Populations

 A group of the same species

living in an area that may
interbreed freely.

 No 2 individuals are exactly

alike (variations)

 More Fit individuals survive &

pass on their traits
 The Gene Pool
Members of a species can interbreed
& produce fertile offspring
 Species have a shared gene pool
 Gene pool – all of the alleles of all
individuals in a population
A population with continuosly
changing gene pool frm 1 generation
to next generation---shows
evolutionaty changes.
Gene pool does not change-- genetic
equilibrium
 Population genetic
The study of inherited variation in a
population.

Allele frequency
• Ratio of any given allele in a
population, relative to the other
alleles of that gene at the same
locus.

Genotype frequency
• percentage of individual with specific
genotype in a population
 Assumptions of the H-W
n Theorem
Large population size
- small populations can have chance
fluctuations in allele frequencies (e.g., fire,
storm).
n No migration
- immigrants can change the frequency of
an allele by bringing in new alleles to a
population.
n No net mutations
- if alleles change from one to another, this
will change the frequency of those alleles
 Assumptions of the H-W
n Theorem
Random mating
- if certain traits are more desirable, then
individuals with those traits will be
selected and this will not allow for
random mixing of alleles.
n No natural selection
- if some individuals survive and
reproduce at a higher rate than others,
then their offspring will carry those
genes and the frequency will change for
the next generation.
 Hardy-Weinberg Equilibrium
                                   
The gene pool of a non-evolving population remains
constant over multiple generations; i.e., the allele
frequency does not change over generations of time.
 
The Hardy-Weinberg Equation:
 
                              p2 + 2pq + q2 = 1
                                               
where p2 = frequency of AA genotype; 2pq = frequency of
Aa plus aA genotype; q2 = frequency of aa genotype
Evolution does occur within populations.

Evolution within a species/population = microevolution.

Microevolution refers to changes in allele frequencies in a

gene pool from generation to generation. Represents a
gradual change in a population.
 
Causes of microevolution:
                       
1)  Genetic drift

11) Natural selection (1 & 2 are most important)

13)Gene flow

15)Mutation
POPULATION
GENETICS

Predicting inheritance in a population

 THE HARDY WEINBERG PRINCIPLE
Step 1
 Calculating the gene frequencies from the genotype

frequencies
 Easily done for codominant alleles.

MN blood group
Sample Phenotypes Type M Type MN Type N
Population
Genotypes MM MN NN
747 Numbers 233 385 129

Contribution 2M 1M 1N 2N
to gene pool alleles allele allele alleles
per per per per
person person person person
MN blood group
Total M alleles = (2 x 233) + (1 x 385) = 851
Total N alleles = (2 x 129) + (1 x 385) = 643
Total of both alleles =1494
= 2 x 747

Frequency of the M allele = 851/1494 = 0.57 or 57%

Frequency of the N allele = 643/1494 = 0.43 or 43%

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
Step 2

 Using the calculated gene frequency to

predict the EXPECTED genotypic
frequencies in the NEXT generation
OR
 to verify that the PRESENT population is

in genetic equilibrium
Assuming all the individuals mate
randomly
NOTE the gene frequencies are the gamete frequencies too

SPERMS

M 0.57 N 0.43

M 0.57 MM MN
0.32 0.25
EGGS
N 0.43 MN NN
0.25 0.18
Close enough for us to
assume genetic equilibrium

Genotypes Expected Observed

frequencies frequencies

MM 0.32 233 ÷ 747 = 0.31

MN 0.50 385 ÷ 747 = 0.52

NN 0.18 129 ÷ 747 = 0.17

In general for a diallellic
gene A and a (or Ax and Ay)
Where the gene frequencies are p and q
Then p + q = 1
and SPERMS

A p a q

A p AA p2 Aa pq
EGGS
a q Aa pq aa q2
THE HARDY WEINBERG EQUATION

So the genotype frequencies are:

AA = p2
Aa = 2pq
aa = q2

or p2 + 2pq + q2 = 1
DEMONSTRATING GENETIC
EQUILIBRIUM
Using the Hardy Weinberg Equation to
determine the genotype frequencies from the
gene frequencies may seem a circular
argument
Only one of the populations below is
in genetic equilibrium. Which one?

