Population Genetics

Gene (or Allelic) Frequencies

 Genetic data for a population can

be expressed as gene or allelic
frequencies
 All genes have at least two alleles
 Frequencies can vary widely
among the alleles in a population
 Two populations of the same
species do not have to have the
same allelic frequencies.
Estimating Allelic Frequencies

 When all genotypes are known

 Example: blood type locus
 two alleles: LM or LN,
 three genotypes: LMLM, LMLN, LNLN
Blood type Genotype Number of individuals
M LMLM 1787
MN LMLN 3039
N LNLN 1303
Total 6129
Estimating Allelic Frequencies

 To determine the allelic frequencies we

simply count the number of LM or LN
alleles and divide by the total number
of alleles
Number of
Genotype Allele LM Allele LN
individuals
LMLM 1,787 3,574 0
LMLN 3,039 3,039 3,039
LNLN 1,303 0 2,606
Total 6,129 6,613 5,645
Total alleles 12,258
Estimating Allelic Frequencies

Number of
Genotype Allele LM Allele LN
individuals
LMLM 1,787 3,574 0
LMLN 3,039 3,039 3,039
LNLN 1,303 0 2,606
Total 6,129
Total alleles 12,258

 f(LM) = (3,574 + 3,039)/12,258 = 0.5395

 f(LN) = (3,039 + 2,606)/12,258 = 0.4605.
Estimating Allelic Frequencies

 By convention one of the alleles is

given the designation p and the
other q
 Also p + q = 1
 p (LM) = 0.5395 and q (LN) = 0.4605
Estimating Allelic Frequencies

 Using the genotypic frequencies

Percentage
Location
MM MN NN Total

Greenland 83.5 15.6 0.90 100

Iceland 31.2 51.5 17.30 100

 Percent
Location
MM MN NN
Greenland 83.5 15.6 0.90

Estimating Allelic Frequencies

Iceland 31.2 51.5 17.30

 Let p = f(M) and q = f(N)

 Thus, p = f(MM) + ½ f(MN) and

q = f(NN) + ½ f(MN)

 So the results of the above data are:

 Percent
Location
MM MN NN
Greenland 83.5 15.6 0.90

Estimating Allelic Frequencies Iceland 31.2 51.5 17.30

Greenland:

 p(M) = 0.835 + ½ (0.156) = 0.913;

 q(N) = 0.009 + ½ (0.156)=0.087

Iceland:

 p(M) = 0.312 + ½ (0.515) = 0.569; and

q(N) = 0.173 + ½ (0.515)=0.431

 Clearly the allelic frequencies vary between

these populations.
The Hardy-Weinberg Law

 The unifying concept of population

genetics
 The law predicts how gene
frequencies will be transmitted from
generation to generation with some
assumptions:
 Population large
 Random mating population
 No mutation
 No migration
 No natural selection.
The Hardy-Weinberg Law

For one gene with two alleles

(p + q)2 = p2 + 2pq + q2 and

p+q=1
where:
p2 is frequency for the AA genotype
2pq is frequency for the Aa genotype, and
q2 is frequency for the aa genotype.
The Hardy-Weinberg Law

 the gene frequencies will not

change over time, and the
frequencies in the next generation
will be:
 p2 for the AA genotype
 2pq for the Aa genotype, and
 q2 for the aa genotype.
The Hardy-Weinberg Law

 If p equals the frequency of allele A

in a population and q is the
frequency of allele a in the same
population, union of gametes
would occur with the following
genotypic frequencies:
Female Male gametes
gametes
p (A) q (a)
p (A) p2(AA) pq(Aa)
q (a) pq(Aa) q2(aa)
Some examples

1. Assume that a community of

10,000 people on an island is in
Hardy-Weinberg equilibrium and
there are 100 sickle cell individuals
(homozygous recessives).
a. What are the frequencies of the
alleles (sickle cell and normal)?
b. What is expected number of
heterozygous carriers in the
community?
 Assume that a community of 10,000 people
on an island is in Hardy-Weinberg
equilibrium and there are 100 sickle cell
individuals (homozygous recessives).
a. What are the frequencies of the alleles

Some examples (sickle cell and normal)?

b. What is expected number of
heterozygous carriers in the
community?

