LESSON 8: Genetic issues in fisheries
management
Using the tools so far learnt one can
address at least 3 major issues:
• Intentional and unintentional alterations of
the genetic makeup of hatchery stocks
• Inadvertent effects of management and
exploitation on the genetics of wild stocks
• Accidental or purposeful release of
transgenic fish into natural waters and their
possible effects on wild populations
Genetics and fitness of hatchery stocks
Mating techniques, intentional and
inadvertent selection, domestication, and
inbreeding all affect the genetics and
fitness of fish.
In general, hatchery managers should try
to maintain genetic variation in breeding
populations while producing fish that are
suitable for their intended use.
Hatchery bred fish may be stocked in an
aquacultural facility for food production, in
a natural environment, or in some captive
setting as broodstock.
The reproductive fitness of fish destined for
slaughter is not important; in fact,
reproduction is often undesirable.
o In contrast, the fitness of fish used as
broodstock or for stocking in natural
environments is of paramount
importance because the fitness of
future generations depends upon their
genetic characteristics.
Principal hatchery concerns are:
1) Hatchery practices may detrimentally
alter survival, yield or reproduction,
and,
2) Small effective population sizes in
hatcheries can lead to inbreeding and
loss of genetic diversity.
Principal factors affecting inbreeding and
effective size of hatchery populations are:
1) Number of breeding individuals in the
population,
2) Sex ratio,
3) Variation in the reproductive success
of individual spawners, and
4) Effective population size during
previous generations.
Unintentional inbreeding, which occurs in
all populations of finite size, is an important
concern in hatchery management.
Inbreeding results in loss of genetic
diversity (loss of alleles) and increased
homozygosity, leading potentially to
inbreeding depression.
o The rate of inbreeding in a population is
inversely related to the effective size of
the population; i.e., it is low in large
populations and high in small
populations.
o Inbreeding is cumulative because it
increases from one generation to the
next.
Population size
In an idealized population, numbers of
individuals, i.e., one that is infinitely large,
random variation in reproductive success,
non-overlapping generations, and balanced
sex ratio, the effective size is simply the
number of individuals in the population.
In real populations the effective size is
almost always less than the number of
individuals in the population.
o The first requirement, therefore, for the
reduction of inbreeding in hatcheries is
the capability to hold large numbers of
spawners.
There is no guarantee that
inbreeding will be minimized in
large populations because the
effective population size also
depends on other factors like sex
ratios and variation in reproductive
success.
Sex ratio
Consider a population with Nm males and
Nf females in which the number of males
does not necessarily equal the number of
females.
The effective population size and the rate
of inbreeding are given approximately by:
o Ne = 4 Nm Nf / (Nm + Nf )
o ∆F = 1/ (2Ne ) = 1 / (8Nm) + 1 / (8Nf )
Note that Ne = N and ∆F = 1/ (2N) when
the sex ratio is balanced (Nm = Nf ).
o An unfortunate consequence of these
relationships is that unbalanced sex
ratios have large effects on Ne and ∆F.
o Consider two hatchery populations of
50 individuals. In the first population
(with equal numbers of males and
females) the effective population size
and rate of inbreeding for the
population are 50 and 1percent,
respectively;
In the second population (with 40
females and 10 males) the
effective size and rate of
inbreeding for the population are
32 and 1.6%, respectively.
o The unbalanced sex ratio reduced the
effective population size by 36 percent
and increased the rate of inbreeding
by 60%.
Variation in reproductive success
Non-random variation among individuals in
reproductive success can be due to
differences in fecundity, fertility, and
longevity (fish that live longer have more
opportunities to reproduce), variable
conditions or disturbances on the spawning
grounds, and accidents in the hatchery
(e.g., fungus infections).
The effective population size accounting for
variation in family size (Vk) is given
(approximately) by:
o Ne = 4N / (Vk + 2)
o In an ideal population with random
variation in family size, Vk = 2, and
therefore Ne = N.
In real populations a few successful
individuals may produce numerous
offspring whereas many produce few or
none.
o This increases Vk , which decreases
the ratio Ne /N.
Falconer and MacKay (1996) state that
differences in reproductive success in real
populations are “the most important cause
of Ne being less than N.”
