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Lecture 8
Genetic Variation in
Individuals and Populations:
Mutation and Polymorphism
FACTORS THAT DISTURB HARDYWEINBERG EQUILIBRIUM

A number of assumptions underlie the HardyWeinberg law:
1. Population is large and mating is random.
2. Allele frequencies are not changing over time.
- no migration in or out of the population by
groups whose allele frequencies at a locus of
interest are radically different
3. Selection for or against particular alleles and
new mutations adding alleles are not
significant
Exception to Large Population with
Random Mating

In human populations, nonrandom mating
may occur because of three distinct but
related phenomena: stratification,
assortative mating, and consanguinity.
Stratification

Stratification describes a population in
which there are a number of subgroups that
have remained relatively genetically
separate during modern times.
 For example, the U.S. population is
stratified into many subgroups including
whites, African Americans, and numerous
Native American, Asian, and Hispanic
groups.

When mate selection in a population is restricted
to members of one particular subgroup within that
population, the result for any locus with more than
one allele is an excess of homozygotes in the
population as a whole and a corresponding
deficiency of heterozygotes compared with what
one would predict under random mating from
allele frequencies in the population as a whole.

By way of comparison, stratification has no
effect on the frequency of autosomal dominant
disease and would have only a minor effect on
the frequency of X-linked disease by increasing
the small number of females homozygous for
the mutant allele.
Assortative Mating

Assortative mating is the choice of a mate because
the mate possesses some particular trait.
 Assortative mating is usually positive; that is,
people tend to choose mates who resemble
themselves (e.g., in native language, intelligence,
stature, skin color, etc.)
 To the extent that the characteristic shared by the
partners is genetically determined, the overall
genetic effect of positive assortative mating is an
increase in the proportion of the homozygous
genotypes at the expense of the heterozygous
genotype.

A clinically important aspect of assortative mating
is the tendency to choose partners with similar
medical problems, such as congenital deafness or
blindness or exceptionally short stature (dwarfism).
 In such a case, the expectations of Hardy-Weinberg
equilibrium do not apply because the genotype of
the mate at the disease locus is not determined by
the allele frequencies found in the general
population.
 For example, in the case of two parents with
achondroplasia, offspring homozygous for the
achondroplasia gene have a severe, lethal form of
dwarfism that is almost never seen unless both
parents are achondroplasia heterozygotes.
Consanguinity and Inbreeding

Consanguinity, like stratification and positive
assortative mating, brings about an increase in the
frequency of autosomal recessive disease by
increasing the frequency with which carriers of an
autosomal recessive disorder mate.
 Unlike the disorders in stratified populations, in
which each subgroup is likely to have a high
frequency of a few alleles, the kinds of recessive
disorders seen in the offspring of related parents
may be very rare and unusual because
consanguineous mating allows uncommon alleles
to become homozygous.
Exceptions to Constant Allele
Frequencies
Genetic Drift in Small Populations

Chance events can have a much greater effect on
allele frequencies in a small population than in a
large one.
 If the population is small, random effects, such as
increased fertility or survival of the carriers of a
mutation, occurring for reasons unrelated to
carrying the mutant allele (which would be
selection, not a random event), may cause the allele
frequency to change from one generation to the next.

In a large population, such random effects would
average out, but in a small population, allele
frequencies can fluctuate from generation to
generation by chance.
 This phenomenon, known as genetic drift, can
explain how allele frequencies can change as a
result of chance operating on the small gene pool
contained within a small population.
Mutation and Selection

Changes in allele frequency due to selection
or mutation usually occur slowly, in small
increments, and cause much less deviation
from Hardy-Weinberg equilibrium, at least
for recessive diseases.
 Mutation rates are generally well below the
frequency of heterozygotes for autosomal
recessive diseases, and so new mutation
would have little effect in the short term on
allele frequencies for such diseases.

