POPULATION GENETICS

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Rombel 1 - Biology Education
 POPULATIONS GENETICS

Population genetics examines allelic variation among individuals, the

transmission of allelic variants from parents to offspring generation after
generation, and the temporal changes that occur in the genetic makeup of a
population because of systematic and random evolutionary forces.
The theory of population genetics is a theory of allele frequencies. Each
gene in the genome exists in different allelic states, and, if we focus on a
particular gene, a diploid individual is either a homozygote or a
heterozygote. Within a population of individuals, we can calculate the
frequencies of the different types of homozygotes and heterozygotes of a
gene, and from these frequencies we can estimate the frequency of each of
the genes alleles. These calculations are the foundation for population
genetics theory.
 Hardy-Weinberg Law

In a large random mating population in the absence of mutation,

migration, selection and random drift, allele frequency remains the
same from generation to generation. Furthermore, there is a simple
relationship between allele frequency and genotypic frequency
Ideal population of the Hardy-Weinberg principle
1. Two sexes and the population consist of sexually mature individuals
2. Mating between male and female are equal in probability (independent
of distance between mates, type of genotype, age of individuals
3. Population is large and actual frequency of each mating is equal to
Mendelian expectation
4. Meiosis is fair.
5. All mating produce the same number of offspring, on average.
6. Generations do not overlap
7. There is no difference among genotype groups in the probability of
survival
8. There is no migration, mutation, drift and selection
 RELATING GENOTYPE FREQUENCIES TO ALLELE
FREQUENCIES: THE HARDYWEINBERG PRINCIPLE

In a population a particular gene is segregating two alleles, A and a,

The random mating, the predicted
frequencies of the three genotypes
in the population are:
and that the frequency of A is p and that of a is q.
The probability that an egg (or sperm) carries A is p, and the
probability that it carries a is q.
The probability of producing an AA homozygote in the population is
simply p x p = p2
The probability of producing an aa homozygote is q x q = q2.
For the Aa heterozygotes, there are two possibilities: An A sperm can
unite with an a egg, or an a sperm can unite with an A egg. Each of
these events occurs with probability p x q, and because they are
equally likely, the total probability of forming an Aa zygote is 2pq.
These predicted frequencies can be obtained by expanding the
binomial expression (p x q)2 = p2 + 2pq + q2.
 How good is the random mating assumption in
actual populations?

The chief criteria necessary for a population to be H-W equilibrium is

random mating among individuals in the population.
These are some of the conditions that affect random mating assumption
and therefore may affect H-W equilibrium:
 Inbreeding

Since the inbreeders are related, its more likely than random mating that for
one characteristic they will have matching alleles. This includes recessive
alleles. Therefore, the frequency of homozygotes increases (as the genes
the offspring receives from both related parents are more likely to be the
same) and the frequency of heterozygotes decreases. Consider the
interaction of the following three cases:
 Genetic Drift

Random changes in allele frequencies because of chance fluctuations in

population size is called genetic drift.
Any natural disaster that causes a population crash will have a high
probability of changing allele frequencies in the next generation, e.g. Natural
disasters : fires, floods, earthquake, severe winters.
The result is that the gene pool of the small number of survivors may not be
representative of the original population - a situation known as The
Bottleneck effect.
 Mutation

A mutation is any change in the nucleotide sequence of an organisms DNA.

A new mutation that is transmitted in the gametes can change the gene pool
of a population by substituting one allele for another.
For any one gene locus, mutation alone does not have much quantitative
effect on a large population in a single generation. This is because the
occurrence of a mutation at any given gene locus is a very rare event -
typically 1 in 105 to 106 gametes.
Mutation can have an extremely powerful effect on the rate of
evolution especially if a mutation confers a major adaptive or
selective advantage.
Mutation is also the original source of the genetic variation that
serves as the raw material for natural selection.
 Gene Flow

