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Lectures for Week 8
Selection, Gene Flow, and
Mutation
Andrea Hatlen
Announcements

• 

The workshop is this week. The assessment completed
during the workshop will count for 20% of your score in
this course.

• 

Please go through the PopG tutorial, you will be tested
upon entering the workshop.

• 

Please bring a pencil (and eraser)







• 

Make sure you know your Student ID number

• 

Don’t forget:
– 
– 
– 

Tuesday 12 Nov. 14:00-17:00, FB 1.15a à C800, F850, Z100
Thursday 14 Nov. 15:00-18:00, FB 115a à C300, C400, C431
Friday 15 Nov. 14:00-17:00, FB 1.23 à C100
Lecture Outline
1)  Types of Selection
2)  Gene Flow
3)  Mutation
4)  Mini Review Session
The Drift Practical
Selection

Mutation

Gene Flow
Summary of Week 6 Lectures
1)  Defined our terms
– 

Gene, Locus, Allele, Genotype, Phenotype, Gamete, Zygote,
Dominant, Recessive

2)  Introduced genetic drift
– 
– 
– 

Stochastic change in allele frequencies
Can lead to fixation or loss of alleles.
Stronger in small populations, eg. in founder events.

3)  Touched on Selection
– 
– 

Selection occurs against a background of drift
Related to ‘fitness’ of a particular genotype

Any Questions?
Darwin on Selection
In 1859 Darwin rocked the foundations of modern science with
the publication of his seminal work “On the Origin of Species by
Means of Natural Selection”
“When on board H.M.S. “Beagle”,
as a naturalist, I was much struck
with certain facts in the distribution of
the inhabitants of South America, and
in the geological relations of the present
to the past inhabitants of that
continent. These facts seemed to me to
throw some light on the origin of
species – that mystery of mysteries, as
it has been called by one of our
greatest philosophers.”


Sold for £103,250 in 2009
Darwin on Selection
Darwin looked at selection, both artificially and in the wild, and
concluded that it could lead to systematic changes over long
timescales.
“That most skillful breeder, Sir John Sebright,
used to say, with respect to pigeons, that ‘he
would produce any given feather in three years,
but it would take him six years to obtain a
head and beak’”

“I can see no good reason to doubt that female
birds, be selecting, during thousands of
generations, the most melodious or beautiful
males, according to their standard of beauty,
might produce a marked effect.”
Darwin on Selection
Darwin was unaware of Gregor
Mendel’s work on heredity, and as
such many of the details of Darwin’s
theory were wrong (see “Pangenesis”).
However, the central principles of
evolution by natural selection hold 
true to this day.
We can use our rigorous notation
from earlier lectures to obtain a more
up-to-date perspective on selection.
Darwin on Selection
Selection occurs at the level of
the…

Gene

Locus


Allele Population


Phenotype

Nucleotide

But genes can relate to phenotypes in various

different ways…
Types of Selection
If an allele is dominant then the heterozygote has the same phenotype as the
homozygote.




A is dominant


If an allele is recessive then the heterozygote has the same phenotype as the
other homozygote.


A is recessive
Types of Selection
If A is dominant then the heterozygote has the same fitness as the
homozygote




wAA = 1

wAB = 1

wBB = 0.8


If A is recessive then the heterozygote has the same fitness as the other
homozygote


wAA = 1


wAB = 0.8


wBB = 0.8
Types of Selection
Recall the picture of drift + selection from earlier lectures…

Don’t be seduced by the smoothness of these lines – drift is still occurring in
the background!
Types of Selection

Q. How can we explain the shape of this curve?
Types of Selection
When A is at high frequency B is rare, and
therefore B is most often present in
heterozygotes.

From a fitness point of view there is nothing
to differentiate AA from AB individuals, and
so there is very little phenotypic variation
for selection to operate on.
This is the same reason it is difficult
to eliminate deleterious recessive
alleles from a population, for example
in Ellis-van Creveld syndrome.
Types of Selection

Q. How can we explain the shape of this curve?
Types of Selection
Even when the A allele is at high
frequency the B allele is always ‘visible’

From a fitness point of view selection is
always acting to drive out B alleles

Dominant disorders can be driven out
of a population more easily than
recessive disorders, and hence there
are less of them around.

