Module 4

Genetic Models and Genetic Diversity

At the end of this module you are expected to:
1. Understand the principles of genetic models and genetic diversity;
2. Appreciate the role of environment on the expression of a phenotype;
3. Recognize the importance of genetic diversity relative to animal breeding in order
to prevent occurrence of inbreeding depressions.

Genetic Models

Even though for some animal species the full genome has been mapped, we still cannot
“see” which in a population of animals would be the genetically superior ones. We cannot
read the working of the DNA in full detail yet. So instead we need to make an estimate of
the genetic potential of the animal based on its phenotype.

For example, is a cow that produces an average of 25 kg per day in her lactation indeed
a genetically better cow than a cow that produces 15 kg per day? Is a horse that always
has high scores in a dressage test indeed a genetically better horse than the one that
scores much lower? And why is the full sister of that excellent hunting dog not also
performing at top level with that same trainer?

Phenotype and environment during life history

Generally, not all variation in observed phenotypes is a result of differences in genetic

makeup between animals. Part of it is determined by variation in what we call the
environment.

Often the environment has a

very important influence on
the animal’s phenotype. An
impression of what type of
influence the environment
has in the phenotype is given
in figure. The figure
represents the life span of an
animal, indicated by the
green arrow. The vertical
bars in the arrow represent
important events in life that
indicate the start of a new
phase in the life history of the
animals.

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A. Events before birth
● The life history of an animal starts with the fusion of an oocyte and a
spermatozoid: the conception. What happened to these two before
conception has an influence on their quality, and thus with the start-up
conditions of the animal.
● The next important phase is that of development through embryonic and
fetal phase to the birth of the animal.
o In mammals, this phase occurs in the uterus and the mother has
more or less continuous influence, in egg laying species it occurs
in the egg and the mother’s influence mainly lays in the composition
of the yolk and white components.
o During its time until birth, the animal encounters certain so-called
windows of development: periods during which certain parts
should develop.
o These windows often have a fixed time-frame. That means that
the development has to take place during that time-frame. After the
window closes again, development in that aspect is no longer
possible.
o The development will depend on the genetics of the animal, but
also on the environment. If that is not sufficient, the development
will be sub-optimal.

B. Events after birth

● After birth or hatch, the influence of the mother continues, provided the
offspring is allowed to be with the mother.
● However, the influence of the environment prior to birth is still present.
● So, if there was shortage of something in the uterus or egg, then the
development will have adjusted accordingly.
● After birth there may be compensatory growth, but if the organs were not
optimally developed then that is a given fact that cannot be corrected
anymore.
● The development continues after birth, also with a number of windows of
development.
o Post-birth development does not only involve development of the
physical part of the animal, but also of the emotional part.
o Many components of the character are developed during the
first few weeks after birth.
o A sub-optimal early environment can have irreversible influence on
the emotional development of the animal.
o Until weaning the environment of the animal is influenced by the
maternal care, including food provision, but also by the other
members of the environment, for example litter mates.

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C. Events after weaning
● After weaning, the irreversible part of the influence of the early environment
on the development of the animal remains.
● On top of that, the current environment of the individual animal will have its
influence.
o For example, whether there is food and water and of what quality,
what type of housing, how other animals influence its development,
etc.
● The development of the animal continues until it has finished growing.
● This may be after it has matured in the sense of after the start of its
reproductive life.
● The first estrus or fertile sperm production, and sometimes the birth of the
first offspring, occur before the animal has finished growing.
● Therefore, the term maturity is a bit misleading in the figure. It often
represents the age at first reproduction, but in this case, it represents the
end of the animal’s development.

