Human Evolution – Parts 1 and 2
How to use this to ACTIVELY RECALL:
Bullet-point Question/Answer format
Based on Lectures and Knowledge Clips provided by the VU
Colour the questions RED until you perfect them. Colour them GREEN once you’ve mastered
them. Then, ONLY practice the red question, until they’re all green.
Follow lecture and knowledge clip slides to view images and visuals corresponding to the notes.
Lectures 1: Skipped as it is a formal course introduction.
Lectures 2 and 3 – Population genetics
Population genetics
Genetics are associated with
geography - so people living in
certain areas can have certain
genetic traits.
Say you see a huge association
with geography and genetic data
when you’ve tested 100,000
people. What if you took only
100 of them? Then you would
see a lot less differences
between them, because those
disparities are caused by very tiny
variations. So the more you zoom out,
the more differences you will see.
What are loci? Number of
people/samples. So Loci number
matters when looking at trends in
geographical DNA.
Explain what is in the genetic structure plot alongside. Each vertical line is very thin and
represents a person’s DNA - and this person comes from a cultural community. The colour
represents the continental region their DNA matches. There is a bit of overlap.
What is a genetic cluster? Different groups of people that have DNA patterns.
What are some causes of genetic variation in a population? Mutations, linkage disequilibrium,
migration, genetic drift, and natural selection pressures.
HW Equilibrium
What are the traits of an ideal population? No migration, no mutation, no selection, a large
population (no genetic drift) and Panmixia.
What is Panmixia? Random mating in a population - the
likelihood that any individual breeds within another
individual is the same for all individuals.
Why do population geneticists use the ideal Hardy
Weinberg equilibrium model? Because they want to create
a null model with a clean slate, so that they can then see
what the affecting factors in the population are.
What is a locus? Position in the genome. Alleles are
variants at a locus - every individual has 2 alleles at each
locus.
What is the genotype? The two alleles at a locus.
, What is allele frequency? The proportion of a specific allele in a population
What is the allele frequency of this bunny? 0.5 → (½ for each)
What is the genotype frequency of this
bunny in its own population? 1
What are the allele frequencies and
genotype frequencies in the second
bunny picture?
What is a HWE in terms of allele and
genotype frequencies? If the allele
frequencies for a locus with two alleles
are equal to p and q, then the frequencies
of the three genotypes they form are
equal to p^2, 2pq and q^2
What are the allele frequencies in the T and t
picture alongside? So after solving it, you can
compare it to the actual observed frequencies to
see if equilibrium actually exists.
What does a HW disequilibrium show in a
population? That some change is going on.
How does human footprint index affect distance
travelled by species? As human footprint index
increases, the distance goes down.
How can a mutation lead to change in HWE and
cause selection? Will change the kind of allele
expressed, that can lead to natural selection.
In the picture alongside, which of the 3
populations is in HWE and why? Population 2 because of the math.
What is wrong with pop1 - why is it not meeting the HWE? Has much more homozygous
than the heterozygous version. Probably due to a preference of homozygous individuals to
breed with each other for some reason.
What is wrong with population 3? Much more heterozygous version and none of the
homozygous recessive. This could be because it was a lethal combination of alleles that killed
before birth so none of those genotypes actually remain in the population.
Neutral evolution: genetic drift, founder effect and bottleneck
What is the neutral theory of evolution? Not all aspects of an organism are because of natural
selection - there are other processes (like genetic drift) that cause change over time. So not all
elements are neutral, but some definitely are.
So what is our initial assumption about ideal allele frequency? P + q = 1. So they are both 0.5.
Then certain factors cause this ratio to change over time.
What will happen to the ideal 0.5 and 0.5 allele frequencies if there is No migration, no
mutation, no selection, lots of Panmixia, but the population is not infinitely large? Then these
ratios (allele frequencies) will change.
So what happens if you have a very large population within initial allele frequencies of 0.5
and 0.5 after say 500 generations vs 40000 generations? After 500 generations, there will be
some variation in the ratio but not much at all (like maybe 0.6 to 0.4). After 40000
generations, it turns to a ratio where some individuals have a 1.0 to 0 ratio, some have 0 to 1.0
(allele fixation) and a few are still maintaining both alleles.