Marfan syndrome
Types of Selection
Other types of selection include heterozygote advantage (overdominance)…





wAA = 0.8

 wAB = 1

wBB = 0.8


and heterozygote disadvantage (underdominance)…


wAA = 1


wAB = 0.8


wBB =1
Types of Selection

Q. How can we explain the shape of this curve?
Types of Selection
There is a balance between having enough A alleles and having
too many!

A alleles rare: mostly
present in
heterozygotes


Selection for A


A alleles common:
mostly present in
homozygotes


Selection against A


The equilibrium frequency is the

point at which these forces balance out
Types of Selection
A classic example of heterozygote advantage is sickle-cell anemia.
Types of Selection
A classic example of heterozygote advantage is sickle-cell anemia.
–  The sickle-cell allele (HbS) is autosomal recessive; meaning only
homozygotes are affected
–  However, HbS also confers partial resistance to malaria, meaning in
certain parts of the world the heterozygote has the highest fitness

Historical distribution of malaria and HbS allele
Types of Selection
Types of Selection

Q. How can we explain the shape of this curve?
Types of Selection
One cause of heterozygote disadvantage is the formation of
hybrids, but more on this later…

Questions?
Announcements

• 

The workshop is this week. The assessment completed
during the workshop will count for 20% of your score in
this course.

• 

Please go through the PopG tutorial, you will be tested
upon entering the workshop.

• 

Please bring a pencil (and eraser)







• 

Make sure you know your Student ID number

• 

Don’t forget:
– 
– 
– 

Tuesday 12 Nov. 14:00-17:00, FB 1.15a à C800, F850, Z100
Thursday 14 Nov. 15:00-18:00, FB 115a à C300, C400, C431
Friday 15 Nov. 14:00-17:00, FB 1.23 à C100
Lecture Outline
1)  Types of Selection
2)  Gene Flow
3)  Mutation
4)  Mini Review Session
Gene Flow
So far we have only looked at the effects of drift and selection within a single
panmictic population. To understand how evolution works across different
populations we must talk in terms of “gene flow”.
Gene flow describes the processes by which individuals genes (or
alleles) move from one population to another.

•  Gene flow can be one-directional
or multi-directional
•  Movement of individuals does
not necessarily imply movement
of genes!
Gene Flow
In the absence of gene flow populations tend to become genetically
differentiated from one another.
Gene Flow
In the absence of gene flow populations tend to become genetically
differentiated from one another.
Gene Flow
In the absence of gene flow populations tend to become genetically
differentiated from one another.


This is mainly visible in neutral loci, which are evolving under drift alone.
Gene Flow
Gene flow homogenises populations, and can recover lost genetic variation
Gene Flow
Many populations are isolated, experiencing limited or zero gene flow.
In this case we expect drift to lead to differentiation between
populations.

Smaller numbers of differences are expected between close branches,
larger differences between more distant branches
Gene Flow
•  Branching patterns can also be
constrained by geographic
boundaries within species. In
this case, as before, drift leads
to differentiation between
distinct populations.

•  Patterns reflect the consequences of the
spread of populations since the last ice age
(ending 10,000 years ago), at the height of
which most of Europe was inhospitable for
the species that currently inhabit it.
•  Populations were restricted to refugia, and
they become a relic population of a once
more widespread species
Lecture Outline
1)  Types of Selection
2)  Gene Flow
3)  Mutation
4)  Mini Review Session
Mutation
Consider the following questions…
1)  What is mutation?
2)  What are some ways of classifying mutation?
3)  How does mutation interact with drift and selection?
Mutation
Mutation
•  The processes producing genetic variation
•  The original source of all genetic variation
•  A permanent structural alteration in DNA

In most cases, DNA changes either have no effect or cause harm, but
occasionally a mutation can improve an organism's chance of
surviving and passing the beneficial change on to its descendants.
Mutation
Point Mutation
One base exchanged for another