D. Events after maturity

● After maturity there is the rest of the animal’s life.
● It will depend on the environmental quality how that will influence the
animal’s phenotype.
● However, the animal has finished development so many of the
environmental influences will be reversible.
● It may start its reproductive life and create its own influences on its offspring.
● And because it was influenced by its parents itself, you can imagine that
those influences may still be of influence on the development of the animal’s
offspring.
● In fact, these influences of the parents of the animal of the development of
its offspring would be trans generational effects.
● This is a relatively new area of research and not a lot is known about the
importance of trans generational effects.
o An example is that of food deprivation of the mother of the animal
during pregnancy or before laying the egg. This will have influenced
the development of the animal. And because the development was
influenced, this in turn may influence the development of its
offspring.
o For example, if the growth of the animal was restricted and it
remained small as adult, this will have influenced the size of the
uterus as well, and thus the environment of its developing offspring.

E. Events after reproductive phase

● After the reproductive phase, some domestic animals are allowed to retire.
● Also, with its own environmental influences on top of its past experiences
during life. In nature animals usually do not retire but die before they reach
that age.

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 ● Farm animals are usually culled even before the end of the reproductive
period.
● Note that environmental influences early in life may influence the phenotype
later in life.
● However, not ALL early influences have a lasting effect. Some of the
influences will be reversible or of insignificant influence.

Phenotype in a model

● As we have seen, anything that has happened during the life history of the animal
may have an influence on the current phenotype.
o For example, if you measure the height of an animal, then that is its
phenotype. Genetics will play a role in the height because if the genes
determine that the animals will stay small, it can eat as much as it likes but
it will never grow big: the genetic makeup sets the boundary.
o However, if that same animal does not get fed properly, or gets ill, or lives
in a very cold climate, or his mother was ill when she was pregnant of the
animal, the animal will not even reach that boundary and stay smaller than
an animal of the same genetic makeup that had the best circumstances for
growth.
● These environmental influences are not always easy to pinpoint because they start
so early (oocyte and sperm experience environmental influences as well), but also
because it is not always clear what is of influence and what not.

The environment can be defined as anything that influences the animal’s performance
that is not related to the genetic makeup of the animal, starting at the earliest possible
moment in life, even before conception.

● Basic Model for the expression of a Phenotype

P=G+E

These symbols P and G and E are important to remember as they are very
commonly used to describe phenotype, genotype, and environment.

Monogenic genetic variation

Genetic differences
between animals are
a result of
differences in their
DNA. If a trait is
determined by only a
single gene, such as
for example in the
case of having horns

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in cattle or not, then the phenotype depends on the combination of alleles for that single
gene.

Having horns only occurs in case of homozygosity for the recessive allele h. Being polled
(having no horns) is a dominant trait, so both Hh and HH animals are polled, and only hh
cattle have horns. Especially in dairy cattle the calves are de-horned when they are still
very young. However, also in the Holstein-Friesian some animals are naturally polled
because they carry the H-allele.

Some aspects of coat color are also determined by only a single gene with two alleles.
But that may result in more phenotypic variation than in the example of having horns or
not in cattle. In chestnut horse, for example, horses with no dilution factor (DD) are
chestnut (brown coat and brown mane and tail). But if they have a single dilution allele
(Dd) they are palomino (lighter manes and tail, slightly lighter coat), and with a double
dilution allele (dd) they are cremello (almost white in coat and mane and tail, and also
lighter eyes). So, this dilution gene results in 3 different phenotypes, whereas the polled
gene only produced 2.

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It may seem that monogenic traits are never influenced by the environment, so P = G.
This is not always the case. An example of a gene that is influenced by the environment
is the gene that causes phenylketonuria or PKU in humans. It is a rare recessively
inherited metabolic disorder. Only if two carriers have a child, that child can have PKU. In
the Netherlands, 1 in 18,000 children has it, but all are tested for it as newborn baby in
the blood collected with the heel pinch. In people with PKU, the enzyme Phenylalanine
hydroxylases is not present or not functioning, so that it cannot break down the amino
acid Phenylalanine. This is thus accumulating in the blood and the spinal fluid, which
causes damage to nerve cells, eventually resulting in brain damage. Patients with
untreated PKU are usually mentally retarded with behavior problems, and often suffer
from skin diseases. The treatment is very basic: a lifelong diet with very little protein and
no intake of aspartame as that contains phenylalanine. Patients do get amino-acid
additives to prevent deficiencies. Thus, the expression of this monogenic traits can be
influenced by the environment, by the diet in this example.

