of stray spawners in a natural
population, not simply population size, determines the rate at
which local alleles are replaced by hatchery alleles. However,
at small effective population sizes (Ne << 1,000),
the loss of adaptive genetic diversity will be greatly accelerated
by genetic drift. Deleterious alleles with effects less than
the reciprocal of twice the effective population size (s
< 1/2Ne) will not be eliminated by selection, and beneficial
alleles with effects less 1/2Ne will be lost due to random
drift.
The panelists attempted to predict the magnitude of genetic effects
of non-native strays on local populations that results from altering
the population structure and demographic factors listed in Table
1.
Genetic distance between hatchery and natural populations
In general, measures of genetic distance among salmon populations
are based on biochemical and molecular markers that are assumed
to be largely neutral to selection. Thus, biochemical and molecular
genetic distances may provide better estimates of the time that
populations have been separated, or of the magnitude of gene flow,
than the measurement of adaptive traits subject to natural selection.
However, the longer two populations have been isolated from each
other, the more likely it is that they have diverged genetically,
even for adaptive phenotypes shared by the populations. Similar
phenotypes in two reproductively isolated populations may be due
to convergence in which different genotypes produce the same phenotype
through different genetic mechanisms. Thus, although genetic distance
based on neutral traits may not be a linear indicator of the type
and extent of adaptive differences between populations, the consequences
of straying on adaptive traits are likely to increase with increasing
genetic distance between populations. For neutral alleles, gene
flow from a hatchery population may result in the replacement
of local alleles with non-native alleles regardless of the genetic
distance between the populations (Equation 1). The loss of genetic
diversity within a population will be modified by any population
substructuring (e.g., metapopulation structure), and the loss
of diversity among populations will be determined by the number
of populations receiving strays from the same hatchery stock.
Life-history similarity between the non-native hatchery and
local populations
As indicated above, salmon populations that appear to be phenotypically
similar for adaptive traits may be genetically different. Conversely,
life-history differences between populations may reflect environmental
rather than genetic differentiation. Thus, the level of phenotypic
similarity exhibited by hatchery and local populations is not
a reliable estimator of the amount of outbreeding depression (and
hence loss of productivity) that can follow hybridization. Outbreeding
depression is experimentally difficult to demonstrate because
hybridization and reciprocal translocation experiments over several
generations are required. The type and extent of outbreeding
depression in salmonids is unknown, although it probably does
occur.
Magnitude of straying
Persistent one-way straying at any level will eventually lead
to the loss of effectively neutral genes in a local population
(Equation 1), except when selection against F1 hybrids is absolute.
Even genes under positive selection in a local population will
be replaced if the proportion of effective strays, m, is
greater than the coefficient of selection, s, for local
advantageous alleles. Natural selection, however, is expected
to maintain genes with high fitnesses in local populations in
spite of immigration, except when population sizes are very small.
There are few reliable estimates of selection coefficients associated
with alleles producing adaptive phenotypes in salmonid populations.
The number of genes influencing the variability of a morphological
or life-history trait is generally unknown, so the selective value
of the trait itself provides an upper limit to the selective value
of any one locus influencing the trait. Traits may be selectively
advantageous at one life-history stage in one set of environmental
circumstances, and selectively disadvantageous at another life-history
stage or in another set of environmental circumstances. Thus,
the differential in fitness between alternative phenotypes must
be evaluated over the salmonid life cycle, and even then may vary
over time depending on environmental conditions. It is experimentally
more difficult to detect small selection coefficients than large
ones, and difficult to measure the adaptive value of a trait over
time. Thus, published selection coefficients are higher, on average,
than values for most adaptive alleles, which likely have selection
coefficients of less than 0.05 (5%). Such alleles would be lost
from local populations experiencing consistent levels of gene
flow of 5% and higher.
Reproductive success of hatchery strays
The reproductive success of hatchery strays is one factor that
affects the magnitude of gene flow resulting from straying, as
discussed above. If the reproductive successes of strays are
low, the effective stray rate, m, and the rate of replacement
of local genes are lower than would be estimated by simply calculating
the proportion of strays in the local population. However, implications
for the genetic diversity and productivity of local populations
differ if selection operates on the migrants themselves rather
than on their hybrid progeny. If hatchery migrants fail to compete
for mates and do not otherwise disrupt normal spawning in the
local population, the rate of introgression will be low, and productivity
of the local population may be little affected. However, if migrants
hybridize extensively with local fish but fail to produce viable
progeny, much of the local, as well as the non-native, contribution
to the next generation may be lost by selection against hybrid
progeny. Thus, at high rates of immigration and hybridization,
losses in productivity and genetic diversity in local populations
may be substantial even if the reproductive success of hatchery
migrants, as measured by surviving progeny, is low.