Insertion
Extra base pair(s) inserted

Deletion
Base pair(s) lost

Frameshift
Applies to insertions and deletions. Anything
which changes the amino acid sequence being
coded for
Mutation
There are also some larger mutational events
that can occur, including…
•  Large-scale deletion/insertion events
•  Duplication
•  Inversion
•  Translocation
and some very large…
•  Polysomy
•  Whole genome duplication
Mutation

Without some process generating variation, eventually all alleles will become
either fixed or lost over enough time
Mutation

Mutation can re-introduce lost genetic variation into a population
Mutation
•  Each gene copy experiences mutation at a rate μ
•  In a population of 2N genes this is a total mutation rate of 2Nμ
•  The chance of any one new allele going to fixation is 1/(2N)
•  Therefore…the probability of a new mutant allele going to fixation under
drift alone is 1/(2N) * 2Nμ = μ



The rate of substitution is independent

of the population size
Questions?
Sneak Peek: The Workshop
•  What happens when you make a population bigger? smaller?
(with drift or drift and selection)
•  What about if you change the fitness of one genotype or
another (aka change selection pressures)? 
•  What about if there is mutation? or migration?
Mini Revision Session
Short questions…
1.  Define the terms Dominant and Recessive. 
2.  How are relative and absolute fitness calculated?
3.  Is genetic drift stronger or weaker in a small population? Why?
Longer questions…
1.  Explain how random sampling from a finite population leads to stochastic
changes in allele frequencies.
2.  Why do we expect many more carriers of recessive deleterious alleles than
affected individuals?
3.  For an allele that is at a high frequency in a population, would selection be
able to bring it to fixation faster if it is dominant or recessive? Why?
Mini Revision Session
I will not be providing model answers for all of the mini-revision session
questions, as it is far more important that you think about these
questions yourselves! All of the answers are contained within the lecture
notes of the past two weeks – once you familiarise yourself with this
material these questions should seem fairly straightforward.