Polygenic genetic variation

Many traits are determined by more

than a single gene. The figure shows an
example of three genes that together
determine skin color. You can see that
with three genes you can already form
64 different genotypes! But these 64
genotypes do not result in 64, but only
6 different phenotypes due to epistasis:
The expression of the genes depend on
the combination of alleles and these 64
genotypes result in only 6 different
grades of expression. If you would plot
the frequency at which these genotypes
occur per phenotype then you get this
bell-shape curve. The intermediate
phenotype occurs most frequent and
both extremes the least frequent. The
more genes are involved in expression
of a trait, the more the frequency plot
will resemble a smooth bell-shape. This
bell-shape is a very common shape when you look at frequency distributions of traits with
discrete values.

In animal breeding a general assumption is that traits are determined by an infinite

number of genes, each with a very small effect, so that the bell-shape is very smooth. It
is also assumed that this infinite number of gene effects are all additive. The model
underlying this assumption is called the infinitesimal model.

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The infinitesimal model assumes that all traits are determined by an infinite number of
genes, each with an infinitely small effect. This assumption results in a smooth bell-
shaped distribution that can be described by the Normal Distribution. This distribution
comes with a number of rules that animal breeding theory is built on.

Variance components

The variation in a population can be quantified using statistics related to the Normal
Distribution and is expressed as a so-called variance component. In symbols this
generally is indicated with a2. So, the phenotypic variance is called 2P, the genetic
variance is called 2G, and the environmental variance is called 2E.

Our model of P = G + E is also applicable to variance components:

2 2 2
P= G+ E+ 2covgG, E

= 2G + 2E

The covariance between G and E is assumed to be 0. In other words: there is no

dependency of the genotype on the environment, or vice versa. The genotype does not
change if the environment changes. This assumption generally is justified as we usually
only consider a single type of environment when estimating variance components. In the
chapter about evaluation of the breeding program we will see that this is not always the
case. But for now, we will just follow the general assumption that there is no mutual
dependency between genotype and environment.

Variation in a population is expressed in a variance component. The symbol for a

variance component is 2 and the subscript indicates what type of variance component it
is: 2 P, G, or E.

For estimating these variance components, we make use of the fact that if a trait is
heritable it would mean that brothers and sisters perform more alike than unrelated
individuals. So, we combine the phenotypic information on the animals with their genetic
relationships (i.e. the pedigree), and then the only component we have no real information
about is the environment. Of course, we can identify certain components of the
environment, like housing and nutrition. But because the influence of the environment
already starts at conception, we cannot identify all components of the environment. And
some components we are not even aware of, like the potential influence of the weather
three weeks ago on the performance today. We can estimate 2E by subtracting 2G from
2P. So, E = P – G. Because this is not a very accurate way of. estimating the variance due
to environmental influences, this variance component is called error variance, rather than
environmental variance.

The 2E is called the error variance. This includes the variance caused by environmental
2 E error variance influences, but also by some other effects.

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Simplify the genetic model

The G in our model P = G + E is quite complex as it has a number of underlying

components.

This can be modelled as:

Genotype = additive effect + dominance effect + epistatic effect

or

G=A+D+

The genetic component consists of three underlying effects:

a. The epistatic effect: interaction between genes. The epistatic effects indicate that
there are genes interacting with each other. This is, for example, the case if one
gene needs the product of another gene to come to expression, resulting in so-
called gene-pathways. Expression of one gene thus depends on the allele
combination in another gene.

b. The dominance effect: interaction between alleles of the same gene. The
dominance effects indicate that expression of the gene itself depends on the allele
combination in that gene. Two recessive genes will result in a different expression
from one recessive and one dominant allele.

c. The additive effect: everything that is left over after correcting for the interacting
effects. The additive effects indicate the effect of the gene without the dominance
and epistatic effects. So irrespective of the allele combinations of the gene itself or
of other genes. What remains are effects that you can add up.

