POPULATION

GENETICS

PATRICK JUMAR S. BUENAFLOR, RMT, MSMT(c)

Population genetics
• Gene pool
► the complete set of genetic information in all
individuals within a population
• Genotype frequency
► proportion of individuals in a population with a
specific genotype
► Genotype frequencies may differ from one
population to another
• Allele frequency
► proportion of any specific allele in a population
► Allele frequencies are estimated from genotype
frequencies
 GENE
POOL
RED = DOMINANT TRAIT
BLUEGREEN = RECESSIVE TRAIT
Population genetics
Hardy-Weinberg Principle
• The Hardy-Weinberg Law provides an equation to relate
the genotype frequencies and allele frequencies in a
randomly mating population:

p2 + 2pq + q2 = 1 (for 2 alleles such as A and a)

• If no forces act on a population in Hardy-Weinberg
equilibrium, proportion of genotypes will stay the same
p+q=1
p2 + 2pq + q2 = 1
p+q=1
Population genetics
Hardy-Weinberg Law
Homozygous Heterozygous Homozygous
Dominant Recessive

p2 + 2pq + q2 = 1
Where,
p = Frequency of dominant alleles
q = Frequency of recessive alleles
 = pq

= pp or p2

= qq or q2

= qp

GRAY = DOMINANT TRAIT

GREEN = RECESSIVE TRAIT =p =q
Population genetics
Hardy-Weinberg Law
 How does genetic structure
change?
changes in allele frequencies and/or
• mutation genotype frequencies through time
• migration
• natural selection
• genetic drift
• non-random mating
 How does genetic structure
change?
• mutation spontaneous change in DNA
• creates new alleles
• migration
• ultimate source of all
• natural selection genetic variation

• genetic drift

• non-random mating
 How does genetic structure
change?
• mutation

• migration individuals move into population

• introduces new alleles
• natural selection “gene flow”

• genetic drift

• non-random mating
 Migration
POPULATION A POPULATION B NEW POPULATION B
 How does genetic structure
change?
• mutation certain genotypes produce
more offspring
• migration • differences in survival
or reproduction
• natural selection differences in“fitness”

• leads to adaptation
• genetic drift

• non-random mating
Natural selection
Resistance to antibacterial soap
Generation 1: 1.00 not resistant
0.00 resistant
Natural selection
Resistance to antibacterial soap
Generation 1: 1.00 not resistant
0.00 resistant
Natural selection
Resistance to antibacterial soap
Generation 1: 1.00 not resistant
0.00 resistant

Generation 2: 0.96 not resistant

0.04 resistant

mutation!
Natural selection
Resistance to antibacterial soap
Generation 1: 1.00 not resistant
0.00 resistant

Generation 2: 0.96 not resistant

0.04 resistant

Generation 3: 0.76 not resistant

mutation! 0.24 resistant
Natural selection
Resistance to antibacterial soap
Generation 1: 1.00 not resistant
0.00 resistant

Generation 2: 0.96 not resistant

0.04 resistant

Generation 3: 0.76 not resistant

0.24 resistant

Generation 4: 0.12 not resistant

0.88 resistant
Natural selection can cause
populations to diverge

divergence
Selection on sickle-cell allele

aa – abnormal ß hemoglobin very low

fitness
sickle-cell anemia

AA – normal ß hemoglobin intermed.

fitness
vulnerable to malaria

Aa – both ß hemoglobins high

fitness
resistant to malaria
Selection favors heterozygotes (Aa).
Both alleles maintained in population (a at low level).
 How does genetic structure
change?
• mutation

• migration
genetic change by chance alone
• natural selection • sampling error
• misrepresentation
• small populations
• genetic drift

• non-random mating
Genetic drift
Before:
8 RR 0.50 R
8 rr 0.50 r

After:
2 RR 0.25 R
6 rr 0.75 r
 How does genetic structure
change?
• mutation

• migration cause changes in

allele frequencies
• natural selection

• genetic drift

• non-random mating
 How does genetic structure
change?
• mutation

• migration mating combines alleles

into genotypes
• natural selection
• non-random mating
• genetic drift non-random
allele combinations
• non-random mating
 A A
A aa x aa AA x AA
A A a
A A aa AA
a
A
A a
0.8 0.2
allele frequencies:
A = 0.8
a = 0.2
A AA Aa
0.8 0.8 x 0.8 0.8 x 0.2

genotype frequencies:
a AA = 0.8 x 0.8 = 0.64
0.2 aA aa
0.2 x 0.8 0.2 x 0.2 Aa = 2(0.8 x0.2) = 0.32
aa = 0.2 x 0.2 = 0.04
 Genetic Equilibrium
• Genetic drift
All can affect the
• Mutation
• Mating choice
transmission of genes
• Migration from generation to
• Natural selection generation