So what happens if you have a very small population within initial allele frequencies of 0.5
and 0.5 after say 500 generations vs 40000 generations? After 500 generations, there will be
way more variation than in the large sample (0.8 to 0.2 is possible for example). After 40000,
it will be even more! Many will have lost an allele as the ratio becomes 1.0 to 0 or vice versa.
The more generations, the more variation regardless of population size.
What is allele fixation and what is polymorphism? Allele fixation is when the frequency of
one allele becomes 100%, so 1. Polymorphism is when some ratio of both is maintained.
, How can you
mathematically describe
the likelihood of a
fixation of new
mutations? There are 2n
alleles in a diploid
population (2 per person, so n is the population number). The likelihood that a new mutation
fixes is k = 1/2n. The mutation rate is R per generation, so probability of fixation happening
per generation is 2nR.
What real world aspect can cause a difference in the calculated fixation and the real fixation?
The pop size n is assumed that everyone reproduces and that the ratio of males to females is
even, but this is not always the case.
What does a smaller N effective (so a smaller breeding population than actually expected)
mean? Faster genetic drift, more interbreeding, loss of genetic diversity → genetic drift is
high, which causes random alleles to be lost quicker, reducing genetic diversity.
How to calculate Ne?
What is genetic drift? Evolution and random mutations that occur by chance, and not by
advantage.
Migration - Fst and isolation by distance
What is genetic distance? A number
indicating the degree to which
populations differ in allele frequency.
Measured using F(st) - measures how
much variation is actually caused by
population structure.
How is F(st) calculated?
What do different F(st) values
indicate?
What does the graph for the ibex, wolf
and bear show? Ibex has highest F(st),
showing that there is the most
variation. The slope is also the steepest
showing this variation occurs within
the smallest geographical distance.
What is isolation by distance? More
distance between species = more
genetic difference between them.
The ibex has a strong signal of
isolation by distance due to less
mobility and less gene flow.
Why do the wolf and bear have less
isolation by difference? Maybe
more room to move and to cause
less fixation or loss of alleles.
Population size could be different
as well.
So usually as you move further from a location,
you see the Fst increasing and the number of
alleles present declines. This genetic diversity is
lost maybe because of inbreeding (caused by
isolation or lower population due to migration
and venturing into new territories – population
bottleneck).
How to use this to ACTIVELY RECALL:
Bullet-point Question/Answer format
Based on Lectures and Knowledge Clips provided by the VU
Colour the questions RED until you perfect them. Colour them GREEN once you’ve mastered
them. Then, ONLY practice the red question, until they’re all green.
Follow lecture and knowledge clip slides to view images and visuals corresponding to the notes.
Lectures 1: Skipped as it is a formal course introduction.
Lectures 2 and 3 – Population genetics
Population genetics
Genetics are associated with
geography - so people living in
certain areas can have certain
genetic traits.
Say you see a huge association
with geography and genetic data
when you’ve tested 100,000
people. What if you took only
100 of them? Then you would
see a lot less differences
between them, because those
disparities are caused by very tiny
variations. So the more you zoom out,
the more differences you will see.
What are loci? Number of
people/samples. So Loci number
matters when looking at trends in
geographical DNA.
Explain what is in the genetic structure plot alongside. Each vertical line is very thin and
represents a person’s DNA - and this person comes from a cultural community. The colour
represents the continental region their DNA matches. There is a bit of overlap.
What is a genetic cluster? Different groups of people that have DNA patterns.
What are some causes of genetic variation in a population? Mutations, linkage disequilibrium,
migration, genetic drift, and natural selection pressures.
HW Equilibrium
What are the traits of an ideal population? No migration, no mutation, no selection, a large
population (no genetic drift) and Panmixia.
What is Panmixia? Random mating in a population - the
likelihood that any individual breeds within another
individual is the same for all individuals.
Why do population geneticists use the ideal Hardy
Weinberg equilibrium model? Because they want to create
a null model with a clean slate, so that they can then see
what the affecting factors in the population are.
What is a locus? Position in the genome. Alleles are
variants at a locus - every individual has 2 alleles at each
locus.
What is the genotype? The two alleles at a locus.
, What is allele frequency? The proportion of a specific allele in a population
What is the allele frequency of this bunny? 0.5 → (½ for each)
What is the genotype frequency of this
bunny in its own population? 1
What are the allele frequencies and
genotype frequencies in the second
bunny picture?