Population sample Genotypes Gene frequencies

AA Aa aa A a
100 20 80 0
100 36 48 16
100 50 20 30
100 60 0 40
Only one of the populations below is
in genetic equilibrium. Which one?

Population sample Genotypes Gene 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
Only one of the populations below is
in genetic equilibrium. Which one?

Population sample Genotypes Gene 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
SICKLE CELL ANAEMIA IN WEST
AFRICA, A BALANCED
POLYMORPHISM
β haemoglobin gene
 Normal allele HbN

 Sickle allele HbS

Phenotypes Normal Sickle Sickle Cell Alleles

Cell Trait Anaemia
Genotypes HbNHbN HbN HbS HbS HbS HbN HbS
Observed 0.56 0.4 0.04
frequencies
Expected
frequencies
SICKLE CELL ANAEMIA IN WEST
AFRICA, A BALANCED
POLYMORPHISM
β haemoglobin gene
 Normal allele HbN

 Sickle allele HbS

Phenotypes Normal Sickle Sickle Cell Alleles

Cell Trait Anaemia
Genotypes HbNHbN HbN HbS HbS HbS HbN HbS
Observed 0.56 0.4 0.04 0.76 0.24
frequencies
Expected 0.58 0.36 0.06
frequencies
SICKLE CELL ANAEMIA IN THE
AMERICAN BLACK POPULATION

Phenotypes Normal Sickle Sickle Cell Alleles

Cell Trait Anaemia
Genotypes HbNHbN HbN HbS HbS HbS HbN HbS
Observed 0.9075 0.09 0.0025
frequencies
Expected
frequencies
SICKLE CELL ANAEMIA IN THE
AMERICAN BLACK POPULATION

Phenotypes Normal Sickle Sickle Cell Alleles

Cell Trait Anaemia
Genotypes HbNHbN HbN HbS HbS HbS HbN HbS
Observed 0.9075 0.09 0.0025 0.91 0.09
frequencies
Expected 0.8281 0.16 0.0081
frequencies
RECESSIVE ALLELES

EXAMPLE ALBINISM IN THE BRITISH

POPULATION
Frequency of the albino phenotype
= 1 in 20 000 or 0.00005
A = Normal skin pigmentation allele
Frequency = p
a = Albino (no pigment) allele
Frequency = q
Phenotypes Genotypes Hardy Observed
Weinberg frequencies
frequencies
Normal AA p2
0.99995
Normal Aa 2pq

Albino aa q2 0.00005
Albinism gene frequencies

Normal allele =A=p=?

Albino allele = q = √ (0.00005) = 0.007 or 7%
HOW MANY PEOPLE IN BRITAIN
ARE CARRIERS FOR THE ALBINO
ALLELE (Aa)?
a allele = 0.007 =q
A allele =p
But p+q =1
Therefore p = 1- q
= 1 – 0.007
= 0.993 or 99.3%
The frequency of heterozygotes (Aa) = 2pq
= 2 x 0.993 x 0.007
= 0.014 or 1.4%
Heterozygotes for rare
recessive alleles can be
quite common
 Genetic inbreeding leads to rare recessive

mutant alleles coming together more

frequently
 Therefore outbreeding is better
 Outbreeding leads to hybrid vigour
Example: Rhesus blood
group in Europe
What is the probability of a woman who
knows she is rhesus negative (rhrh)
marrying a man who may put her child at
risk (rhesus incompatibility Rh– mother and
a Rh+ foetus)?
Rhesus blood group

A rhesus positive foetus is possible if the father

is rhesus positive
RhRh x rhrh → 100% chance
Rhrh x rhrh → 50% chance
Rhesus blood group

Rhesus positive allele is dominant Rh

Frequency = p
Rhesus negative allele is recessive rh
Frequency = q
Frequency of rh allele = 0.4 = q
If p+q=1
Therefore Rh allele = p = 1 – q
= 1 – 0.4
= 0.6
Rhesus blood group

 Frequency of the rhesus positive phenotype

= RhRh + Rhrh
 = p2 + 2pq
 = (0.6)2 + (2 x 0.6 x 0.4)
 = 0.84 or 84%
Rhesus blood group
Phenotypes Genotypes Hardy Observed
Weinberg frequencies
frequencies
Rhesus positive RhRh p2
0.84
Rhesus positive Rhrh 2pq