In variance component terms the genetic variance can thus be written as;

2 2 2 2
G = A + D+ I

To be precise, this equation should be extended by “+2cov A, D + 2covA, I + 2covD, I”,

however these co-variances are zero by definition and are, therefore, left out of the
equation.

Next generation: transmission model

The dominance and epistatic effects depend on allele combinations. They are broken in
the gamete production and established again in the offspring, but it is unpredictable how.
The additive effects, however, are predictable because they do not depend on specific
combination of alleles. To be able to predict the additive genetic effects, we need to

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develop another model that
describes the transmission of
the genetic potential from
both parents to their offspring.
To illustrate that, let us see a
picture of a family of rabbits.
The parents each have two
different copies of each gene,
but they pass only 1 on to
their offspring and you don’t
know which one. So, for each
gene there are two alleles per
parents, and four different
combinations of those alleles
possible in the offspring.

Fact is that each animal receives half of its genes from its father (sire) and half from its
mother (dam). But you can see from the figure that with this formula you cannot predict
what will be the offspring performance as you will need to know WHICH half of the genes
are passed on to the offspring. And that is a chance factor, also called the Mendelian
Sampling term. So, a part you know: half from sire and half from dam, and the other part
is the Mendelian Sampling term (MS).

The Mendelian Sampling term indicates the chance factor in distributing half the genetic
material from each parent to their offspring.

Remember that in breeding we are only interested in the additive genetic effect (A), as
half of that is inherited to the offspring. This is also called the true breeding value of an
animal.

The true breeding value (A) of an animal is its additive genetic component, half is which
is inherited by the offspring.

In model terms you can write the breeding value of an offspring as;

Aoffspring = ½ Asire + ½ Adam + MS

Heritability

Because in animal breeding we only make use of the prediction of A, and not of G, we
should simplify the model of P = G + E to P = A + E. Note that this last E is larger than
before because as we cannot estimate them, E also contains the D and I components. It
now becomes more obvious why we call the 2E error variance because it contains more
than only the effect of the environment.

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The additive genetic effect is the part of the genetic component that is passed on from
both parents to their offspring. In other words: the additive genetic effect is heritable. To
indicate how heritable a certain trait is, a parameter is defined that indicates what
proportion of the variation you observe (the phenotypic variance) is determined by
(additive) genetic differences between animals (the additive genetic variance). This
parameter is called the heritability and is indicated with the symbol h2.

The heritability (h2) indicates what proportion of the total phenotypic variation is due to
genetic variation among individuals.

In formula: h2 = 2A / 2P

Boundaries between 0 and 1!

It is possible to estimate the heritability for a trait in a population if phenotypes and genetic
relationships (pedigree) is available. A h2 of 0.3 indicates that 30% of the variation you
observe in your phenotypes is due to additive genetic differences between the animals.
If ALL phenotypic differences are due to genetic differences, then the h2 will be 1.0. Larger
than 1.0 by definition is not possible. Similarly, if the differences between animals are
NOT determined by their genetics, then the h2 = 0.0. Smaller than 0.0 by definition is also
not possible.

Restrictions to estimates of the heritability

The estimated heritability is always specific for a trait, but also for a particular population
in a particular environment. This has two important reasons.
● First, the influence of the environment will, of course, depend on the environment.
● Second, as we have seen in the example about genetic variation in human hair
color, genetic variation for a trait may vary between populations.

A heritability always is estimated for a specific population in a specific environment

because it reflects the genetic variation for a trait in that specific population relative to the
phenotypic population.

If phenotypes are recorded in more than one environment, but for the same population,
then there may be a third reason for difference in heritability.

Misconceptions about the heritability

Misconception 1.” A heritability of 0.40 indicates that 40% of the trait is determined by
genetics”
● A heritability of 0.40 indicates that 40% of all the phenotypic variation for that trait
is due to variation in genotypes for that trait.