Temporal variability in effective
population size
Inbreeding and loss of genetic diversity
accumulate with each new generation so
that the degree to which a population is
inbred depends on the effective population
size during each of the previous
generations.
It is important to consider how temporary
reductions in the effective population size
(population bottlenecks) affect the loss of
genetic diversity in the long-term.
The mean effective population size of a
population over a period of n generations
can be calculated (approximately) as the
harmonic mean of the effective population
sizes during each of the generations:
1 / Ne = (1 / N1 + 1 / N2 + … + 1 / Nn
)/n
The mean rate of inbreeding can be
obtained from Ne in the usual way.
It is important to realize that population
bottlenecks (small values of Ni ) have large
effects on Ne , inbreeding, and the loss of
genetic diversity.
o Consider a population with the following
effective population sizes during ten
consecutive generations: 100, 50, 10, 50,
100, 100, 100, 100, 100, 100.
o The mean effective size and mean rate of
inbreeding are 47.6 and 1%, respectively.
With no three-year population
bottleneck, the effective size and
mean rate of inbreeding would have
been 100 and 0.5%, respectively.
A population bottleneck that lasted
only three generations reduced the
mean effective size by 54% and
doubled the mean rate of inbreeding.
Recommendations for effective size of
hatchery populations
The effective size of hatchery populations
should be as large as possible in order to
minimize loss of genetic diversity.
Recommended values for Ne reflect
compromises involving the value of the
genetic diversity in a population (which is
very difficult to measure), the rate at which
genetic diversity is lost and the costs of
raising fish and managing a hatchery.
Recommendations for the minimum
effective population size of hatchery
populations vary tremendously.
o The Ne is said to ranging from 60 to
200 for a fisheries stock.
This variation results from uncertainty
about the minimum amount of genetic
variation required for populations to persist
in unpredictable natural environments.
Domestic animals seem to tolerate
inbreeding at the rate of about one percent
per generation (equivalent to Ne = 50)
without showing inbreeding depression.
The figure Ne = 50 is thus a lower bound
on the acceptable values of Ne for
populations used in aquaculture.
o Acceptable values for hatchery
populations used in stocking programs
are higher.
o Kincaid (1983), for example, suggests
that the effective size of a breeding
population should be at least 100
(equivalent to ∆F = 0.5%) and
Allendorf and Ryman (1987)
recommended a minimum of 200.
In the conservation genetics, a minimum
Ne of 500 is recommended for conserving
long-term evolutionary potential (Franklin
1980) and even higher minimums of a few
thousand have been suggested.
Therefor considering this uncertainty, an
Ne of 100 – 200 should be regarded as a
minimum acceptable range for hatchery
populations that are used for enhancement
of wild stocks.
For restoration of severely depleted
populations, this number will not always be
achievable.
o Studies however have shown that
problems associated with small
populations can be reduced if restoration
is successful and the population rapidly
increases in size.
As we have seen, the effective size of a
population is often less than the number of
fish in the spawning population.
o How many fish are required to insure
that the effective size of a population is at
least some specified value?
o The answer is not simple and will depend
on the sex ratio of the stock, the breeding
technique used, the means by which
spawners are selected, etc.
o When the sex ratio is balanced and all
spawners enjoy equal reproductive
success, fewer fish will be required to
obtain a given value of effective
population size.
o In a hatchery it may be possible to
maximize Ne by equalizing family size. (Vk
= 0) resulting in an Ne that is almost
twice as large as N.
Note that family size is measured as
the number of offspring that reach
maturity and reproduce.
Equalizing family size, therefore,
requires a means of tracking family
membership until maturity (e.g.,
separate rearing, physical tags, or
genetic markers).
As a matter of practicality, some
hatchery programs have equalized
family size at an earlier life stage (e.g.,
eyed-eggs) to reduce the variance in
family size attributable to fecundity
and fertility differences.
Other hatchery practices can be used
to directly reduce inbreeding.
One approach is to employ a line
crossing scheme such as rotational line
crossing (Kincaid 1977) that minimizes
matings between related individuals.
o In special cases involving captive
broodstock for restoration of critically
small populations, geneticists have used
molecular genetic markers to pedigree
fish to avoid mating close relatives.
Mating techniques
The rate at which genetic diversity is lost in
a hatchery program due to inbreeding and
genetic drift depends partly on how the fish
are mated.