Rhesus negative Rhrh q2 0.16

 Therefore, a rhesus negative, European woman in Europe has

an 84% chance of having husband who is rhesus positive…
 of which 36% will only produce rhesus positive children and 48%
will produce rhesus positive child one birth in two
Estimating Allele Frequencies
from Recessive Homozygote
Frequency
 If Hardy-Weinberg equilibrium is assumed (an assumption we will
examine shortly), it is possible to estimate the allele frequencies for a
gene that shows complete dominance even though heterozygotes can’t
be distinguished from the dominant homozygotes.
 The frequency of recessive homozygotes is q2. Thus, the frequency of
the recessive allele is the square root of this. Very simple.
 For example, the recessive genetic disease PKU has a frequency in the
population of about 1 in 10,000. q2 thus equals 0.0001 (10-4). The
square root of this is 0.01 (10-2), which implies that the frequency of the
PKU allele is 0.01 and the frequency of the normal allele is 0.99. Thus
the frequency of the heterozygous genotype is 2 * 0.99 * 0.01 = 0.198.
Abut 2% of the population is a carrier of the PKU allele.

 Note again: this ASSUMES H-W equilibrium, and this assumption is not
always true.
 Necessary Conditions for Hardy-
Weinberg Equilibrium
 The relationship between allele frequencies and genotype frequencies
expressed by the H-W equation only holds if these 5 conditions are met.
None of them is completely realistic, but all are met approximately in many
populations.

 If a population is not in equilibrium, it takes only 1 generation of meeting these

conditions to bring it into equilibrium. Once in equilibrium, a population will
stay there as long as these conditions continue to be met.

 1. no new mutations
 2. no migration in or out of the population
 3. no selection (all genotypes have equal fitness)
 4. random mating
 5. very large population
Testing for H-W Equilibrium
 If a population where we can distinguish all 3 genotypes,
we can use chi-square test to see if the population is in H-
W equilibrium.
 The steps:
1. Count the numbers of each genotype to get the observed genotype
numbers, then calculate the observed genotype frequencies.
2. Calculate the allele frequencies from the observed genotype
frequencies.
3. Calculate the expected genotype frequencies based on the H-W
equation, then multiply by the total number of offspring to get
expected genotype numbers.
4. Calculate the chi-square value using the observed and expected
genotype numbers.
5. Use 1 degree of freedom (because there are only 2 alleles).
 Example
• Data: 26 MM, 68 MN, 106 NN, with a total population of 200 individuals.
• 1. Observed genotype frequencies:
– MM: 26/200 = 0.13
– MN: 68/200 = 0.34
– NN:106/200 = 0.53
• 2. Allele frequencies:
– M: 0.13 + 1/2 * 0.34 = 0.30
– N: 0.53 + 1/2 * 0.34 = 0.70
• 3. Expected genotype frequencies and numbers:
– MM: p2 = (0.30)2 = 0.09 (freq) x 200 = 18
– MN: 2pq = 2 * 0.3 * 0.7 = 0.42 (freq) * 200 = 84
– NN: q2 = (0.70)2 = 0.49 (freq) * 200 = 98
• 4. Chi-square value:
– (26 - 18)2 / 18 + (68 - 84)2 / 84 + (106 - 98)2 / 98
– = 3.56 + 3.05 + 0.65
– = 7.26
• 5. Conclusion: The critical chi-square value for 1 degree of freedom is
3.841. Since 7.26 is greater than this, we reject the null hypothesis
that the population is in Hardy-Weinberg equilibrium.
 Japanese Blood Type Personality Chart

My Boyfriend Best Traits

Type A
Conservative, reserved, patient, punctual,

is Type B
perfectionist and good with plants.
Worst Introverted, obsessive, stubborn, self conscious,
Traits and uptight

Type B
Best Traits Creative and passionate. Animal loving.
Optimistic and flexible
Worst Forgetful, irresponsible, individualist
Traits

Type AB
Best Traits Cool, controlled, rational. Sociable and popular.
Empathic
Worst Aloof, critical, indecisive and unforgiving
Traits

Type O
Best Traits Ambitious, athletic, robust and self-confident.
Natural leaders
Worst Arrogant, vain and insensitive. Ruthless
Traits
 1) Genetic drift

Genetic drift = alteration of the gene pool of a small

population due to chance.