A precondition of Hardy-Weinberg equilibrium is that the gene pool is a

closed system i.e. closed to influences from other gene pools . Therefore a
population may gain new alleles or lose alleles as a result of a process
called Gene Flow.
Gene Flow is genetic exchange between different gene pools (populations)
due to the migration of fertile individuals or gametes Gene flow between
plant communities might take place entirely by exchange of gametes i.e.
pollen carried on the wind or by bees Gene flow tends to reduce gene pool
differences between populations.
 Migration
When individuals from populations with different allele frequencies mix, the
combined population will be in H-W equilibrium after one generation of random
mating. The combined population will be out of equilibrium to the extent that
mating is assortatative.
If we are considering rare alleles we can make the following approximations
allowing us to avoid a lot of messy algebra in our calculations.

For f(a) = q, and f(A) = p, If q << 1 then p 1

From H-W: f(A/A) = p2 1, f(A/a) = 2pq 2q, f(a/a) = q2

Since most genetic diseases are rare, these approximations are valid for many
of the population genetics calculations that are of medical importance.
Calculating Gene
Frequencies
 1. The Genotype Frequency For Recessive Dominant Genes

RUMUS !!
p2 (AA) + 2pq (Aa) +q2 (aa)

p+q=1
Example :
In a population that has been mating randomly for many generations, two phenotypes are
segregating; one is due to a dominant allele G, the other to a recessive allele g. The
frequencies of the dominant and recessive phenotypes are 0.35 and 0,65, respectively.
Estimate the frequencies of the dominant and recessive alleles
Answer:
Dominant (GG) = p2 = 0.35 recessive (gg)= q2 = 0.65
the frequencies of the dominant (G) and recessive (g) alleles?
G = 0,35 = 0,59
G + g = 1 g = 1- G = 1- 0,59 = 0,41
So, the frequencies of the dominant and recessive alleles is 0,59 and 0,41
2. The Genotype Frequency For Multiple Allele

RUMUS!!
p2 (IAIA) + 2pr (Iai) + q2 (IBIB)+ 2qr (Ibi) + 2pq (IAIB) + r2 (ii)

p + q + r =1
Example :
The ABO blood types of 1000 people from an isolated village were
determined to obtain the following data:

Number of people blood A = 42

Number of people blood B = 672
Number of people blood AB = 36
Number of people blood O = 250.

Estimate the frequencies of the IA, IB, and i alleles of the ABO blood group
gene from these data!
Answer:
Symbolize the frequencies of the IA, IB, and i alleles of the I gene as p, q, and r,
IA = p
IB = q
i=r
To estimate r r2 = 250 / 1000 r = , = 0,500
To estimate p (p + r)2 = p2 + 2pr + r2 corresponds to the combined frequencies of the A
(p2 + 2pr) and O (r2) blood types.
(p + r)2 = (42+250) / 1000 = 0,292
p + r = 0,292 = 0,540
p = 0,540 - r = 0,540 0,500 = 0,040
To estimate q p + q + r = 1
q = 1 (p+r)
= 1 (0,040 + 0,500)
q = 0,460
3. The Genotype Frequency For Sex-Linked Allele
RUMUS !!
Untuk betina
p2 (AA) + 2pq (Aa) +q2 (aa)
Untuk jantan
p (A-) + q (a-)

Example :
8 out of 100 men are color blind, how much woman are
color blind?
 Answer :
Consider a recessive sex-linked gene causing color blindness. If 8 out
of 100 (8%) men are color blind (XaY), then the allele frequency can be
directly calculated as q = 0.08 and p = 0.92. Then the H-W principle
can be applied to calculate the expected frequency in women:

Fenotype Genotype Expected Frequencies

Woman Normal XA XA (p2) 0,8464 (84,64%)
Woman c/b Carrier XA Xa (2pq) 0,1472 (14,72%)
Woman c/b Xa Xa (q2) 0,0064 (0,64%)
Total 1,0000 (100%)

So while 8 out of 100 men are color blind, fewer than 1 out of 100
women are color blind.
4. The Genotype Frequency For Sex-Influenced Allele
Example :
Diasumsikan bahwa pada kelompok sapi ayrshire terdapat 200 ekor sapi yang
terdiri dari 49 ekor sapi betina yang berwarna mahogany, dan 51 ekor sapi
betina yang berwarna merah, 91 ekor sapi jantan berwarna mahogany, dan 9
ekor sapi jantan berwarna merah. Bagaimana frekuensi gen mahogany dan
frekuensi gen merah pada populasi?