In addition, most deleterious recessive alleles are
hidden in heterozygotes and not subject to
selection. As a consequence, selection is not likely
to have major short-term effects on the allele
frequency of these recessive alleles.
 Therefore, to a first approximation, HardyWeinberg equilibrium may apply even for alleles
that cause severe autosomal recessive disease.
 For dominant or X-linked disease, however,
mutation and selection do perturb allele
frequencies from what would be expected under
Hardy-Weinberg equilibrium by substantially
reducing or increasing certain genotypes.

Fitness is the chief factor that determines
whether a mutation is lost immediately,
becomes stable in the population, or even
becomes, over time, the predominant allele
at the locus concerned.
 The frequency of an allele in a population
represents a balance between the rate at
which mutant alleles appear through
mutation and the effects of selection.
 If either the mutation rate or the
effectiveness of selection is altered, the
allele frequency is expected to change.

Whether an allele is transmitted to the succeeding
generation depends on its fitness (f), which is a
measure of the number of offspring of affected
persons who survive to reproductive age,
compared with an appropriate control group.
 If a mutant allele is just as likely as the normal
allele to be represented in the next generation, f
equals 1. If an allele causes death or sterility,
selection acts against it completely, and f equals 0.
 A related parameter is the coefficient of selection,
s, which is a measure of the loss of fitness and is
defined as 1 - f, that is, the proportion of mutant
alleles that are not passed on and are therefore lost
as a result of selection.

In the genetic sense, a mutation that
prevents reproduction by an adult is just as
lethal as one that causes a very early
miscarriage of an embryo, because in
neither case is the mutation transmitted to
the next generation.
 Fitness is thus the outcome of the joint
effects of survival and fertility.
Selection in Recessive Disease

Selection against harmful recessive mutations has
far less effect on the population frequency of the
mutant allele than does selection against dominant
mutations because only a small proportion of the
genes are present in homozygotes and are
therefore exposed to selective forces.
 Even if there were complete selection against
homozygotes (f = 0), as in many lethal autosomal
recessive conditions, it would take many
generations to reduce the gene frequency
appreciably because most of the mutant alleles are
carried by heterozygotes with normal fitness.

For example, the frequency of mutant alleles
causing phenylketonuria q, is approximately 1%
in many white populations. Two percent of the
population (2 × p × q) is heterozygous, with one
mutant allele, whereas only 1 individual in 10,000
(q2) is a homozygote with two mutant alleles. The
proportion of mutant alleles in homozygotes is
given by:

Thus, as long as mating is random, genotypes
in autosomal recessive diseases can be
considered to be in Hardy-Weinberg
equilibrium, despite selection against
homozygotes for the recessive allele.
 The mathematical relationship between
genotype and allele frequencies described in
the Hardy-Weinberg law holds for most
practical purposes in recessive disease.
Selection in Dominant Disorders

Dominant mutant alleles are directly exposed to
selection, in contrast to recessive mutant alleles,
most of which are "hidden" in heterozygotes.
 Consequently, the effects of selection and mutation
are more obvious and can be more readily measured
for dominant traits.
 A genetic lethal dominant allele, if fully penetrant, is
exposed to selection in heterozygotes, removing all
alleles responsible for the disorder in a single
generation.
 Several human diseases are thought or known to be
autosomal dominant traits with zero or near-zero
fitness and thus always result from new rather than
inherited autosomal dominant mutations.
Mutation and Selection Balance
in Dominant Disease

If a dominant disease is deleterious but not lethal,
affected persons may reproduce but will
nevertheless contribute fewer than the average
number of offspring to the next generation; that is,
their fitness, f, may be reduced.
 Such a mutation is lost through selection at a rate
proportional to the loss of fitness of heterozygotes.
 The frequency of the mutant alleles responsible
for the disease in the population therefore
represents a balance between loss of mutant alleles
through the effects of selection and gain of mutant
alleles through recurrent mutation.