Duration of hatchery straying
The proportion of effectively neutral native alleles lost in a
local population as a result of continuous one-way straying by
non-native fish increases asymptotically with time (Equation 1).
Long-term straying will lead to the replacement of local alleles
with non-native alleles at effectively neutral loci (s
< m). If migration from a hatchery population occurs
for a short period of time (1-2 generations), or occurs only sporadically,
natural selection may eliminate much of the hatchery contribution
to the local population. Outbreeding depression resulting from
this selection may be concentrated in the first generation after
hybridization or may occur over several generations, depending
on the nature of the outbreeding depression.
Local population size and structure
The proportion of migrant genes that are incorportated into the
local population, not the absolute size of the local population
alone, determines the effect of gene flow on the genetic composition
of the local population. Populations with an Ne of 1,000
or more tend to act like populations of infinite size, so that
little genetic diversity is lost through random drift. However,
even in these large populations, the replacement of local alleles
with hatchery alleles will proceed through gene flow (Equation
1).
There are few estimates of effective population size, Ne,
for salmon populations. Many populations are currently of such
small size that if Ne were only one-third to one-tenth
the number of spawners, even summing numbers of spawners over
the generation time yields estimates of Ne less than 50.
This indicates that as few as 1 or 2 migrants spawning in the
populations each year would have a large impact within 10 generations.
While many salmonid populations are at historical low levels
of abundance, some species (e.g., rainbow trout, steelhead, coho
salmon) appear to have persisted in small populations over time
without obvious signs of inbreeding depression. Salmonids may
therefore form metapopulations consisting of small, partially
isolated subpopulations with some natural level of reproductively
effective straying between them. Straying may not be continuous
or symmetrical among subpopulations and may occur only when triggered
by particular environmental or demographic conditions.
Metapopulation structure can affect the rate of introgression
of hatchery alleles into local subpopulations in two ways. First,
the Ne of importance in determining what proportion of
the population hatchery spawners represent is the Ne of
the entire metapopulation. If hatchery strays enter only one
or a few local subpopulations, they constitute a much smaller
proportion of the metapopulation than the local populations to
which they strayed. Second, if hatchery strays spawn in only
a few of the local subpopulations, hatchery alleles replace local
alleles in those subpopulations at a slow rate because strays
from other subpopulations replenish native genes. The flow of
hatchery alleles into subpopulations not directly receiving strays
would also occur, but might be greatly slowed if natural straying
between the subpopulations followed a stepping-stone model of
migration.
Number of populations affected
Genetic differentiation among populations can decrease, if non-native
fish stray into several local populations. This is true whether
the populations are isolated from one another or whether they
are subunits of a larger metapopulation. When hatchery straying
occurs, hatchery alleles ultimately enter all the subpopulations
of a metapopulation, but the replacement of local alleles is slower
in subpopulations not directly receiving hatchery migrants. Therefore,
local adaptations shared among subpopulations are less likely
to be lost from the metapopulation as a whole if straying occurs
into only one or a few local populations.
Salmon have evolved so that genetic differences, both neutral
and adaptive, exist between populations in the presence of natural
levels of gene flow. However, we do not know which of the following
is the reason that observed population structure is maintained:
Without knowing whether salmon populations, finely tuned to their
environments, are structured to withstand high levels of gene
flow, or whether the natural level of gene flow is low, it is
difficult to predict the consequences of increased amounts of
straying from genetically dissimilar populations. If the reproductive
success of strays is low, the direct genetic consequences of increased
straying from non-native populations may be relatively small,
although indirect effects may still be important. On the other
hand, natural strays may be generally reproductively successful
but would not destroy population structure, either because they
are from nearby genetically similar populations or because straying
is sporadic. Under these circumstances, hatchery strays, which
are genetically dissimilar to natural populations and which are
genetically or environmentally predisposed to straying, will have
a greater detrimental effect on both the diversity and the fitness
of a natural population.
The expected loss of genetic diversity from gene flow is based
on populations that behave as if they were infinite, with effective
sizes greater than 1,000 fish. The replacement of local genes
by non-native genes for neutral traits follows the predictions
of Equation 1, on average, and genes with selective coefficients
greater than the immigration rate will be replaced. The suggestion
that large populations, because of their size, can withstand the
loss of productivity from outbreeding depression is based on the
assumption that local populations are currently well adapted to
their environments and are currently productive enough to seed
the environment to carrying capacity even with diminished fry
or smolt production, or both. However, the assumptions of well-adapted
populations and productivity may not be true for many populations.
