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Evolutionary Forces Flashcards

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1
Q

How can evolutionary forces be seen

A

They must be deduced from genetic variation, fitness, phenotype, behaviour

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2
Q

How can evolutionary forces be studied

A

The forces leave signatures in the genome. This can be studied by looking into
Genetic variation of individuals (e.g. observed heterozygosity, Ho)
Comparing variation across populations (e.g. population differentiation, FST

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3
Q

What are the evolutionary forces

A 
Mutation
Random genetic drift
Recombination
Gene Flow
Natural and Sexual selection
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4
Q

What are the effects of the evolutionary force mutation

A

Increases variation (Ho) and population differentiation (FST)

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5
Q

What are the effects of the evolutionary force random genetic drift

A

Decreases variation but increase population differentiation

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6
Q

What are the effects of the evolutionary force recombination

A

Tends to reduce variation and differentiation

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7
Q

What are the effects of the evolutionary force gene flow

A

Increases genetic variation but reduces population differentiation

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8
Q

What are the effects of the evolutionary forces natural and sexual selection

A

Depends on the selection coefficients

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9
Q

How do you quantify the effects of evolutionary forces

A

population genetics - changes in allele haplotype and genotype frequencies
quantitative genetics - changes in fitness, behaviour or phenotype
phylogenetics and macro-evolution - footprints in the genome

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10
Q

How do the evo forces affect natural populations

A

They reach an equilibrium and researchers study these equilibriums, or experiment and cause deviation

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11
Q

What is a gene

A

A gene is a piece of DNA located on a particular location of a chromosome (or a locus)

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12
Q

How many alleles on locus on a sexually reproducing diploid organism

A

There are 2 - one allele originates from the mother the other from the father (except for sex chromosomes)

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13
Q

What is the hardy-weinberg equilibrium model

A

Useful null model to predict genotype frequencies from allele frequencies

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14
Q

What is a population that is in Hardy-Weinberg equilibrium is called

A

a panmictic population

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15
Q

What are the assumptions of hardy-weinberg

A

(1) Organism is diploid
(2) Reproduction is sexual
(3) Generations are non-overlapping
(4) Mating occurs at random
(5) Population size is very large
(6) Migration is zero
(7) Mutation is zero
(8) No natural selection acting gene

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16
Q

What would you conclude if you found an deficit of heterozygotes AB?
32 : 16 : 2 (expected numbers)
40 : 0 : 10 (observed)

A

(1) Extreme inbreeding (e.g. selfing),
(2) Sampling two separate populations fixed for different alleles, and/or
(3) Underdominance (heterozygotes are less fit), (4) Null alleles

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17
Q

If you would find a significant excess in a particular genotype in H-W, this suggest:

A

Selection, inbreeding (random genetic drift), gene flow (but not recombination)

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18
Q

What does a mutation do

A

Changes the DNA, the genetic code

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19
Q

What are the different types of mutations

A

Point mutations (single nucleotide polymorphisms, SNPs)
DNA replication slippage (microsatellites)
Deletion insertions (indels or frame shift mutations)
Gene duplication and deletion
Transposable elements

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20
Q

What are the fitness effects of mutation

A

Many mutations are (nearly) neutral (~ 10%, synonymous substitutions ):
Many are detrimental (90% Non-synonymous substitutions)
Very few are beneficial (~ 1-2%)

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21
Q

Why do you think that non-synonymous mutations are often detrimental (or neutral)?

A

The original genetic code is “tested & proven” over millions of years of evolution. Hence, random improvements are extremely rare!

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22
Q

What symbol is used for base mutation rate?

A

μ

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23
Q

What is the equation for the probability of an allele to stay unchanged

A

(1-μ)

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24
Q

What are the equations for the rate of mutation over time

A

pt = p0(1 - μ)t

pt=p0xe^ut

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25
Q

What is the mutation (genetic) load

A

it is the reduction in fitness caused by mutations

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26
Q

What is the mutation -selection balance

A

deleterious mutations are being generated all the time. Bad mutations are removed by selection

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27
Q

Are the majority of mutations recessive or dominant and what is the impact

A

Recessive
Their (bad) fitness effects are not expressed in the heterozygote genotypes
In heterozygote condition, recessive deleterious mutations cannot be detected
Consequently, recessive mutations generally reach a higher equilibrium frequency