For a fixed number of breeders, effective
population size is maximized (inbreeding
and genetic drift are minimized) when
there are equal numbers of males and
females and all breeders contribute equal
numbers of progeny to the next generation.
Miller and Kapuscinski (2003) provide
guidelines for mating schemes.
o A baseline for making crosses is by pairs
of a single male and a single female.
In some situations, unequal numbers of
each sex will be available and the
potential for gamete inviability should
be taken into account.
If one sex is in excess, divide gametes
from individuals of the less numerous
sex to allow crosses with all of the
excess sex.
Sperm from a single male is preferred
for each cross because the alternative
of using pooled sperm may cause
unequal contribution of gametes from
some males due to differences in
potency of their sperm.
An exception is when it is suspected
that many males are infertile.
In this case, pool sperm from
overlapping pairs of males and use
each pooled pair to fertilize eggs of
one female.
Pooling pairs of males will reduce the
incidence of unsuccessful fertilization
because at least one of the pair is
likely to be fertile.
The degree of sperm potency
differences versus numbers of
completely infertile males will
determine whether or not overlapping
males is advantageous.
o Another scheme used to increase
genotypic diversity and Ne is factorial
matings.
Factorial matings involve dividing
gametes from several individuals and
making all possible crosses between
males and females.
Factorial matings increase diversity by
creating more genotype combinations
and may increase Ne by reducing
extremes in reproductive success
Selection
Artificial selection is useful for improving
broodstocks in captive aquaculture and is
usually intentional and desirable.
o Conversely, artificial selection of hatchery
fish destined for stocking in natural
environments may be unintentional and
raises concerns.
Artificially selecting hatchery populations
that supply a stocking program may
improve hatchery performance at the
expense of the fitness of fish released in
natural environments.
Domestication selection is any change in
the selection regime of a cultured
population relative to that experienced by
the natural population.
o The end result is that the genetic
composition of a hatchery population will
likely differ from that of its wild source.
Domestication may be desirable in fish that
are used for aquaculture but it is almost
certainly undesirable in fish destined for
stocking in the wild.
A premise of our application of genetic
principles to hatchery management is that
natural selection can best produce
distributions of genetically determined
traits and that any significant alterations of
these distributions should reduce a
population’s fitness in the wild.
Domestication selection can take one of
several forms.
o The most obvious is intentional selection
on traits such as size or run timing.
o In addition to directly changing a selected
trait, intentional selection may adversely
affect other correlated traits, particularly
those traits that are fitness related.
o Improperly designed selection programs
also reduce effective population size and
encourage inbreeding and loss of genetic
diversity.
Inadvertent selection is unintentional
artificial selection in hatcheries resulting
from two causes.
The first cause is non-random collection of
broodstock.
o It is different from intentional selection
because there is no purposeful selection
on a trait.
For example, gametes may be collected
as soon as a spawning period begins
and end when sufficient numbers are
taken.
The parents have been unintentionally
selected for early spawning time, a trait
known to have a genetic component in
some fish species.
Inadvertent selection may occur if the
average size, age, or spawning locations
of the spawners used in hatcheries are
different from the averages for the
entire population.
The second cause of inadvertent
selection is the unintentional selection
that occurs in the hatchery
environment.
For example, changes in agonistic
behaviour due to crowding, rearing
conditions, or feeding methods.
The final form of domestication
selection is the relaxation of natural
selection in the hatchery environment.
Fish that would have been selected
against in the wild may survive in the
hatchery and pass on their genes that
are maladaptive in the natural
environment.
Domestication selection can be reduced,
although not entirely avoided, by collecting
large, random samples of broodstock,
minimizing hatchery mortalities, collecting
broodstock from the wild, and minimizing
the time fish are held before stocking.
o However, that even these efforts might
not prevent loss of fitness in the wild.
Importantly, he found that the effect of
domestication on the fitness of hatchery
fish in the wild is sensitive to the carrying
capacity of the environment and the
population growth rate it can support.
o It is therefore important to first
restore or maintain good habitats
before considering population
supplementation by stocking.