Human activity and natural events have changed the habitats of
many salmon populations so rapidly in recent decades that populations
may not be as well adapted to their environments as was historically
the case. Salmon populations have already experienced a loss
of productivity, because of natural selection against some genotypes
that occur naturally at high frequencies in the population. Heavily
exploited populations may, at least in some years, possess fewer
spawners than necessary to produce optimal numbers of juvenile
fish. Current populations of salmon may not be able to maintain
adequate levels of fitness, because they are smaller than they
were historically, and because of rapidly changing environmental
conditions. Gene flow from non-native fish is an additional challenge
which will affect the ability of salmon to adapt to future changes
and which can greatly decrease productivity.
What are the appropriate parameters to consider in evaluating
the effects of straying?
Forces that bring about genetic change in populations are migration,
mutation, natural selection, and random genetic drift. Mutation
rates are typically low for most genes, and mutation was not considered
in detail for the time frame of interest (< 100 years) (but
see Lynch (in press) for more discussion of the role of mutation).
Most of the discussion focused on the relative importance of
drift migration, as well as selection under a variety of scenarios.
Brief descriptions of some key terms and parameters follow.
What other parameters are important in determining the genetic
effects of straying?
Several other parameters also help to determine the genetic consequences
of straying (see Table 1). Some of these are described below.
Do short- and long-term effects of straying differ?
Yes. A short-term infusion of non-native alleles may lead either
to heterosis (increased fitness) or to outbreeding depression
(decreased fitness), or both, in local populations. Although
outbreeding depression and associated reduced productivity might
persist in local populations for several generations after the
straying occurred, selection against deleterious non-native alleles
could result in the retention of primarily local genetic information.
In contrast, long-term straying will eventually replace neutral
genes and those with small adaptive effects (s < m).
In small populations, the loss of genes with greater adaptive
value will be accelerated by genetic drift.
Are the effects of hatchery straying likely to be permanent?
Yes. The changes in genetic structure of local populations resulting
from straying are likely to be permanent. If straying stops,
local populations may recover lost fitness over time through mutation,
but the original genetic composition of the population will not
be restored.
Can hatchery straying be beneficial for natural populations?
Theoretically, short-term straying can be beneficial under certain
circumstances. The initial introduction of non-native alleles
will generally increase genetic diversity in local populations.
In well-adapted populations, this may cause a loss of adaptive
fitness. However, in small populations experiencing inbreeding
depression, the introduction of non-native alleles may mask effects
of deleterious recessive genes and act to increase fitness.
Is there any safe level of hatchery straying that is consistent
with the conservation of natural populations?
There are no "safe" levels of hatchery straying. Any
level of long-term straying will change the structure of local
populations. For neutral genes and genes with small adaptive
effects, persistent straying at any level will lead to replacement
of local alleles. Local alleles with adaptive values greater
than migration (s > m) will be maintained, but
selection against maladaptive non-native alleles will lead to
reductions in productivity.
Can the effects of hatchery straying be predicted with any
certainty?
To the extent that straying leads to one-way gene flow, initial
changes in allele frequencies are predictable, as discussed above.
However, the amount of gene flow resulting from a given level
of straying is seldom known, and it is likely highly variable.
Moreover, the fitness consequences of altered allele frequencies
depend on the adaptive differences between local and non-native
populations, which are seldom known. As a result, the effects
of straying on average fitness in a local population, and on the
long-term ability of a population to persist, are not predictable.
Experimentation and long-term monitoring may be required to determine
the effects of non-native gene flow into local populations. Both
increased fitness from heterosis and decreased fitness from outbreeding
depression may occur. Short-term monitoring of the effects of
hatchery introgression may be overly optimistic because outbreeding
depression may not occur until the second and succeeding generations
after hybridization.
What will occur with straying at the 5% level?
As noted in the previous question, the genetic effects of straying
at any given level cannot reliably be predicted, but some of the
effects of gene flow are predictable. Based on estimates of gene
flow from allozyme frequencies in natural populations, a value
of 5% gene flow is much higher than that generally occurring between
non-local salmon populations. Also based on what is known about
the strength of selection in other animals, this amount of gene
flow would quickly lead to the replacement not only of neutral
genes, but also of locally adapted ones. Most genes in natural
populations probably have selection coefficients less than 5%
and would thus be subject to loss if gene flow occurred at this
level. The panel found no genetic justification for allowing
gene flow from non-native fish at levels as high as 5%.
What research should be undertaken to help resolve uncertainties
of hatchery straying?
The following topics were identified as particularly important
for research:
Lynch, M. In press. Genetic risks of extinction for Pacific salmon. In: A. D. MacCall and T. C. Wainwright (editors), Assessing extinction risk for West Coast salmonids: Proceedings of the workshop. U.S. Dep. Commer., NOAA Tech. Memo.