Solution 1:
a. .q2(aa) = 100/10,000 = 0.01
q(a) = 0.01 = 0.1; p(A) = 1 – 0.1 = 0.9
b. Frequencies heterozygous:
2pq(Aa) = 2 x 0.9 x 0.1 = 0.18
Number of heterozygous carriers = 0.18 x
10,000 = 1800 people.
Some examples

 In a randomly mating laboratory population of

Drosophila melanogaster, 4 percent of the
flies have black body (black is the autosomal
recessive, b) and 96 percent have brown
bodies (the natural color, B). If this population
is assumed to be in Hardy-Weinberg
equilibrium:
 What are the allelic frequency of B and b
 What are the genotype frequency of BB and Bb?
 In a randomly mating laboratory population of
Drosophila melanogaster, 4 percent of the flies
have black body (black is the autosomal
recessive, b) and 96 percent have brown
bodies (the natural color, B). If this population is

Some examples assumed to be in Hardy-Weinberg equilibrium:

a. What are the allelic frequency of B and b
b. What are the genotype frequency of BB
and Bb?

Solution 2:
a. q2(bb) = 0.04; q(b) = 0.04 = 0.2

p(B) = 1 – 0.2 = 0.8

b. p2(BB) = (0.8)2 = 0.64

2pq(Bb) = 2 x 0.8 x 0.2 = 0.32.

Frequencies of multiple alleles

For one gene with two alleles

(p + q)2 = p2 + 2pq + q2 and

p+q=1
where:
p2 is frequency for the AA genotype
2pq is frequency for the Aa genotype, and
q2 is frequency for the aa genotype.
 Frequencies of multiple alleles

 For one gene with three alleles:

(p + q + r)2 = p2 + q2+ r2 + 2pq + 2pr + 2qr
and p+q+r=1
Example of one gene with three
alleles: ABO blood group:
 IA : produce antigen A
 IB : produce antigen B
 i : does not produce any antigen.
Frequencies of multiple alleles

For ABO
Blood type blood group: Frequency
Genotype
IAIA p2
A
IAi 2pr
IBIB q2
B
I Bi 2qr
AB IAIB 2pq
O ii r2
Example

 In the population of 1000 people, there are

42 persons having blood type of A, 672 of
B, 36 of AB and 250 of O.
 What is the frequency of IA?
 What is the frequency of IB?
 What is the frequency of i?
 How many persons from 42 of A type are A
heterozygote?
 How many persons are B homozygote?
In the population of 1000 people, there
are 42 persons having blood type of A,
672 of B, 36 of AB and 250 of O.

 Solution:
 From that data, the frequency of allele
that can directly be calculated is of i
 From 1000 people, there are 250 of O
blood type
 r2(ii) = 250/1000 = 0.25
 r(i) = 0.25 = 0.5
In the population of 1000 people, there
are 42 persons having blood type of A,
672 of B, 36 of AB and 250 of O.

 Now, we add A and O blood types, and

we will have
 A + O = 42 + 250 = 292
 A = p2 + 2pr and O = r2
 p2 + 2pr + r2 = 292/1000 = 0.292
 (p + r)2 = 0.292
 p + r = 0.54
 Since r(i) = 0.5 then p(IA) = 0.54 – 0.50 = 0.04
In the population of 1000 people, there
are 42 persons having blood type of A,
672 of B, 36 of AB and 250 of O..

 What is the frequency of IB?

 p+q+r=1
 q(IB) = 1 – 0.04 – 0.50 = 0.46
In the population of 1000 people, there
are 42 persons having blood type of A,
672 of B, 36 of AB and 250 of O..