What is a HWE in terms of allele and
genotype frequencies? If the allele
frequencies for a locus with two alleles
are equal to p and q, then the frequencies
of the three genotypes they form are
equal to p^2, 2pq and q^2
What are the allele frequencies in the T and t
picture alongside? So after solving it, you can
compare it to the actual observed frequencies to
see if equilibrium actually exists.
What does a HW disequilibrium show in a
population? That some change is going on.
How does human footprint index affect distance
travelled by species? As human footprint index
increases, the distance goes down.
How can a mutation lead to change in HWE and
cause selection? Will change the kind of allele
expressed, that can lead to natural selection.
In the picture alongside, which of the 3
populations is in HWE and why? Population 2 because of the math.
What is wrong with pop1 - why is it not meeting the HWE? Has much more homozygous
than the heterozygous version. Probably due to a preference of homozygous individuals to
breed with each other for some reason.
What is wrong with population 3? Much more heterozygous version and none of the
homozygous recessive. This could be because it was a lethal combination of alleles that killed
before birth so none of those genotypes actually remain in the population.
Neutral evolution: genetic drift, founder effect and bottleneck
What is the neutral theory of evolution? Not all aspects of an organism are because of natural
selection - there are other processes (like genetic drift) that cause change over time. So not all
elements are neutral, but some definitely are.
So what is our initial assumption about ideal allele frequency? P + q = 1. So they are both 0.5.
Then certain factors cause this ratio to change over time.
What will happen to the ideal 0.5 and 0.5 allele frequencies if there is No migration, no
mutation, no selection, lots of Panmixia, but the population is not infinitely large? Then these
ratios (allele frequencies) will change.
So what happens if you have a very large population within initial allele frequencies of 0.5
and 0.5 after say 500 generations vs 40000 generations? After 500 generations, there will be
some variation in the ratio but not much at all (like maybe 0.6 to 0.4). After 40000
generations, it turns to a ratio where some individuals have a 1.0 to 0 ratio, some have 0 to 1.0
(allele fixation) and a few are still maintaining both alleles.
So what happens if you have a very small population within initial allele frequencies of 0.5
and 0.5 after say 500 generations vs 40000 generations? After 500 generations, there will be
way more variation than in the large sample (0.8 to 0.2 is possible for example). After 40000,
it will be even more! Many will have lost an allele as the ratio becomes 1.0 to 0 or vice versa.
The more generations, the more variation regardless of population size.
What is allele fixation and what is polymorphism? Allele fixation is when the frequency of
one allele becomes 100%, so 1. Polymorphism is when some ratio of both is maintained.
, How can you
mathematically describe
the likelihood of a
fixation of new
mutations? There are 2n
alleles in a diploid
population (2 per person, so n is the population number). The likelihood that a new mutation
fixes is k = 1/2n. The mutation rate is R per generation, so probability of fixation happening
per generation is 2nR.
What real world aspect can cause a difference in the calculated fixation and the real fixation?
The pop size n is assumed that everyone reproduces and that the ratio of males to females is
even, but this is not always the case.
What does a smaller N effective (so a smaller breeding population than actually expected)
mean? Faster genetic drift, more interbreeding, loss of genetic diversity → genetic drift is
high, which causes random alleles to be lost quicker, reducing genetic diversity.
How to calculate Ne?
What is genetic drift? Evolution and random mutations that occur by chance, and not by
advantage.
Migration - Fst and isolation by distance
What is genetic distance? A number
indicating the degree to which
populations differ in allele frequency.
Measured using F(st) - measures how
much variation is actually caused by
population structure.
How is F(st) calculated?
What do different F(st) values
indicate?
What does the graph for the ibex, wolf
and bear show? Ibex has highest F(st),
showing that there is the most
variation. The slope is also the steepest
showing this variation occurs within
the smallest geographical distance.
What is isolation by distance? More
distance between species = more
genetic difference between them.
The ibex has a strong signal of
isolation by distance due to less
mobility and less gene flow.
Why do the wolf and bear have less
isolation by difference? Maybe
more room to move and to cause
less fixation or loss of alleles.
Population size could be different
as well.
So usually as you move further from a location,
you see the Fst increasing and the number of
alleles present declines. This genetic diversity is
lost maybe because of inbreeding (caused by
isolation or lower population due to migration
and venturing into new territories – population
bottleneck).