If none of these factors is operating then the

relative proportions of the alleles (the ALLELE
FREQUENCIES) will be constant.
Population genetics
• genetic structure of a population
Population genetics
• genetic structure of a population
group of individuals
of the same species
that can interbreed
Population genetics
• genetic structure of a population
• alleles group of individuals
• genotypes of the same species
that can interbreed

Patterns of genetic variation in populations

Changes in genetic structure through time
Describing genetic structure
• genotype frequencies
• allele frequencies
GENERAL FORMULA FOR FREQUENCY:

No.of individual or Allele that

possess the characteristic
𝐹𝑟𝑒𝑞𝑢𝑒𝑛𝑐𝑦𝑃𝑒𝑟𝑐𝑒𝑛𝑡𝑎𝑔𝑒 = x 100
𝑇𝑜𝑡𝑎𝑙 𝑃𝑜𝑝𝑢𝑙𝑎𝑡𝑖𝑜𝑛 𝑜𝑟 𝐴𝑙𝑙𝑒𝑙𝑒𝑠
Describing genetic structure
• genotype frequencies
• allele frequencies genotype
frequencies:
rr = white = 200
200/1000 = 0.2 rr
Rr = pink = 500
500/1000 = 0.5 Rr
=
RR = red = 300 300/1000 = 0.3 RR

total = 1000 flowers

 RR = RED =5
Rr = ORANGE =4
Rr = BLUEGREEN
TOTAL FISH = 12 =3

GENOTYPIC FREQUENCY
RR = 5/12 = 0.42 or 42%
Rr = ORANGE = 0.33 or 33%
Rr = BLUEGREEN = 0.25 or 25%

RED SCALES = HOMOZYGOUS DOMINANT TRAIT

ORANGE SCALE = HETEROZYGOUS TRAIT
BLUEGREEN SCALES = HOMOZYGOUS RECESSIVE TRAIT
Describing genetic structure
• genotype frequencies
• allele frequencies
allele
200 rr = 400 r frequencies:
900/2000 = 0.45 r
500 Rr = 500 r
= 500 R 1100/2000 = 0.55 R

300 RR = 600 R
total = 2000 alleles
 RR = RED = 5 x 2 = 10
Rr = ORANGE
R=4
r =4
Rr = BLUEGREEN = 3 x 2 = 6
TOTAL ALLELES OF FISH = 24

ALLELE FREQUENCY
R = 10 + 4 = 14/24 = 0.58 or 58%
r = 4 + 6 = 10/24 = 0.42 or 42%

RED SCALES = HOMOZYGOUS DOMINANT TRAIT

ORANGE SCALE = HETEROZYGOUS TRAIT
BLUEGREEN SCALES = HOMOZYGOUS RECESSIVE TRAIT
RR = RED = 5 x 2 = 10
Rr = ORANGE
R=4
r =4
Rr = BLUEGREEN = 3 x 2 = 6
TOTAL ALLELES OF FISH = 24

ALLELE FREQUENCY
R = 10 + 4 = 14/24 = 0.58 or 58%
r = 4 + 6 = 10/24 = 0.42 or 42%

RED SCALES = HOMOZYGOUS DOMINANT TRAIT

ORANGE SCALE = HETEROZYGOUS TRAIT
BLUEGREEN SCALES = HOMOZYGOUS RECESSIVE TRAIT
for a population calculate:
with genotypes:

100 GG Genotype frequencies

160 Gg

Phenotype frequencies

140 gg
Allele frequencies
for a population calculate:
with genotypes:

100 GG Genotype frequencies

100/400 = 0.25 GG
260 160/400 = 0.40 Gg 0.65
160 Gg 140/400 = 0.35 gg

Phenotype frequencies
260/400 = 0.65 green
140/400 = 0.35 brown
140 gg
Allele frequencies
360/800 = 0.45 G
440/800 = 0.55 g
another way to calculate
allele frequencies:

100 GG Genotype frequencies

0.25 GG G 0.25
0.40 Gg G 0.40/2 = 0.20
160 Gg 0.35 gg g 0.40/2 = 0.20
g 0.35

Allele frequencies
140 gg 360/800 = 0.45 G
440/800 = 0.55 g

OR [0.25 + (0.40)/2] = 0.45

[0.35 + (0.40)/2] = 0.65
 THE HARDY WEINBERG PRINCIPLE

Step 1
• Calculating the allele frequencies from the
genotype frequencies
▪Easily done for codominant alleles (each
genotype has a different phenotype).