Now is a good opportunity to ask me any questions
you have before the workshop

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Evolution Lectures WK8

  • 1. Lectures for Week 8 Selection, Gene Flow, and Mutation Andrea Hatlen
  • 2. Announcements •  The workshop is this week. The assessment completed during the workshop will count for 20% of your score in this course. •  Please go through the PopG tutorial, you will be tested upon entering the workshop. •  Please bring a pencil (and eraser) •  Make sure you know your Student ID number •  Don’t forget: –  –  –  Tuesday 12 Nov. 14:00-17:00, FB 1.15a à C800, F850, Z100 Thursday 14 Nov. 15:00-18:00, FB 115a à C300, C400, C431 Friday 15 Nov. 14:00-17:00, FB 1.23 à C100
  • 3. Lecture Outline 1)  Types of Selection 2)  Gene Flow 3)  Mutation 4)  Mini Review Session
  • 5. Summary of Week 6 Lectures 1)  Defined our terms –  Gene, Locus, Allele, Genotype, Phenotype, Gamete, Zygote, Dominant, Recessive 2)  Introduced genetic drift –  –  –  Stochastic change in allele frequencies Can lead to fixation or loss of alleles. Stronger in small populations, eg. in founder events. 3)  Touched on Selection –  –  Selection occurs against a background of drift Related to ‘fitness’ of a particular genotype Any Questions?
  • 6. Darwin on Selection In 1859 Darwin rocked the foundations of modern science with the publication of his seminal work “On the Origin of Species by Means of Natural Selection” “When on board H.M.S. “Beagle”, as a naturalist, I was much struck with certain facts in the distribution of the inhabitants of South America, and in the geological relations of the present to the past inhabitants of that continent. These facts seemed to me to throw some light on the origin of species – that mystery of mysteries, as it has been called by one of our greatest philosophers.” Sold for £103,250 in 2009
  • 7. Darwin on Selection Darwin looked at selection, both artificially and in the wild, and concluded that it could lead to systematic changes over long timescales. “That most skillful breeder, Sir John Sebright, used to say, with respect to pigeons, that ‘he would produce any given feather in three years, but it would take him six years to obtain a head and beak’” “I can see no good reason to doubt that female birds, be selecting, during thousands of generations, the most melodious or beautiful males, according to their standard of beauty, might produce a marked effect.”
  • 8. Darwin on Selection Darwin was unaware of Gregor Mendel’s work on heredity, and as such many of the details of Darwin’s theory were wrong (see “Pangenesis”). However, the central principles of evolution by natural selection hold true to this day. We can use our rigorous notation from earlier lectures to obtain a more up-to-date perspective on selection.
  • 9. Darwin on Selection Selection occurs at the level of the… Gene Locus Allele Population Phenotype Nucleotide But genes can relate to phenotypes in various different ways…
  • 10. Types of Selection If an allele is dominant then the heterozygote has the same phenotype as the homozygote. A is dominant If an allele is recessive then the heterozygote has the same phenotype as the other homozygote. A is recessive
  • 11. Types of Selection If A is dominant then the heterozygote has the same fitness as the homozygote wAA = 1 wAB = 1 wBB = 0.8 If A is recessive then the heterozygote has the same fitness as the other homozygote wAA = 1 wAB = 0.8 wBB = 0.8
  • 12. Types of Selection Recall the picture of drift + selection from earlier lectures… Don’t be seduced by the smoothness of these lines – drift is still occurring in the background!
  • 13. Types of Selection Q. How can we explain the shape of this curve?
  • 14. Types of Selection When A is at high frequency B is rare, and therefore B is most often present in heterozygotes. From a fitness point of view there is nothing to differentiate AA from AB individuals, and so there is very little phenotypic variation for selection to operate on. This is the same reason it is difficult to eliminate deleterious recessive alleles from a population, for example in Ellis-van Creveld syndrome.
  • 15. Types of Selection Q. How can we explain the shape of this curve?
  • 16. Types of Selection Even when the A allele is at high frequency the B allele is always ‘visible’ From a fitness point of view selection is always acting to drive out B alleles Dominant disorders can be driven out of a population more easily than recessive disorders, and hence there are less of them around. Marfan syndrome
  • 17. Types of Selection Other types of selection include heterozygote advantage (overdominance)… wAA = 0.8 wAB = 1 wBB = 0.8 and heterozygote disadvantage (underdominance)… wAA = 1 wAB = 0.8 wBB =1
  • 18. Types of Selection Q. How can we explain the shape of this curve?
  • 19. Types of Selection There is a balance between having enough A alleles and having too many! A alleles rare: mostly present in heterozygotes Selection for A A alleles common: mostly present in homozygotes Selection against A The equilibrium frequency is the point at which these forces balance out
  • 20. Types of Selection A classic example of heterozygote advantage is sickle-cell anemia.
  • 21. Types of Selection A classic example of heterozygote advantage is sickle-cell anemia. –  The sickle-cell allele (HbS) is autosomal recessive; meaning only homozygotes are affected –  However, HbS also confers partial resistance to malaria, meaning in certain parts of the world the heterozygote has the highest fitness Historical distribution of malaria and HbS allele