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28
Q

How to estimate mutation rate

A

DNA sequence divergence and split time of fossil record
Compare genome sequences from children and their parents
Mutation accumulation experiments

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29
Q

What is something extra to consider when estimating mutation rate

A

the generation time - generation times of female and males may differ

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30
Q

What mutation rate do researchers use in fossil record calibration and why

A

typically use a mutation rate of 1 × 10−9 mutations per site per year derived from the observed DNA sequence difference of ~1.3% between the human and chimpanzee and an assumed divergence time of 7 Ma based on fossil record

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31
Q

What is the issue with fossil calibration

A

fraught with its own uncertainty, and the argument is circular
If you “know” the divergence time based on fossils, why bother estimating mutation rates to estimate it?
problem with generation times

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32
Q

two ways to estimate mutation rate

A

based on parent-offspring comparison

from fossil records

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33
Q

How to estimate mutation rate base on parent-offspring comparison

A

From the two trios (parents + offspring) the de novo germline base mutation rate µ=10-8 per base pair per generation
Factor 10 different from what people commonly use!

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34
Q

Example of when we got generation time join when considering mutation rate

A

Previously, researchers assumed 20-25 year human generation time
Currently the estimate is ~29 years (and differs between sexes)
Humans and chimp divergence time recently doubled…!

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35
Q

Why study microsatellite mutation rate of diatoms?

A

Diatoms are most common type of phytoplankton
100,000 extant species
45% of the total oceanic primary production
Many species are clonal or asexual

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36
Q

What are microsatellites

A

Repeating sequences
Generally 2 to 6 base pairs
Very common in genomes

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37
Q

What is the mutation rate of microsatellites compared to other neutral regions of DNA

A

higher rate of mutation

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38
Q

How does the size the of the microsatellite cor change

A

Slippage mutations tend to extend the size of the core repeat (Single-step mutation model (SMM))

When large, drastic deletions reduce the size (Two-phase model (TPM))

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39
Q

Why are micro satellites an important marker in micro-evolution

A

Highly polymorphic (many alleles) and high mutation rate
Microsatellites have been used in 189,000 papers in conservation
High resolution, e.g. to distinguish related individuals
High resolution allows you to observe evolutionary change over short periods of time

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40
Q

Describe how microsatelllites have high resolution

A

Parents tend to have 2 x 2 = 4 distinct alleles
Full-sib offspring have 4 possible genotypes per locus
Using 10 microsatellite loci = >1 million unique genotypes

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41
Q

Why can the high mutation rate of microsatellites be a problem

A

high mutation rate saturates the number of distinct alleles at a given locus, and causes “size homoplasy
Alleles look the same, but are not identical by descent
An individual may be homozygous at a locus, but its parents could be completely unrelated

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42
Q

What type of marker is replacing microsatellites

A

SNP markers - but you need many more SNPs than microsatellite loci to get the same resolution

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43
Q

5 conclusions of microsatellite mutation rate is diatoms

A

Microsatellite mutation rate&raquo_space; base mutation rate (~5 orders of magnitude!)
In diatoms, the rate is relatively high during clonal phase, ca. 3 - 10x higher than in humans
This can generate novel genetic variation in the absence of recombination
Highest rate was observed at start of culturing
Microsatellite mutation rate seems to be unsuitable to calibrate divergence time

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44
Q

What is genetic drift

A

Chance events leading to a loss of genetic variation

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45
Q

Processes leading to random genetic drift

A

Small population size (inbreeding)
Founder effects
Population fluctuations
Population bottlenecks

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46
Q

What trait does genetic drift share with mutation

A

random process

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47
Q

According to the neutral theory of evolution, which forces explain most of the genetic variation

A

drift and mutation

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48
Q

Who came up with neutral theory

A

Kimura 1968

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49
Q

What was the main criticism against neutral theory

A

The average heterozygosity among loci per individual in diverse species, including those with apparently immense population sizes, is mostly restricted to the range 0-20%
(Lewontin, 1974)

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50
Q

What is the symbol for actual population size

A

Ne/N

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51
Q

What is Ne

A

genetic effective population size

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52
Q

What is the relationship between Ne and N

A

Ne<

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53
Q

What causes population size fluctuations

A

Environmental disturbances
Host-parasite and predator-prey coevolution
Other frequency dependent processes