Two factors may cause genetic drift:

                                    
• Bottleneck effect may lead to reduced genetic
variability following some large disturbance that
removes a large portion of the population. The
surviving population often does not represent the
allele frequency in the original population.

• Founder effect may lead to reduced variability when a

few individuals from a large population colonize an
isolated habitat.
*Yes, I realise that this is not really a cheetah.
2) Natural selection
                                   
As previously stated, differential success in reproduction
based on heritable traits results in selected alleles being
passed to relatively more offspring (Darwinian
inheritance).

The only agent that results in adaptation to environment.

 

3) Gene flow
                                   
-is genetic exchange due to the migration of fertile
individuals or gametes between populations.
 
 4) Mutation
                                   
Mutation is a change in an organism’s DNA and is
represented by changing alleles. 
 
Mutations can be transmitted in gametes to offspring,
and immediately affect the composition of the gene pool.

The original source of variation.

Genetic Variation, the Substrate for Natural Selection
           
Genetic (heritable) variation within and between
populations: exists both as what we can see (e.g., eye
color) and what we cannot see (e.g., blood type).
 
Not all variation is heritable.

Environment also can alter an individual’s phenotype [e.g.,

the hydrangea we saw before, and…

…Map butterflies (colour changes are due to seasonal

difference in hormones)].
Mutation
 Mutation is unavoidable. It happens as a result of radiation in the
environment: cosmic rays, radioactive elements in rocks and soil,
etc., as well as mutagenic chemical compounds, both natural
and artificially made, and just as a chance event inherent in the
process of DNA replication.
 However, the rate of mutation is quite low: for any given gene,
about 1 copy in 104 - 106 is a new mutation.
 Mutations provide the necessary raw material for evolutionary
change, but by themselves new mutations do not have a
measurable effect on allele or genotype frequencies.
Migration
 Migration is the movement of individuals in or out of
a population. Migration is necessary to keep a
species from fragmenting into several different
species. Even as low a level as one individual per
generation moving between populations is enough
to keep a species unified.
 Migration can be thought of as combining two
populations with different allele frequencies and
different numbers together into a single population.
After one generation of random mating, the
combined population will once again be in H-W
equilibrium.
Migration Examples
 Population X has 20 individuals with frequency of the A allele = 0.8. Population
Y has 10 individuals with frequency of the A allele = 0.2. The two populations
mix. What is the frequency of A in the final population?
 There are 20 + 10 = 30 individuals in the final population, for a total of 60 copies
of the gene.
 For population X, 40 * 0.8 = 32 copies are A, and 8 are a.
 For population Y, 20 * 0.2 = 4 copies are A, and 16 are a.
 Adding these together, the final population has 32 + 4 = 36 A alleles and 8 + 16 = 24 a
alleles. Out of 60 alleles, the frequency of A is 36/60 = 0.6