PROPORSI SAPI AYRSHIRE YANG BERWARNA MERAH DAN MAHOGANY

PADA POPULASI SAPI JANTAN DAN BETINA

Fenotip
Genotip Frekuensi
Jantan Betina
MM p2 Mahogany Mahogany
Mm 2pq Mahogany Merah
mm q2 Merah Merah
 Answer :
Pada populasi sapi betina
proporsi sapi berwarna mahagony (p2) = 49/100 = 0,49. Jadi, frekuensi gen
mahagony pada populasi ini adalah = 0,7.
frekuensi gen merah = 1 0,7 = 0,3.
Pada populasi jantan
proporsi sapi jantan merah (q2) = 9/100 = 0,09 dan frekuensi gen merah = 0,3.
frekuensi gen mahogany = 1 0,3 = 0,7.

Jumlah individu heterozigot untuk kedua jenis kelamin adalah

2pq = 2(0,7)(0,3) x 100 = 42 ekor.
Pada sapi betina, 42 ekor sapi termasuk diantara 51 ekor sapi betina merah.
Pada sapi jantan, 42 ekor sapi itu termasuk diantara 91 ekor sapi berwarna
mahagony.
 Answer Questions Below
1. The ABO blood group system is governed by a multiple allelic system in which
some codominant relationships exist. Three alleles, IA. IB, and i, form the dominance
hierarchy (IA = IB) > i.
(a) Determine the genotypic and phenotypic expectations for this blood group locus
from a population in genetic equilibrium,
(b) Derive a formula for use in finding the allelic frequencies at the ABO blood group
locus,
(c) Among New York Caucasians, the frequencies of the ABO blood groups were
found to be approximately 49% type O, 36% type A, 12% type B, and 3% type AB.
What are the allelic frequencies in this population?
(d) Given the population in part (c) above, what percentage of type A individuals is
probably homozygous?
2. While wool is dependent upon a dominant allele B and black wool
upon its recessive allele b. Suppose that a sample of 900 sheep of
the Rambouillet breed in Idaho gave the following data: 781 white
and 119 black. Estimate the allelic frequencies!
3. In a population of giraffes, the gene that determines spot size has
two alleles, S for larger spots and s for smaller spots. Giraffes with one
of each allele have medium-sized spots. In one generation, the
frequency of S is p=0.4 and the frequency of s is q=0.6. Since spots
help the giraffes blend in with their surroundings, they are acted upon
by natural selection. In the next generation, 64% of giraffes have small
spots. What percentage of giraffes in the second generation will have
medium spots? Large spots?
4. Among 2,820 Shorthorn cattle, 260 are white, 1,430 are red, and
1,130 are roan. Is this consistent with the assumption that the traits
are controlled by a single pair of autosomal alleles and that mating
has been at random for this allele pair?
5. In Semarang, 16% of the population has Rh negative blood, which is
recessive. If the student population of Universitas Negeri Semarang was
2,000, how many students would you expect for each of the three
possible genotypes?
6. P. D. N. Hebert studied the frequencies of alleles for the gene that
codes for the enzyme malate dehydrogenase (Mdh) in the "water
flea," Daphnia magna, living in ponds near Cambridge, England.
There are three alleles of the Mdh gene, abbreviated S, M and F.
Hebert found the following genotypes:
Genotype Observed Number
SS 3
SM 8
SF 19
MM 15
MF 37
FF 32
Total 114

Calculate the allele frequencies!