A stable allele frequency is reached at whatever
level balances the two opposing forces: one
(selection) that removes mutant alleles from the
gene pool and one (new mutation) that adds new
ones back.
 The mutation rate per generation, μ, at a disease
locus must be sufficient to account for that
fraction of all the mutant alleles (allele frequency
q) that are lost by selection from each generation.
Thus,
μ = sq

When a genetic disorder limits reproduction
so severely that the fitness is zero (s = 1), it
is referred to as a genetic lethal.
 For a dominant genetic lethal disorder,
every allele in the population must be a
new mutation since none can be inherited
(in the absence of gonadal mosaicism).

In achondroplasia, the fitness of affected patients
is not zero, but they have only about one fifth as
many children as people of normal stature in the
population.
 In the subsequent generation, only 20% of current
achondroplasia alleles are passed on from the
current generation to the next. Because the
frequency of achondroplasia is not decreasing,
new mutations must be responsible for replacing
the 80% of mutant genes in the population lost
through selection.

If the fitness of affected persons suddenly
improved (because of medical advances, for
example), the observed incidence of the disease in
the population would increase and reach a new
equilibrium.
 Retinoblastoma and certain other dominant
embryonic tumors with childhood onset are
examples of conditions that now have a greatly
improved prognosis, with a predicted consequence
of increased disease frequency in the population.
 Allele frequency, mutation rate, and fitness are
related; thus, if any two of these three
characteristics are known, the third can be
estimated.
Mutation and Selection Balance
in X-Linked Recessive Mutations

For those X-linked phenotypes of medical interest
that are recessive, or nearly so, selection occurs in
hemizygous males and not in heterozygous
females, except for the small proportion of
females who are manifesting heterozygotes with
low fitness.
 Because males have one X chromosome and
females two, the pool of X-linked alleles in the
entire population's gene pool will be partitioned,
with one third of mutant alleles present in males
and two thirds in females.

As we saw in the case of autosomal dominant
mutations, mutant alleles lost through selection
must be replaced by recurrent new mutations to
maintain the observed disease incidence.
 If the incidence of a serious X-linked disease is
not changing and selection is operating against,
and only against, hemizygous males, the mutation
rate, μ, must equal the coefficient of selection, s
(the proportion of mutant alleles that are not
passed on), times q, the allele frequency, times 1/3
since selection is operating on only one third of
the mutant alleles in the population, that is, those
present in males. Thus,
μ = sq / 3

For an X-linked genetic lethal disease, s = 1 and
one third of all copies of the mutant gene
responsible is lost from each generation.
 Therefore, one third of all persons who have such
X-linked lethal disorders are predicted to carry a
new mutation, and their genetically normal
mothers have a low risk of having subsequent
children with the same disorder (assuming no
mosaicism).
 In less severe disorders such as hemophilia A, the
proportion of affected individuals representing
new mutations is less than one third (currently
about 15%).

Because the treatment of hemophilia is improving
rapidly, the total frequency of mutant alleles can
be expected to rise relatively rapidly and to reach a
new equilibrium, as we saw in the case of
autosomal dominant conditions.
 Assuming that the mutation rate at this locus stays
the same, the proportion of hemophiliacs who
result from a new mutation will decrease, even
though the incidence of the disease increases.
Migration and Gene Flow

Migration can change allele frequency by the
process of gene flow, defined as the slow
diffusion of genes across a barrier.
 Gene flow usually involves a large population and
a gradual change in gene frequencies.
 The genes of migrant populations with their own
characteristic allele frequencies are gradually
merged into the gene pool of the population into
which they have migrated. (The term migrant is
used here in the broad sense of crossing a
reproductive barrier, which may be racial, ethnic,
or cultural and not necessarily geographical and
requiring physical movement from one region to
another.)

The frequencies of the 32-base pair deletion allele
of the CCR5 cytokine receptor gene, ΔCCR5, have
been studied in many populations all over the
world.
 The frequency of the ΔCCR5 allele is highest,
approximately 10%, in western Europe and Russia
and declines to a few percent in the Middle East
and the Indian subcontinent.
 The ΔCCR5 allele is virtually absent from Africa
and the Far East, suggesting that the mutation
originated in whites and diffused into the more
easterly populations.