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54
Q

What reduces Ne/N ratio

A 
Fluctuation in population size
Variance in family size
Unequal sex-ratio
Overlapping generations / age structure
Mode of inheritance (Y chromosomes)
Selection (balancing selection vs Hill-Robertson effects)
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55
Q

What is a high ratio

A

when the difference between the numbers is large

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56
Q

What is a low ration

A

when the difference between the numbers is low e.g. 1:1

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57
Q

What is the common range of Ne/N in natural populations

A

≈0.0001 - 0.1

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58
Q

What does Ne/N largely depend on and give examples

A

Largely dependent on taxonomic group
Cod is mass spawner and has small Ne/N
Life bearing mammals relative high Ne/N

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59
Q

What does Vk stand for

A

Variance in reproductive success

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60
Q

What is the relationship between Vk and Ne/N

A

when reproductive variance Vk > 2, then Ne/N < 1

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61
Q

Can Ne/Ne be larger than unity

A

Yes, when Vk < 2, (minimised inbreeding regime)

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62
Q

What equation links Ne/N and Vk

A

Ne/N (roughly) = 4/Vk+2

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63
Q

What is the harmonic mean population

A

The long-term effective population size

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64
Q

Across generations, how do we determine the loss of genetic variation

A

mostly determined but the generation with the smallest Ne

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65
Q

What tends to b bigger, the harmonic mean or the arithmetic mean

A

harmonic, as it is most influenced by the smallest populations size

66
Q

What is coalescence time

A

the time in generations it takes for 2 alleles to coalesce t=2N

67
Q

Equation for nucleotide diversity

A

pi = 4Nµ

68
Q

What is the Wahlund effect

A

the Wahlund effect is a reduction of heterozygosity (that is when an organism has two different alleles at a locus) in a population caused by subpopulation structure

69
Q

What are the effects of a post-bottleneck drift after a founder event

A

It reduces genetic variation (He)

It increase genetic differentiation (FST) between the founder population and the source population

70
Q

Who developed the F statistic

A

Wright

71
Q

Equation explaining the fixation of alleles due to inbreeding and drift

A

(1 – FIT) = (1 – FIS) (1 – FST)

Loss in Vg = inbreeding x drift

72
Q

What is the equation for Fis

A

FIS = 1 – HO/HS

73
Q

What does Ho stand for

A

it is the mean observed heterozygosity in subpopulations

74
Q

What does Hs stand for

A

it is the mean expected heterozygosity in subpopulations

75
Q

What is the equation for Fst

A

FST = 1 – HS/HT

76
Q

what does Ht stand for

A

the heterozygosity when considering the subpopulations as a single population (averaging the allele frequencies)

77
Q

what does Fis and Fst express together

A

they express how much of the genetic variation is fixed within individuals

78
Q

Whis F is used to measure how much of the genetic variation is fixed due to inbreeding

A

Fis (how much is fixed within a genome as homozygosity)

79
Q

Whis F is used to measure how much of the genetic variation is fixed due to drift

A

FST (how much is fixed between subpopulations due to population fragmentation)

80
Q

Why is fixation a problem

A

Due to fixation, genetic variation is no longer available between individuals, which limits the speed of adaptive evolution

81
Q

Who introduced nearly neutral theory

A

Ohta (1970)

82
Q

Who argued that selection was the most important evolutionary force

A

Fisher 1958

83
Q

Who argued drift to be the most important evolutionary force

A

Wright 1931, 1932

84
Q

What is Wright’s argument about adaptive topography or adaptive landscape

A

With constant genotypic fitnesses and random mating, selection causes the gene frequency to change in such a way that the mean fitness of individuals in the population always increases until at equilibrium it reaches a maximum

85
Q

What are the three phases of wrights shifting balance hypothesis

A

Random genetic drift
Mass selection
Interdemic selection

86
Q

Describe Wright’s genetic drift phase

A

“when the set of gene frequencies drifts at random in the multidimensional space […] around an adaptive peak

87
Q

Describe Wright’s mass selection phase

A

when a set of gene frequencies drifts far enough outside the attraction zone of its own peak to become attracted by another peak

88
Q

Describe Wright’s interdemic selection phase

A

when migrants from the deme on the highest peak take over other subpopulations

89
Q

Explain Wright’s shifting balance hypothesis

A

Genetic drift can be thought of as a process of random exploration of the adaptive zones in a temporarily maladaptive way, on the chance that a new phenotype may be found which will be better adapted.

