Download Lecture 10 Population Genetics

Lecture 10
Population Genetics
CAMPBELL BIOLOGY
Chapter 13
Hox Genes –
Control development –
Hox genes need to be highly
regulated to get expressed at
the right time and correct
level to orchestrate
mammalian development in
utero.
Mario Capecchi won the Nobel Prize in 2007 for his research on Hox genes &
their role in defining the mammalian development plan. Individual Hox
genes were mutated in mice and the effects of the mutations observed.
In TCD last week at History Society!
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The study of populations is intimately related to the study
of evolution.
  It is the population, not the individual that evolves.
  Evolution can be defined in terms of what happens to the genetic
structure of a population over time.
  Typically populations undergo changes in:
Size
Composition
Behaviour
i.e. number of individuals
i.e. the extent of phenotypic variation
i.e. mating behaviour
Charles Darwin saw evolution in these terms.
He agreed with Malthus who proposed that populations could
in theory increase in size exponentially.
But not in practice because of resource limitations: food and space
  Natural Selection
Darwin proposed that in most situations in nature there will be
competition to survive and reproduce and that this was governed
by a process he called natural selection
That any being, if it vary however slightly, in any manner
profitable to itself………will have a better chance of surviving
This implies a better chance of reproducing – leaving offspring
If the variation which increased the chances of survival were to be
inherited, then the offspring would also have a better chance
of survival and reproduction
  Over time any gene variant that contributed to a selective
advantage would increase in frequency in the population
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  Populations, Gene Pools and Gene Frequencies
  A population is defined as: A group of individuals that
interbreed freely and randomly
  In general a population will consist of members of a species
between which breeding can occur
  Such a population shares what is called a Gene Pool
= the sum of all alleles at all gene loci in the population
  As an example imagine a population of wild flowers in which
there are two types which differ in colour
The single flower colour locus has 2 alleles: A for pink flowers
which is completely dominant over the allele a for white flowers
Calculating Allele and Genotype frequencies
Suppose the imaginary population consists of 500 individual plants
  20 of these produce white flowers (homozygous recessive): a a
  The remaining 480 have pink flowers: 320 are homozygous AA
160 are heterozygous A a
We can define the genetic structure of the population i.e.
the composition of the gene pool in terms of:
(1) the genotype frequencies i.e. frequency of AA, Aa and
aa
or
(2) the allele frequencies
i.e. Frequency of A
Frequency of a
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Genetic structure of the parent population s gene pool
1. Calculating Genotype frequencies
Genotype
Frequencies
320
500
160
500
20
500
2. Calculating Allele Frequencies in the population
Genotype
Frequency
320
500
160
500
20
500
x2
Number of
alleles in
gene pool
(640 + 160)
800
1000
Allele
frequency
p = frequency of A = 0.8
x2
(160 + 40)
200
1000
q = frequency of a = 0.2
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  What can allele frequencies tell us about a population?
(1)  Whether the gene pool is stable or undergoing change
(2)  We can estimate the rate of change
(3) If we know the rate of change we can make predictions about
likely future trends
(4) This has important applications in conservation of wild
populations and in captive breeding programmes
Is there any rule which defines how gene pools behave from
generation to generation?
Yes: the Hardy-Weinberg Theorem or Equation
The Hardy-Weinberg theorem
This is a fundamental concept in Population Genetics
It states that:
the frequencies of alleles and genotypes in a population s
gene pool will remain constant from generation to generation
unless
it is acted upon by factors other than sexual recombination
Put another way:
on its own, the shuffling of alleles during meiosis and
fertilization has no effect on the overall genetic structure
of a population over time
The Hardy-Weinberg theorem describes a non-evolving population!
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The Hardy-Weinberg theorem also states the conditions under
which gene frequencies are not expected to change:
1. The population is infinitely large or at least large enough so
that no sampling errors occur
2. Within the population mating occurs at random
3. There is no selective advantage for any genotype
i.e. all gametes are equally viable and fertile
4. There is no mutation
no migration
  These parameters describe a non-evolving population
Deriving the Hardy-Weinberg equation
We saw earlier how we can use genotype frequencies to calculate
allele frequencies in our imaginary wild flower population
p = frequency of A = 0.8
q = frequency of a = 0.2
These actually represent the probabilities of finding a given type
of gamete (A or a) in the gene pool
What happens to genotype frequencies in the next generation?
We can use the rule of multiplication of probabilities, to calculate the
frequencies of the 3 possible genotypes in the next generation
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Allele and genotype frequencies in the second generation
Types of sperm
A
p = 0.8
a
q = 0.2
Types of egg
A
p = 0.8
AA
p2=0.64
a
Aa
aA
pq=0.16
pq=0.16
q = 0.2
aa
q2=0.04
Genotype
Frequencies
Allele Freq s
p2 = 0.64 AA
2pq = 0.32 Aa
p = 0.8 A
q2 = 0.04 aa
q = 0.2 a
From this we can derive a general formula that describes
allele and genotype frequencies in a population
Hardy-Weinberg equation =
p2 + 2pq + q2 = 1
This formula enables us to calculate allele frequencies if we know
the frequency of genotypes
This can be used to calculate the % of the human population
that carries alleles for an inherited disease
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e.g. Cystic Fibrosis a recessive inherited disease in humans
Affected individuals are homozygous recessive cf cf
and occur with a frequency of 1 in 1600 in the population
Therefore q2 = 1/1600
and q = 1/40 = 0.025
The allele frequency of the mutant cf allele is 0.025
The allele frequency of normal / wild type allele CF
is p = 1 – q = 0.975
What is the frequency of CF carriers?