© 2016 Paul Billiet ODWS

 Iceland

Population
• 313 337 (2007 est)
Area
• 103 000 km2
Distance from mainland
Europe
• 970 km

© 2016 Paul Billiet ODWS

 Example Icelandic population: The MN
blood group

Sample Phenotypes Type M Type MN Type N

Population
Genotypes MmMm MmMn MnMn
747 Numbers 233 385 129

Contribution 2 Mm 1 Mm 1 Mn 2 Mn
to gene pool alleles allele allele alleles
per per per per
person person person person

© 2016 Paul Billiet ODWS

 MN blood group in Iceland

Total Mm alleles = (2 x 233) + (1 x 385) = 851

Total Mn alleles = (2 x 129) + (1 x 385)= 643
Total of both alleles =1494
= 2 x 747
(humans are diploid organisms)
Frequency of the Mm allele = 851/1494= 0.57 or 57%
Frequency of the Mn allele = 643/1494 = 0.43 or 43%

© 2016 Paul Billiet ODWS

 In general for a diallellic gene A and a (or Ax
and Ay)

If the frequency of the A allele = p

and the frequency of the a allele = q
Then p+q = 1

© 2016 Paul Billiet ODWS

 Calculated Allele Frequency

•Calculated allele frequency

▪to predict the EXPECTED genotypic
frequencies in the NEXT generation
OR
▪to verify that the PRESENT population is
in genetic equilibrium.

© 2016 Paul Billiet ODWS

 Assuming all the individuals mate
randomly

NOTE: SPERMS
The allele frequencies
are the gamete Mm 0.57 Mn 0.43
frequencies too

Mm 0.57 MmMm MmMn

0.32 0.25
EGGS
Mn 0.43 MmMn MnMn
0.25 0.18

© 2016 Paul Billiet ODWS

Close enough for us to assume genetic
equilibrium
Genotypes Expected Observed
frequencies frequencies

MmMm 0.32 233  747 = 0.31

MmMn 0.50 385  747 = 0.52

MnMn 0.18 129  747 = 0.17

© 2016 Paul Billiet ODWS

 In general for a diallellic gene A and a (or Ax
and Ay)

Where the allele

frequencies are p and q SPERMS
Then p + q = 1
and A p a q
So the genotype frequencies are:
AA = p2
Aa = 2pq A p AA p2 Aa pq
aa = q2 EGGS
or p2 + 2pq + q2 = 1 a q Aa pq aa q2

© 2016 Paul Billiet ODWS

 DEMONSTRATING GENETIC
EQUILIBRIUM

Only one of the populations below is in genetic equilibrium. Which one?

Population sample Genotypes Allele frequencies

AA Aa aa A a
100 20 80 0
100 36 48 16
100 50 20 30
100 60 0 40
© 2016 Paul Billiet ODWS
 DEMONSTRATING GENETIC
EQUILIBRIUM

Population sample Genotypes Allele frequencies

AA Aa aa A a
100 20 80 0 0.6 0.4
100 36 48 16 0.6 0.4
100 50 20 30 0.6 0.4
100 60 0 40 0.6 0.4
© 2016 Paul Billiet ODWS
 DEMONSTRATING GENETIC
EQUILIBRIUM

Population sample Genotypes Allele frequencies

AA Aa aa A a
100 20 80 0 0.6 0.4
100 36 48 16 0.6 0.4
100 50 20 30 0.6 0.4
100 60 0 40 0.6 0.4
© 2016 Paul Billiet ODWS
 DEMONSTRATING GENETIC
EQUILIBRIUM

p2 + 2pq + q2 = 1
(0.6)2 + 2(0.6)(0.4) + (0.4)2 = 1
0.36 + 0.48 + 0.16 = 1 SPERMS
1=1
A p (0.6) a q (0.4)

A p AA 0.36 Aa 0.24
EGGS (0.6)
a q Aa 0.24 aa 0.16
(0.4)
© 2016 Paul Billiet ODWS
 DEMONSTRATING GENETIC
EQUILIBRIUM

Population sample Genotypes Allele frequencies

AA Aa aa A a
100 20 80 0 0.6 0.4
100 36 48 16 0.6 0.4
100 50 20 30 0.6 0.4
100 60 0 40 0.6 0.4
© 2016 Paul Billiet ODWS
 Population genetics
✓ What is population genetics?
✓ Calculate - genotype frequencies
- allele frequencies

Why is genetic variation important?

Genetic variation in space and
time
Why is genetic variation important?
potential for change in genetic structure
• adaptation to environmental change
- conservation
•divergence of populations
- biodiversity
Why is genetic variation important?

global
variation warming survival

EXTINCTION!!

no variation
Why is genetic variation important?

variation

no variation
Why is genetic variation important?

divergence

variation

NO DIVERGENCE!!
no variation