Figure 9-10 Frequency of ΔCCR5 alleles in
populations from Europe, the Middle East, and the
Indian subcontinent.
ETHNIC DIFFERENCES IN THE FREQUENCY OF
VARIOUS GENETIC DISEASES

Why are allele frequencies different in
different populations? In particular, why are
some mutant alleles that are clearly
deleterious when present in homozygotes
relatively common in certain population
groups and not in others?

The human species of more than 6 billion members
is separated into many subpopulations, or ethnic
groups, distinguishable by appearance, geographical
origin, and history.
 Although the 25,000 genes and their location and
order on the chromosomes are nearly identical in all
humans, we saw earlier that extensive polymorphism
exists between individuals in a population.
 Most variation is found in all human populations, at
similar frequencies. Other alleles, however, although
present in all groups, may demonstrate dramatic
differences in frequency among population groups;
and finally, some allelic variants are restricted to
certain populations, although they are not
necessarily present in all members of that group.

It is likely that because modern humans lived in
small isolated settlements until quite recently, as
mutations occurred in the various groups, the
differences in the frequency of certain alleles
persisted and could even become magnified.
 A number of factors are thought to allow
differences in alleles and allele frequencies among
ethnic groups to develop.
 Two such factors are genetic drift, including
nonrandom distribution of alleles among the
individuals who founded particular subpopulations
(founder effect), and heterozygote advantage
under environmental conditions that favor the
reproductive fitness of carriers of deleterious
mutations.

Differences in frequencies of alleles that cause genetic
disease are significant for the medical geneticist and
genetic counselor because they cause different disease
risks in specific population groups.
 Well-known examples include Tay-Sachs disease in
people of Ashkenazi Jewish ancestry, sickle cell
disease in African Americans, and cystic fibrosis and
PKU in white populations.
 The inherited disease of hemoglobin, β-thalassemia, is
a clear example of ethnic differences both in disease
frequency and in which alleles are responsible in
populations with a high incidence of disease.

The disease is common in people of
Mediterranean or East Asian descent and very
rare in other ethnic groups. Even though dozens
of different alleles can cause β-thalassemia,
certain alleles tend to be far more common in
some populations than in others, so that each
population has only a few common alleles.
 For example, the most common β-thalassemia
alleles responsible for more than 90% of the
disease in Mediterranean people are very rare in
people from Southeast Asia or the Asian
subcontinent; similarly, the most common alleles
in Southeast Asians and Asian Indians are quite
rare in the other two unrelated ethnic groups.

This information is of value in genetic
counseling and prenatal diagnosis. For
example, in North America, when persons
of Mediterranean descent are at risk of
having a child with β-thalassemia, testing of
parental DNA for just seven mutant alleles
has a more than 90% probability of
providing the information needed for
prenatal diagnosis
Genetic Drift




Genetic drift can explain a high frequency of a deleterious
disease allele in a population. For example, when a new
mutation occurs in a small population, its frequency is
represented by only one copy among all the copies of that gene
in the population.
Random effects of environment or other chance occurrences
that are independent of the genotype and operating in a small
population can produce significant changes in the frequency of
the disease allele.
During the next few generations, although the population size of
the new group remains small, there may be considerable
fluctuation in gene frequency. These changes are likely to
smooth out as the population increases in size.
In contrast to gene flow, in which allele frequencies change
because of admixture, the mechanism of genetic drift is chance.
Founder Effect



When a small subpopulation breaks off from a larger
population, the gene frequencies in the small population
may be different from those of the population from which
it originated because the new group contains a small,
random sample of the parent group and, by chance, may
not have the same gene frequencies as the parent group.
This form of genetic drift is known as the founder effect. If
one of the original founders of a new group just happens to
carry a relatively rare allele, that allele will have a far
higher frequency than it had in the larger group from
which the new group was derived.
One example is the high incidence of Huntington disease
in the region of Lake Maracaibo, Venezuela, but there are
numerous other examples of founder effect involving other
disease alleles in genetic isolates throughout the world.