Heterozygotes 2pq = 2x0.975x0.025= 0.048
1 in 20 people have the genotype CF cf
i.e. approximately
Heterozygotes are termed carriers of the disease allele
We have discussed:
(1)  How populations can be defined in terms of the alleles
they contain i.e. the Gene Pool
(2) How to calculate genotype and allele frequencies
(3) The Hardy-Weinberg theorem which describes how
allele and genotype frequencies remain the same from
generation to generation unless acted upon by factors
other than recombination
When allele frequencies do not change from generation
to generation the population is said to be in a
Hardy-Weinberg equilibrium
This describes an essentially non-evolving population
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A non-evolving population is the exception rather than the rule
If a population is evolving, then allele frequencies will change
over time i.e. the composition of the gene pool will change from
one generation to the next
Let s look at the kinds of forces that drive changes in allele
frequencies i.e. the forces that drive evolution
Because changes in a population s gene pool is evolution on a small
scale, we refer to it as microevolution
Microevolution occurs even if the frequency of alleles are changing
for only a single locus
If we track allele and genotype frequencies in a population over
many generations, some loci will show a Hardy-Weinberg
equilibrium but alleles at other loci will be changing
  There are 5 causes of microevolution.
Each one is the opposite of the conditions required for a
Hardy-Weinberg equilibrium to be maintained:
Factors promoting equilibrium
Factors driving microevolution
1. A very large population size
1. Genetic drift
2. Isolation from other gene pools
2. Gene flow
3. No mutation
3. Mutation
4. Random mating
4. Non-random mating
5. No selection for
advantageous alleles
5. Natural selection
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1. Genetic drift
Every new generation in a population draws its alleles from the
previous generation
If this occurs at random and the population is very large, then the
allele frequencies in the new generation will be the same
But if the population undergoes a large reduction in size, then
(a) the statistical probabilities can be drastically altered and
(b) the allele frequencies in the new generation can differ
dramatically from the parental generation
  Random changes in allele frequencies because of chance
fluctuations in population size is called: Genetic Drift
We can observe the effects of Genetic Drift on allele frequencies
in an imaginary population over three generations
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www.google.ie/imgres?imgurl=http://evolution.berkeley.edu/evosite/evo101
What might cause 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
Certain alleles will
be over-represented
in the survivor
population and other
alleles will be
under-represented
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Genetic drift may also occur if a new population is established
on an isolated island by a few individuals
The most extreme case would be the founding of a new isolated
population by one pregnant animal or a single plant seed.
Genetic drift caused in this way is said to be due to the Founder Effect.
The Founder Effect probably account for the high frequency of
certain inherited disorders e.g. Huntington s Chorea (neurodegenerative disorder) in regions of South America,
This is thought to be due to the founding of new communities
during the 17th century by individual sailors of European origin
who unwittingly carried the disease allele,
2. 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
Most populations are not completely isolated !
Therefore a population may gain new alleles or lose alleles as a
result of a process called Gene Flow
biology.unm.edu/ccouncil/Biology_203/Images/PopGen/bugflow.gif
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
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www.google.ie/imgres?imgurl=http://evolution.berkeley.edu/evosite/evo101
3. Mutation
A mutation is any change in the nucleotide sequence of an
organism s 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.
If an allele has a frequency of 0.50 in the gene pool and it mutates
to become a new allele at a rate of 0.00001 mutations per generation,
it would take 2000 generations to reduce the frequency of the original
allele from 0.50 to 0.49
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If a new mutant allele increases its frequency by a significant
amount in a population:
  its not because mutation is generating the new allele in
abundance
  its because individuals carrying the mutant allele are producing
a disproportionate number of offspring as a result of natural
selection or genetic drift
Mutation can have an extremely powerful effect on the rate of
evolution especially if a mutation confers a major adaptive
or selective advantage
e.g. a mutant allele which confers resistance to rat poison
Mutation is also the original source of the genetic variation that
serves as the raw material for natural selection
4. Non-random mating
For a population to be in Hardy-Weinberg equilibrium an
individual
of any genotype must be able to choose mates at random
In practice, individuals usually mate more often with close
Neighbours than with more distant members of the same
population especially in species that do not disperse far
This gives rise to neighbourhood effects which in turn can lead to
inbreeding
The most extreme case of inbreeding is self-fertilization which is
particularly common in species that are both male and female
i.e. hermaphrodites e.g. many plants can self-fertilize
Inbreeding causes the relative frequency of genotypes to deviate
from what is expected from Hardy-Weinberg equilibrium
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5. Natural Selection
Hardy-Weinberg equilibrium requires that all individuals in a
population are equal in their ability to survive and produce
viable, fertile offspring.
This condition is probably never completely met.
Populations consist of varied individuals and on average some
variants leave more offspring than others.
This differential success in reproduction is due to natural selection.
Of all the agents driving microevolution, selection is the most likely
to adapt a population to its environment.
An interesting example of how powerful a force natural selection
can be, is provided by the peppered moth Biston betularia.
Before 1850 – 99% of moths were light-coloured and wellcamoflaged against their predators.
As the Industrial Revolution advanced, pollutants especially soot,
darkened the surfaces on which the moths would land.
Light-coloured moths on dark surfaces were easy prey for birds.
The previously rare dark-coloured moths suddenly gained a huge
selective advantage.
A single dominant allele C was responsible for
dark colour. Over a 50 year period, there was a
rapid increase in the frequency of the C allele.
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The wonderful wildlife on the Galapagos Islands,
for example, the blue-footed boobies, Sula nebouxii excisa
was such an inspiration to Charles Darwin
that it prompted him to formulate his theory of
evolution (1861).
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