  • 23. Types of Selection Q. How can we explain the shape of this curve?
  • 24. Types of Selection One cause of heterozygote disadvantage is the formation of hybrids, but more on this later… Questions?
  • 25. Announcements •  The workshop is this week. The assessment completed during the workshop will count for 20% of your score in this course. •  Please go through the PopG tutorial, you will be tested upon entering the workshop. •  Please bring a pencil (and eraser) •  Make sure you know your Student ID number •  Don’t forget: –  –  –  Tuesday 12 Nov. 14:00-17:00, FB 1.15a à C800, F850, Z100 Thursday 14 Nov. 15:00-18:00, FB 115a à C300, C400, C431 Friday 15 Nov. 14:00-17:00, FB 1.23 à C100
  • 26. Lecture Outline 1)  Types of Selection 2)  Gene Flow 3)  Mutation 4)  Mini Review Session
  • 27. Gene Flow So far we have only looked at the effects of drift and selection within a single panmictic population. To understand how evolution works across different populations we must talk in terms of “gene flow”. Gene flow describes the processes by which individuals genes (or alleles) move from one population to another. •  Gene flow can be one-directional or multi-directional •  Movement of individuals does not necessarily imply movement of genes!
  • 28. Gene Flow In the absence of gene flow populations tend to become genetically differentiated from one another.
  • 29. Gene Flow In the absence of gene flow populations tend to become genetically differentiated from one another.
  • 30. Gene Flow In the absence of gene flow populations tend to become genetically differentiated from one another. This is mainly visible in neutral loci, which are evolving under drift alone.
  • 31. Gene Flow Gene flow homogenises populations, and can recover lost genetic variation
  • 32. Gene Flow Many populations are isolated, experiencing limited or zero gene flow. In this case we expect drift to lead to differentiation between populations. Smaller numbers of differences are expected between close branches, larger differences between more distant branches
  • 33. Gene Flow •  Branching patterns can also be constrained by geographic boundaries within species. In this case, as before, drift leads to differentiation between distinct populations. •  Patterns reflect the consequences of the spread of populations since the last ice age (ending 10,000 years ago), at the height of which most of Europe was inhospitable for the species that currently inhabit it. •  Populations were restricted to refugia, and they become a relic population of a once more widespread species
  • 34. Lecture Outline 1)  Types of Selection 2)  Gene Flow 3)  Mutation 4)  Mini Review Session
  • 35. Mutation Consider the following questions… 1)  What is mutation? 2)  What are some ways of classifying mutation? 3)  How does mutation interact with drift and selection?
  • 36. Mutation Mutation •  The processes producing genetic variation •  The original source of all genetic variation •  A permanent structural alteration in DNA In most cases, DNA changes either have no effect or cause harm, but occasionally a mutation can improve an organism's chance of surviving and passing the beneficial change on to its descendants.
  • 37. Mutation Point Mutation One base exchanged for another Insertion Extra base pair(s) inserted Deletion Base pair(s) lost Frameshift Applies to insertions and deletions. Anything which changes the amino acid sequence being coded for
  • 38. Mutation There are also some larger mutational events that can occur, including… •  Large-scale deletion/insertion events •  Duplication •  Inversion •  Translocation and some very large… •  Polysomy •  Whole genome duplication
  • 39. Mutation Without some process generating variation, eventually all alleles will become either fixed or lost over enough time
  • 40. Mutation Mutation can re-introduce lost genetic variation into a population
  • 41. Mutation •  Each gene copy experiences mutation at a rate μ •  In a population of 2N genes this is a total mutation rate of 2Nμ •  The chance of any one new allele going to fixation is 1/(2N) •  Therefore…the probability of a new mutant allele going to fixation under drift alone is 1/(2N) * 2Nμ = μ The rate of substitution is independent of the population size
  • 43. Sneak Peek: The Workshop •  What happens when you make a population bigger? smaller? (with drift or drift and selection) •  What about if you change the fitness of one genotype or another (aka change selection pressures)? •  What about if there is mutation? or migration?
  • 44. Mini Revision Session Short questions… 1.  Define the terms Dominant and Recessive. 2.  How are relative and absolute fitness calculated? 3.  Is genetic drift stronger or weaker in a small population? Why? Longer questions… 1.  Explain how random sampling from a finite population leads to stochastic changes in allele frequencies. 2.  Why do we expect many more carriers of recessive deleterious alleles than affected individuals? 3.  For an allele that is at a high frequency in a population, would selection be able to bring it to fixation faster if it is dominant or recessive? Why?
  • 45. Mini Revision Session I will not be providing model answers for all of the mini-revision session questions, as it is far more important that you think about these questions yourselves! All of the answers are contained within the lecture notes of the past two weeks – once you familiarise yourself with this material these questions should seem fairly straightforward. Now is a good opportunity to ask me any questions you have before the workshop