 How many persons from 42 of A

type are A heterozygote?
 The frequency of heterozygous A is 2pr
 2 x 0.04 x 0.5 x 1000 = 40 persons
In the population of 1000 people, there
are 42 persons having blood type of A,
672 of B, 36 of AB and 250 of O.

 How many persons are B

homozygote?
 The frequency of homozygous B is q2
 0.462 x 1000 = 212 persons
Selection against the recessive

 Selection (s) against the recessive is

relative compared to the dominant
types
 The proportion selected of a given
genotype is given the symbol s,
which do not reproduce in every
generation
 Therefore, the fitness is equal to 1-s.
Selection against the recessive

Table formulating selection:

Genotype AA Aa aa Total
Frequency p2 2pq q2 1.00
Fitness 1 1 1-s
Proportion p2 2pq q2(1-s) 1-sq2
after selection
Selection against the recessive

 Let’s assume that initially

 the frequency of A is p = 0.5,
 the frequency of a is q = 0.5 and
 s1 = 0.1
Genotype AA Aa aa
Relative fitness 1 1 1-0.1 = 0.9
Frequency p2 = 0.25 2pq = 0.50 q2= 0.25
(at fertilization)
Selection against the recessive

 In forming the next generation,

each genotype will contribute
gametes in proportion to its
frequency and relative fitness
Genotype AA Aa aa
Relative (0.25) x 1 = (0.50) x 1 = (0.25) x 0.9 =
contribution to 0.25 0.50 0.225
next generation
Selection against the recessive

 If we divide each of these relative

contribution by their sum (0.25 + 0.50
+ 0.225 = 0.975) we obtain
Genotype AA Aa aa
Proportional 0.256 0.513 0.231
contribution to
next generation
Selection against the recessive

 The frequency of the a allele after

one generation of selection is from
homozygote aa and from half of
heterozygote Aa:

q‘(a) = 0.231 + (1/2)(0.513) = 0.487

Selection against the recessive

 The frequency q' represents the genes which

survive and therefore corresponds to the gene
frequency in the next generation before
selection

 The formula can be applied repeatedly

generation after generation

 In the right side of the formula q' is calculated

in the preceding generation and so forth.
Selection against the recessive
Selection against the recessive

 The figure shows such an

application. By strong selection
(s=1) the gene frequencies change
very rapidly at high gene frequencies

 If the gene frequency in contrasts is low, the

selection will hardly affect the frequency

 by weak selection pressure the changes in the

gene frequency are always very slow.
Try these

1. The ability to taste the compound PTC is

controlled by a dominant allele T, while the
individuals homozygous for the recessive
allele t are unable to taste this compound. In
a genetics class of 125 students, 88 were
able to taste PTC, 37 could not.
a. Calculate the frequency of the T and t allele in
this population.
b. Calculate the frequency of the genotypes.
Try these

2. In a given population, only the "A" and

"B" alleles are present in the ABO system;
there are no individuals with type "O"
blood or with O alleles in this particular
population. If 200 people have type A
blood, 75 have type AB blood, and 25
have type B blood, what are the alleleic
frequencies of this population (i.e., what
are p and q)?
Try these

3. Cystic fibrosis is a recessive condition that affects

about 1 in 2,500 babies in the Caucasian
population of the United States. Please calculate
the following.

a. The frequency of the recessive allele in the population

b. The frequency of the dominant allele in the
population
c. The percentage of heterozygous individuals (carriers)
in the population
Try these

4. You sample 1,000 individuals from a large

population for the MN blood group:
Number of Resulting
Blood type Genotype
individuals frequency
M MM 490 0.49
MN MN 420 0.42
N NN 90 0.09

Calculate the following:

a. The frequency of each allele in the population.
b. Supposing the matings are random, the frequencies of the matings
c. The probability of each genotype resulting from each potential
cross.
Any question?
Thank you