The founder effect is well illustrated by the Old
Order Amish, a religious isolate of European
descent that settled in Pennsylvania and gave rise to
a number of small, genetically isolated
subpopulations throughout the United States and
Canada.
 The Old Order Amish tend to have large families
and a high frequency of consanguineous marriage.
 The incidence of specific rare autosomal recessive
syndromes such as the Ellis-van Creveld
syndrome of short-limbed dwarfism, polydactyly,
abnormal nails and teeth, and high incidence of
congenital heart defects in some Amish
communities, but not in others, is an illustration of
the founder effect.

Figure 9-11 The hands of a patient with Ellis-van
Creveld syndrome, a very rare disorder seen with
increased frequency in some Amish groups.

The population of Finland, long isolated
genetically by geography, language, and culture,
has expanded in the past 300 years from 400,000
to about 5 million.
 The isolation and population expansion have
allowed the Finnish population to develop a
distinctive pattern of single-gene disorders.
 There is a high frequency of at least 20 diseases
that are rare elsewhere. For example,
choroideremia, an X-linked degenerative eye
disease, is very rare worldwide; only about 400
cases have been described.
 Fully one third of the total number of patients,
however, are from a small region in Finland,
populated by a large extended family descended
from a founding couple born in the 1640s.

Another Finnish genetic disease is hyperornithinemia
with gyrate atrophy of the choroid and retina, an
autosomal recessive condition caused by deficiency of
ornithine aminotransferase and leading to loss of
vision in young adulthood.
 As one might expect with a founder effect, one
mutation was found in homozygous form in the
majority of apparently unrelated cases of gyrate
atrophy in Finland, but it was not observed at all in
non-Finnish cases.
 Conversely, disorders that are common in other
European populations, such as PKU, are quite rare in
Finland.

Thus, one of the outcomes of the founder effect
and genetic drift is that each population may be
characterized by its own particular mutant alleles
as well as by an increase or decrease in specific
diseases.
 As these examples show, genetic drift and founder
effect can favor the establishment at high
incidence of alleles that are not favorable or even
neutral but are actually harmful.
 The relative mobility of most present-day
populations, in comparison with their ancestors of
only a few generations ago, may reduce the effect
of genetic drift in the future while increasing the
effect of gene flow.
Positive Selection for Heterozygotes
(Heterozygote Advantage)

Although certain mutant alleles may be deleterious in
homozygotes, there may be environmental conditions
in which heterozygotes for some diseases have
increased fitness not only over homozygotes for the
mutant allele but also over homozygotes for the
normal allele, a situation termed heterozygote
advantage.
 Even a slight heterozygote advantage can lead to an
increase in frequency of an allele that is severely
detrimental in homozygotes, because heterozygotes
greatly outnumber homozygotes in the population. A
situation in which selective forces operate both to
maintain a deleterious allele and to remove it from the
gene pool is described as a balanced polymorphism.
Malaria and Hemoglobinopathies

A well-known example of heterozygote advantage
is resistance to malaria in heterozygotes for the
sickle cell disease mutation.
 The sickle cell allele has reached its highest
frequency in certain regions of West Africa, where
heterozygotes are more fit than either type of
homozygote because heterozygotes are relatively
more resistant to the malarial organism.
 In regions where malaria is endemic, normal
homozygotes are susceptible to malaria; many
become infected and are severely, even fatally,
affected, leading to reduced fitness.

Sickle cell homozygotes are even more seriously
disadvantaged, with a fitness approaching zero,
because of their severe hematological disease.
 Heterozygotes for sickle cell disease have red cells
that are inhospitable to the malaria organism but
do not undergo sickling under normal
environmental conditions; the heterozygotes are
relatively more fit than either homozygote and
reproduce at a higher rate.
 Thus, over time, the sickle cell mutant allele has
reached a frequency as high as 0.15 in some areas
of West Africa that are endemic for malaria, far
higher than could be accounted for by recurrent
mutation.