Misconception 2. “A low heritability means that traits are not determined by genes”

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 ● For example, number of fingers on a hand is very much genetically determined,
but because by far most people have five fingers on each hand, the genetic
variance is very low.

Misconception 3. “A low heritability means that genetic differences are small”

● A low heritability not automatically indicates that the genetic variance is small. It
can also mean that the error variance is large. And this can be caused by large
influence of the environment, but also by inaccurate phenotype recording.

Misconception 4. “A heritability is a fixed value”

● The heritability reflects the relative weight of the genetic variance component in
the phenotypic variance in a specific population and based on observations that
were taken on a specific moment in time.
● The size of the heritability depends on genetic variance in a population, but also
on the influence of the environment and on the accuracy of the observations.
● The genetic variance in one population may be (somewhat) different from that in
another population. Especially if that other population is of a different breed. But
also, within a population the heritability can change in time.
o For example, if the new set of phenotypic observations were collected using
a more accurate recording method.
o Or if the housing system has changed since the last recording, so that the
influence of the environment has changed. It, therefore, is wise to re-
estimate the heritability at regular basis.

To summarize: The heritability indicates what proportion of the phenotypic variance is

determined by the additive genetic variance, for a specific population in a specific
environment. The specific population dictates the additive genetic variance, the specific
environment influences the size of the environmental variance, as is the accuracy of
recording of the phenotype so that differences between animals are revealed.

Non-genetic influences: The variance due to a Common Environment

The environment that an animal has experienced in its life in general is very difficult to
monitor in detail. But there are components that the animal has shared with others during
their development that may have influenced them all in a similar way. The size of that
influence can be estimated because we can compare individuals that shared that same
common environment to others that had another environment in common. An example of
a common environment is the mother, shared by animals in the same litter (think about
pigs, dogs, sheep, rabbits, mice, etc.). Those animals shared the same intrauterine
environment, the same milk composition, approximately the same levels of milk
production and maternal care. This shared early environment will have shaped these
animals in a similar way. But also, animals that were not born in a litter can have a
common environment. For example, chicks that were hatched at the same time in the
same incubator (or under the same hen), young animals in general that share their first
indoor housing (cage or pen). Outdoor housing is much more variable and therefore much
less of similar influence on all that shared the environment.

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A common environment can, of course, also exist in the adult life of animals. However, in
animal breeding we no longer call that a ‘common environment’. A common environment
refers to the environment during the development of an animal and has irreversible
consequences. If the common environment was abundant, the development of the
animals sharing that environment will be according to their potential. However, if animals
develop in a restricted environment, then their development will not be according to their
potential and the consequences of this suboptimal development are irreversible. A
restricted environment during adult life, however, mostly has reversible consequences.

A common environment is an environment that is shared with others during the

development of an animal and that, therefore, is expected to have the same influence on
the development of all animals that share a common environment. The quality of an
environment may have irreversible consequences if experienced during development

Importance of common environment

Why would you be interested in the common environmental variance (c 2)?

● Most important reason is that its size provides insight in the influence of the
common environment on the variation in phenotypes observed. This common
environment does not have to be shared at the moment of the recording of the
phenotype. For example, age at maturation (first estrus cycle) in female animals
may be influenced by the common environment (e.g. shared litter) months or even
years earlier. If the common environment was of good quality this may result in an
earlier age at maturation.
● The benefit of knowing that these joint shared environmental experiences exist is
that being able to quantify the variation in effects of those experiences allows to
estimate the heritability more accurately. This is because it is difficult to disentangle
the effect of the common environment from the genetic component as closely
related animals experience the same common environment.
● Taking the common environment into account when estimating the variance
components helps to “clean” the genetic variance from actual environmental
influences that related animals have in common. And it also provides insight in the
size of the influence of the early environment on the phenotype.