Impacts on the genetics of wild stocks
Stocking
It is possible that the fitness of stocked fish
will be less than the fitness of the wild
population residing at a particular location.
o This is especially true for stock transfers
but may also be true when stocking
hatchery reared fish derived from the
local population.
Stocked fish could affect the fitness and
long-term adaptability of the population.
Stocked fish could directly affect the
genetics of native populations through
hybridization, resulting in loss of
between population genetic diversity
and outbreeding depression. Stocked
fish also could impose indirect genetic
effects by reducing or fragmenting
populations.
These indirect effects could be induced
through increased harvest, introduced
diseases, or range reductions due to
displacement of native fish.
Recommendations
Whenever possible, manage wild
populations so that stocking is unnecessary.
When stocking is necessary, try to stock fish
that are well adapted to the local
environment.
The best way to improve the chances that
stocked fish will have high fitness in a
particular environment is to choose a
source stock following three similarity
criteria:
o Similarity in genetic lineage, which for
the case of hatchery fish, is best assured
by using the wild population as the
source for broodstock. If this is not
practical, then broodstock should be
obtained with similar life histories.
o Similarity in life history patterns partly
reflects similarity in genetic makeup for
these evolutionarily important traits and
increase the chances that life history
patterns of stocked fish will be adaptive
in the new environment.
o Similarity in ecology of the originating
environment.
A similar originating environment
is indicative of similarity of
evolutionary history and increases
the chances that the source
population will be adaptive in the
environment targeted for stocking.
A number of other methods can be used to
help insure that stocked fish have high
fitness.
o Broodstock should be obtained by
sampling randomly from spawners in a
wild population in order to avoid
inadvertent selection for body size,
spawning time, etc.
o Mating schemes and hatchery
management should aim to maximize
effective population size.
o The hatchery rearing period for
broodstock and production stock should
be minimized because consequences of
hatchery culture (i.e., domestication,
inadvertent selection and inbreeding)
accumulate with time.
o Finally, fish should be stocked at a size,
time, and place so that they are similar to
wild fish and integrate with wild fish
rather than displace them.
Harvest management
Harvest management affects the genetics of
wild fish stocks in at least two ways.
o First, high exploitation rates reduce the
effective size of a stock so that the rates
of genetic drift and inbreeding are
increased.
o Second, fishing methods that “select”
individual fish for harvest on the basis
of some characteristic (e.g., size
selectivity in a gillnet fishery) amount to
artificial selection programs that can
cause genetic changes in the stock over
time.
Loss of genetic variation is recognized in
the conservation as a problem that could
reduce population fitness.
Harvest and alteration of spawning habitats
may directly reduce population size, thus
reducing the effective population size
(which is inversely related to the rate of
loss of genetic variation).
Harvest and habitat alteration may also
alter demographic factors (sex ratio and
variance in family size) that reduce the
ratio of effective to census population size.
Because growth rates can differ between
the sexes, size regulations or angler
selection may preferentially target one sex,
thus skewing the sex ratio.
Disturbances on spawning grounds may
destroy the offspring of entire families and
increase the variance in reproductive
success among adults in the population.
Although many plausible scenarios can be
described that would result in genetic
losses, declines in the productivity of wild
populations from inbreeding and loss of
alleles due to genetic drift have not been
documented in fish species suggests that
this is due in part to the lack of relevant
data and confounding effects of other
factors of decline.
Unintentional selection
Many fisheries amount to artificial
selection programs that act on fitness
related traits or traits genetically
correlated with fitness.
Fish taken by a fishery are seldom a
random sample from the population
because fishing techniques and gear
select individuals with certain
characteristics.
o Consequently, fish that live to spawn
will be different, on average, than fish
in the population before exploitation.
o If the differences are heritable, then
the next generation will be genetically
and phenotypically different from the
previous generation.
o This process can occur in every
generation until substantial changes
have occurred in the population.
It is possible that inadvertent artificial
selection will produce a stock of fish with
inferior commercial value or reduced
fitness.
Growth rate is a heritable characteristic
and reduced growth rates have been
observed in several stocks following
exploitation.
Traits genetically correlated with growth
rate, such as average age at sexual
maturity, may also change in response to
selection by the fishery.
Inadvertent selection is not limited to
commercial fisheries.