The heterozygote advantage in sickle cell disease
demonstrates how violating one of the fundamental
assumptions of Hardy-Weinberg equilibrium-that
allele frequencies are not significantly altered by
selection-causes the mathematical relationship
between allele and genotype frequencies to diverge
from what is expected under the Hardy-Weinberg
law.
 Consider two alleles, the normal A allele and the
mutant S allele, which give rise to three genotypes:
A/A (normal), A/S (heterozygous carriers), and S/S
(sickle cell disease).
 In a sample of 12,387 individuals from an adult
West African population, the three genotypes were
detected in the following proportions: 9365 A/A :
2993 A/S : 29 S/S.

By counting the A and S alleles in these three
genotypes, one can determine the allele
frequencies to be p = 0.877 for the A allele and q =
0.123 for the S allele.
 Under Hardy-Weinberg equilibrium, the ratio of
genotypes should be A/A : A/S : S/S = p2 : 2pq :
q2 = 9527 : 2672 : 188. The observed ratios,
however, A/A : A/S : S/S = 9365 : 2993 : 29, differ
significantly from expectations.
 The example of the sickle cell allele illustrates
how the forces of selection, operating not only on
the relatively rare S/S genotype but also on the
other two, much more frequent A/A and A/S
genotypes, distort the transmission of the A and S
alleles and cause a deviation from HardyWeinberg equilibrium in a population.

Change in the selective pressures would be
expected to lead to a rapid change in the relative
frequency of the sickle cell allele. Today, many
sickle cell heterozygotes live in non-malarial
regions, and even in malarial areas, major efforts
are being made to eradicate the mosquito
responsible for transmitting the disease.
 There is evidence that in the African American
population in the United States, the frequency of
the sickle cell gene may already be falling from its
high level in the original African population of
several generations ago, although other factors,
such as the introduction of alleles from nonAfrican populations into the African American
gene pool, may also be playing a role.

Some other deleterious alleles, including genes for
hemoglobin C, the thalassemias, and glucose-6phosphate dehydrogenase deficiency, as well as
the benign FY allele of the Duffy blood group
system, are also thought to be maintained at their
present high frequencies in certain populations
because of the protection that they provide against
malaria.
 Heterozygote advantage has also been proposed to
explain the high frequencies of cystic fibrosis in
white populations and of Tay-Sachs disease and
other disorders affecting sphingolipid metabolism
in the Ashkenazi Jewish population.
Drift Versus Heterozygote Advantage
 Determining whether drift or heterozygote
advantage is responsible for the increased
frequency of some deleterious alleles in certain
populations is not simple to do.
 The environmental selective pressure responsible
for heterozygote advantage may have been
operating in the past and not be identifiable in
modern times. The northwest to southeast gradient
in the frequency of the ΔCCR5 allele, for example,
reflects major differences in the frequency of this
allele in different ethnic groups.
For example, the highest frequency of the ΔCCR5
allele is 21%, seen among Ashkenazi Jews, and it is
nearly that high in Iceland and the British Isles. The
current AIDS pandemic is too recent to have affected
gene frequencies through selection; the variation in
allele frequencies in Europe itself is most consistent
with genetic drift acting on a neutral polymorphism.
 It is, however, possible that another selective factor
(perhaps another infectious disease such as bubonic
plague) may have elevated the frequency of the
ΔCCR5 allele in northern European populations
during a period of intense selection. Thus, geneticists
continue to debate whether genetic drift or
heterozygote advantage (or both) adequately
accounts for the unusually high frequencies that
some deleterious alleles achieve in some populations.


Population genetics uses quantitative methods to
explain why and how differences in the frequency of
genetic disease and the alleles responsible for them
arose among different individuals and ethnic groups.
 Population genetics is also important to our attempts to
identify susceptibility alleles for common, complex
disorders by use of population-based association
methods.
 Not only can the fascinating history of our species be
read in the patterns of genetic variation we now see,
but genetic heterogeneity also has important practical
implications for professionals seeking to deliver
appropriate, personalized health care to the world's
populations in ways that are both efficient and
sensitive.