Special cases of a common environmental effect

● Maternal effect
o The maternal effect can be a special case of the common environment. It is
the effect of the environment that is defined by the mother. It starts already
prior to birth, and continues for as long as the mother has an influence on
the development of her offspring. In case of multiple offspring
simultaneously, such as in a litter, the maternal effect can be an important
part of the common environmental effect. But also, the development of
animals that are born as singletons are influenced by their mother. If the
mother has multiple offspring, but not at the same time, it is possible to

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 estimate the effect of the specific maternal environment that is shared by all
offspring. For example, the size of the uterus, or the temperament of the
mother, resulting in a specific type of maternal care.
o A complicating factor is that the maternal effect has an environmental
component, but also a genetic one! It will depend on the genetics of the
mother what uterine environment she can create for the developing
offspring. And also, how wide her birth canal is, or how much milk she can
produce and of what quality. So, the maternal effect in fact is an
environmental effect for the offspring, but depending on the genetics of the
mother.

The maternal effect is defined as the effect of the environment created by the mother on
the development of her offspring. The maternal effect is partly determined by the genetics
of the mother.

***Note that this maternal effect is part of the breeding goal in a number of animal species.
After all, having good mothering abilities can be an important component in the breeding
program. Maternal effects are included in the breeding goals of, for example, dairy cattle
(ease of birth), beef cattle and sheep (ease of birth, mothering ability), pigs and rabbits
(the mothers are a very important component in number and quality of offspring).

● Social genetic effect (indirect effect)

o Looking into situations, it is not only your mother who has influenced your
development. It was also, for example, your brothers and sisters, and the
children in your school, some of whom were your friends and some may
have bullied you. In other words: many people in your surrounding have had
an influence on who you are today. Part of this influence was due to what
those other people had experienced themselves. But part of it also was
because of the genetics of those people. It should now be clear why we also
call this indirect effect the social genetic effect.
o The phenotype of an animal that is influenced by others. The others are part
of the environment of the animal, where, just as with the maternal effect, the
“environment” has a genetic component: the genetics of the other animals.
In other words: the phenotype of each animal is influenced by a direct
genetic effect (its own genes) and its own environment, but also indirectly
by phenotypic effects of animals in the surrounding of the animal. Just like
the maternal effect, the social phenotype has a genetic and an
environmental component.
o For example, a pen with 4 pigs, Pig 1 has a phenotype due to its own
genetics and own environment, but is also influenced by the social
phenotypes of its pen mates Pig 2, 3, and 4. You can imagine that if these
pen mates of Pig 1 are quiet and friendly, it will perform much better than
when the pen mates are bullying Pig 1 around or preventing it from reaching
the feed. Social effects may play a role anytime animals are kept in social
structures such as pigs in a pen, but also chickens in a cage, horses or
cows in a herd, sheep in a flock, etc.

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The indirect or social effect describes the effect that the phenotypes of others have on
the performance of an animal. Just like with the maternal effect, the social effects are
phenotypes that consist of combinations of genetics and environments of the other
animals.

Genetic Diversity and Inbreeding

Diversity is another word for variation: the presence of differences among whatever you
consider. Related to genetics, most obvious is the genetic diversity between populations.
Different breeds, for example, have specific genetically determined characteristics.

Genetic diversity also exists within a population, and is related to the genetic differences
between animals in that population. It is possible, but very rare, that there is no genetic
variation in a population. This occurs in populations that are fully inbred: animals are
genetically completely identical to each other. But like said, this is a very rare situation
that may occur in genetic lines of laboratory animals that are especially created for that
purpose. The purpose of those populations is to provide animals that are as genetically
equal as possible so that genetic differences are not a cause of variation in, for example,
testing new medicines. A population of clones would be even better from the point of view
of having genetically equal animals.

Clone (animal) is an individual that is genetically identical to another or a group of

individuals that are genetically identical to each other.

Genetic diversity represents the presence of genetic differences between animals within
species, both between and within populations.

The number of alleles that are present in a population is a measure of genetic diversity.
The more alleles are present, the larger the genetic diversity is. The frequency at which
these alleles occur in the population also have an influence on the size of genetic
diversity. The more equal the allele frequencies are, the larger the diversity is.