 A real example: African Americans have a large proportion of African ancestry,

but also some European ancestry. The Duffy blood group has an allele with a
frequency of 0 among West African populations, and an average frequency of
0.43 among European populations. Other blood groups can also be used in this
technique: very little assortative mating occurs on the basis of blood group.
 In Oakland CA, African-Americans are reported to have about 22% European ancestry
 In Charleston South Carolina, the proportion is about 3.7%
Selection
 Selection is the primary factor driving evolution. Genes that confer
increased fitness tend to take over a population. Note that random
events also play a big factor: sometimes a “good” gene is lost due to
chance events. Also, a gene that confers increased fitness in one
environment may confer decreased fitness in another environment.
 Selection can occur at many places in the life cycle: the embryo might
be defective, the fetus might not survive to birth, the immature offspring
might be killed, the individual might not be able to find a mate or might
be sterile.
 We will simplify all of this by assuming that the gametes are produced at
random and combine at random, to produce a population of zygotes in
H-W equilibrium. Then, we will apply selection to the zygotes, killing off
different proportions of the different genotypes.
 Fitness is a function of the genotype. We will define the “relative
fitness” of the best genotype as equal to 1.0, and the fitnesses of the
two other genotypes as equal to or less than 1.
Selection Against Recessive
Homozygote
 This situation is what happens with a recessive genetic disease. Heterozygotes
and dominant homozygotes are indistinguishable and have the same relative
fitness: 1.0. The recessive homozygote has the genetic disease and a fitness
less than 1. The exact fitness depends on the nature of the disease.
 Start with a population where p = 0.6 and q = 0.4, and assume that the aa
homozygote has a relative fitness of 0.1 (i.e. 90% of the aa offspring die without
reproducing).
 The zygotes produces (in H-W equilibrium) are 0.36 AA, 0.48 Aa, and 0.16 aa.
 Selection on the zygotes reduces the aa’s by 90%, to 0.016.
 However, proportions must add to 1.0, so we divide each proportion by a
correction factor. The correction factor is the sum of the remaining proportions:
0.36 + 0.48 + 0.016 = 0.856.
 So, after selection, the frequency of AA is 0.36 / 0.856 = 0.42. The frequency of
Aa is 0.48 / 0.856 = 0.56. The frequency of aa is 0.016 / 0.856 = 0.019.
 Final allele frequencies: A = 0.42 + 1/2 * 0.56 = 0.70. a = 1 - freq(A) = 0.3.
Selection Favouring the
Heterozygote
 Some genes maintain 2 alleles in the population by having the
heterozygote more fit than either homozygote.
 An example is HbS, the sickle cell hemoglobin allele. In rural
West Africa, where malaria is endemic and medical support is
rudimentary, the relative fitness of the HbA homozygote is
estimated at 0.85, due to susceptibility to malaria. The relative
fitness of the HbS homozygote is estimated at approximately 0,
with almost none reaching reproductive age due to sickle cell
disease. The heterozygote is the most fit, so it given a relative
fitness of 1.0. Under these conditions, it is possible to predict an
equilibrium frequency of the HbS allele of about 0.13. This is
approximately what is seen in various West African countries.
Genetic Drift
 Genetic drift is the random changes in allele frequencies. Genetic drift
occurs in all populations, but it has a major effect on small populations.
 For Darwin and the neo-Darwinians, selection was the only force that
had a significant effect on evolution. More recently it has been
recognized that random changes, genetic drift, can also significantly
influence evolutionary change. It is thought that most major events
occur in small isolated populations.

 Simple example: A population of 1 female and 2 males, where the

female chooses only 1 male to mate with. Assume that the female has
the Aa genotype, male #1 is AA, and male #2 is aa.
 initially the allele frequencies are 0.5 A and 0.5 a
 if male #1 gets to mate, the offspring will have a 0.75 A, 0.25 a frequency
 if male #2 mates, the offspring will be 0.25 A and 0.75 a.
Population Bottlenecks and
Founder Effect
 Bottlenecks and the founder effect are closely related
phenomena.
 Founder effect: If a small group of individuals leaves
a larger population and develops into a separate,
isolated population, the allele frequencies in the new
population are determined by the allele frequencies
in the founders. Since these frequencies are
probably different from those found in the general
population, the new population will have a different
set of frequencies.
 This is especially true for rare alleles, which can
suddenly become prominent if one of the founders
has the rare allele.
Founder Effect Example
 Founder effect example: the Amish are a
group descended from 30 Swiss
founders who renounced technological
progress. Most Amish mate within the
group. One of the founders had Ellis-van
Crevald syndrome, which causes short
stature, extra fingers and toes, and heart
defects. Today about 1 in 200 Amish are
homozygous for this syndrome, which is
very rare in the larger US population.
 Note the effect inbreeding has here: the
problem comes from this recessive
condition becoming homozygous due to
the mating of closely related people.
Bottlenecks
 A population bottleneck is essentially the same phenomenon as the
founder effect, except that in a bottleneck, the entire species is wiped
out except for a small group of survivors. The allele frequencies in the
survivors determines the allele frequencies in the population after it
grows large once again.
 Example: Pingalop atoll is an island in the South Pacific. A typhoon in
1780 killed all but 30 people. One of survivors was a man who was
heterozygous for the recessive genetic disease achromatopsia. This
condition caused complete color blindness. Today the island has about
2000 people on it, nearly all descended from these 30 survivors. About
10% of the population is homozygous for achromatopsia This implies
an allele frequency of about 0.26.