Habitat alteration
Changes in the environment can affect the
genetics of wild populations in two familiar
ways:
1) By depressing the effective size of the
population, which causes a loss of
genetic diversity; and
2) By natural selection for increased
fitness in the new environment, which
may decrease the value of the resource.
Depression of effective population size
(leading to increased inbreeding, increased
genetic drift, and loss of genetic diversity)
is a certain consequence of environmental
changes that reduce habitat size (e.g.,
obstruction of spawning streams), kill fish
(e.g., pollution), or limit reproductive
success (e.g., acid rain).
Population fitness may be reduced by a
major change in habitat because
characteristics that maximize fitness in the
old environment may not maximize fitness
in the new environment.
Selection that increases fitness in the new
environment is a natural and constructive
response of the population to an
environmental change.
A number of related consequences,
however, should be kept in mind. Fish
adapted to the new environment (e.g.,
tolerant of polluted water) may not be
desirable for human consumption.
Productivity of the population may remain
low even after the population adapts to the
new environment.
Many generations might elapse before the
population adapts to the new environment
because the response to natural selection
may be slow (although examples of rapid
evolution in fish populations are being
found.
The population may never adapt if the
environment continues to change.
Environmental effects of transgenic fish
The ongoing development of transgenic
fish and shellfish raises the need to assess
and manage environmental risks imposed
by intentional introductions and
unintended escapes of transgenic fish into
natural waters.
This should involve a case-by-case
consideration of the production system
(aquaculture or otherwise) in which the
fish would be used and characteristics of
the transgenic fish line and potentially
affected ecosystems.
Most transgenic fish have been developed
for aquaculture and many aquaculture
systems are extremely vulnerable to
accidental releases into the natural
environment (e.g., damage to ocean net
pens, flooding of outdoor ponds).
Each line of transgenic fishshould be
assessed for how transgenic escapees
might affect wild fish and other organisms
through gene flow and ecological
interactions.
o It is a challenge to prospectively
assess these effects before transgenic
fish enter a natural ecosystem.
o Therefore, efforts are underway to
develop and validate environmental
risk assessment and management
methodologies that integrate confined
experiments on transgenic fish and
data on potentially affected
ecosystems.
Gene flow from transgenic individuals to
wild relatives
Gene flow from transgenic individuals to
wild relatives is a major process through
which transgenic fish may affect wild fish
populations.
The main concern is whether gene flow
results in introgression (incorporation) of
the transgenic genotype into the gene
pool of wild relatives.
Predicting the fate of transgenes requires
data, obtained from well-confined
experiments, on how the transgenic
genotype affects the net fitness of the
fish, as well as evidence of how the
genetic background of the fish population
and genotype-environment interactions
might alter this net fitness (Kapuscinski et
al. 2007-a).
Also required are specific baseline data
about the wild relatives, such as
population genetic structure and spatial
distribution of breeding adults.
Application of a ‘net fitness’ method,
involving aquarium experiments and
computer simulations, has suggested
three potential scenarios of gene flow.
o In a purging scenario, the net fitness
of a transgenic fish is much lower than
that of its wild relatives and natural
selection purges any transgenes
inherited by wild relatives.
This is the most benign outcome
but not completely risk free
because purging is not
instantaneous and may take a
number of generations.
If the affected wild population is
already in decline, inheritance of
maladaptive transgenes in some
individuals could increase the loss
of genetic variation and risk of
extinction.
o In a spread scenario, introgression of
transgenes could result in altered
frequencies of native alleles, loss of
genetic distinctiveness, and loss of
genetic variation in the affected wild
population.
These genetic changes can
undermine current adaptation of
wild populations to their
environment and their ability to
adapt to future environmental
change. In the worst-case
scenario, transgene spread under
very specific conditions would
trigger a population crash
(Howard et al. 2004).
Such predictions based on net
fitness models need to be validated
using more complete data about
the transgenic fish line, wild
populations, and particular
ecosystem.
Ecological effects
Transgenic fish may have ecological
effects beyond their possible effects on
the genetics of wild populations.
Ecological effects are even possible when
there is no gene flow and introgression of
transgenes into wild populations.
Consider, for example, a line of
goldfish with antifreeze protein
transgenes giving them increased
cold tolerance.
o Large-scale aquaculture of these
fish would raise the possibility
that they could invade a broader
range