Forces that influence genetic diversity

There are a number of forces that influence genetic diversity. Some can be influenced by
us; others occur by coincidence. At population level there are forces that increase genetic
diversity, and forces that decrease it.
a. Mutations are events that create new alleles. When it happens in germ cells it has
an increasing effect on genetic diversity.
b. Migration may have an increasing effect, but only immigration (new animals
moving into the population). Emigration (animals moving out of the population)
usually has a decreasing effect on genetic diversity, especially when the population
size is small.

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 c. Selection has a decreasing effect: only animals with a specific genetic make-up
are allowed to breed, at the expense of others. This will have an effect on allele
frequencies, away from the equal frequencies.
d. A final force with a decreasing effect on genetic diversity is the force of coincidence
(genetic drift), and related to that is inbreeding. Genetic drift cannot directly be
influenced by our selection decisions.

Change in diversity: inbreeding

Inbreeding is the result of mating two related individuals. Related individuals genetically
are more alike than non-related individuals because they share alleles. They share alleles
because they have an ancestor in common. This common ancestor passed on the same
alleles to multiple offspring, who passed them on again, so that eventually they ended up
in both related animals. Mating those animals creates the chance that both of them pass
the same alleles on to their offspring, resulting in homozygosity in the offspring. The level
of inbreeding in an animal depends on the level of relatedness between its parents, and
thus the probability that both will pass the same allele on to their offspring. The level of
inbreeding in an animal can be expressed in the inbreeding coefficient.

The inbreeding coefficient indicates the probability that an individual receives the same
allele from both his parents, because his parents are related. Inbreeding is the result of
mating related individuals. The inbreeding coefficient takes values between 0 (0% or not
inbred) and 1 (100% or fully inbred). Important to keep in mind is that inbreeding increases
homozygosity (and decreases genetic diversity).

Definition: Inbreeding level or inbreeding coefficient indicates the probability that an

animal receives the same allele from both parents because they are related.

Causes of inbreeding

There are two causes of inbreeding: inbreeding due to genetic drift and inbreeding due to
nonrandom mating. Or in other words: inbreeding due to coincidence and inbreeding on
purpose, inevitable and evitable inbreeding.

A. Genetic drift causes a loss in genetic diversity due to loss of alleles, which leads
to an increase in homozygosity and this is also called inevitable inbreeding.
Imagine that at some moment in history a mutation occurred. You may assume
that this mutation only occurred in a single animal, as it is unlikely that exactly the
same mutation also occurred in another animal. Animals that carry the allele today,
therefore, must be related because they have that original animal as common
ancestor. This is the case for all mutations, even if the animal in which the mutation
occurred lived a VERY long time ago. Given the definition that inbreeding is the
result of mating related individuals, animals that are homozygous for the allele
must be inbred.
Homozygosity in a population is an indication of size of allele frequencies. If all
animals are homozygous, the other allele(s) is/are lost from the population.

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 Inbreeding due to genetic drift results in a permanent loss of genetic diversity
because alleles are lost for ever.

B. Non-random mating can cause inbreeding, but this is evitable (evitable

inbreeding). Mating closely related animals on purpose, like brother and sister or
father and daughter matings, results in an increased probability that the offspring
of the mating will receive the same allele from both parents. This results in
increased homozygosity, and thus in inbreeding. However, this is a temporary loss
of genetic diversity because if you would stop mating closely related animals on
purpose, but use random mating instead, this cause of inbreeding would
disappear.

Why is genetic diversity important?

There are three main reasons why would we care about genetic diversity;

a. Genetic diversity allows for flexibility in a population.

o Different genotypes may be more suitable and selection pressure will
change.
b. Potentially with devastating consequences, inbreeding (increase in homozygosity)
causes inbreeding depression.
o Inbred animals tend to be less healthy, live shorter, and have reduced
reproductive capacity.
c. Reduced genetic diversity results in increased homozygosity, also of alleles that
have deleterious effects.
o More inbred animals mean more animals that suffer from monogenic
recessive disorders.

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