90
Q

Describe Kimura’s 1968 neutral theory of molecular evolution

A

that the vast majority of evolutionary changes at the molecular level are caused by random drift of selectively neutral mutants which do not affect fitness
(In genomes of existing species, the vast majority of molecular differences are selectively “neutral“)

91
Q

Why is neutral theory a cornerstone of population genetics

A

It states the null model- deviations from it imply selection

92
Q

Explain Ohta’s nearly neutral theory

A

Many polymorphisms behave neutrally, where selection is too weak to counter the drift. However, when population size is large, small selective advantages can become fixed by selection

93
Q

What causes gene flow

A

Migration can result in gene flow when the migrants successfully reproduce in the recipient population

94
Q

What does gene flow do to genetic variation

A

Gene flow tends to increase genetic variation at a local (subpopulation) level and reduces global genetic variation at the metapopulation level by reducingcoalescence time

95
Q

How are is mutations and geneflow similar

A

Like mutations, gene flow introduces novel genetic variation that is available to selection
(Reduces inbreeding but disrupts local adaptation )

96
Q

How is mutations and migration different

A

migration is a non-random process - it can be phenotype of sex dependent

97
Q

What are the concerns over genetic rescue in conservation

A

outbreeding depression/upsetting local genetic adaptation/local purity and provenance,
limited quantitative information on the expected consequences of outcrossing,
lack of clear guidelines,
costs,
risks of disease, pest and parasite spread,
disrupting social systems in some animals,
moving biological material across political jurisdictions,
regulatory barriers

98
Q

How does gene flow constrain evolutionary change

A

Darwin emphasised that isolation of populations was one factor promoting evolution.

99
Q

What was Mayr’s (1996) view on species

A

That they were ‘real’, not man-made definitions

100
Q

What was Mayr’s argument about biological species

A

He argued that a system that prevented unrestricted out-crossing to be superior as it would destroy selective advantages to particular ecological situations

101
Q

What are the flaws in the biological species concept

A

It has been disproven several times
can not apply to asexual species as they do not have sex
many recognised species of plant can hyrbridise
gene flow challenges BSC concept as it undermines species identity

102
Q

What is the BSC definition of a species

A

species is a group of organisms that can potentially interbreed, or mate, with one another to produce viable, fertile offspring.

103
Q

How can gene flow be a generating force in evolution

A

Due to wright’s shifting balance hypothesis and adaptive landscapes:
With natural selection alone, a species would be trapped on one adaptive peak even if there were higher adaptive peaks representing better adapted combinations of characters.
Gene flow allows species to explore the entire adaptive landscape by creating new gene combinations (i.e. epistasis)

104
Q

What is under-dominance

A

It is the selection against the heterozygote, causing disruptive selection and divergent genotypes

105
Q

Will gene flow have a large affect on small of large population when there is underdominance

A

In a large pop, if a BB migrant enters an AA pop, the inferior heterozygotes are likely to get lost
But in a small pop there is a high chance two inferior heterozygotes will mate and selection then favours the superior BB genotype.
A new adaptive peak is found

106
Q

Does gene flow have a bigger impact on large or small populations

A

Small - Due to chance, favourable allele or gene combinations may be generated in small populations

107
Q

what influences the rate of gene flow

A

The migration capacity of the species

108
Q

What is the effect of balancing selection on gene flow?

A

It increases the effective rate of gene flow by favouring rare genotypes (heterozygotes or rare alleles)

109
Q

What is a fragmented population called

A

a meta population

110
Q

What are the different metapopulation models

A

Mainland-island
Stepping stone
Levin’s type metapopulations

111
Q

What needs to be considered in the SLoSS debate

A 
Genetic variation within and between subpopulations
F-statistics
Effects of gene flow
Inbreeding depression
Disease outbreak
Local extinction
Local adaptation
112
Q

What is gene flows impact on Fst

A

It reduces it as gene flow homogenises allele frequency across subpopulations

113
Q

How does population sub-structuring affect coalescence time of alleles

A

It increases it:
Alleles cannot coalesce if they are in different subpopulations
Hence, more different alleles can be maintained
But these alleles are more likely to be in homozygous state (smaller subpopulation gene pool)  Wahlund effect

114
Q

What does it mean when Fst is zero

A

There are no subdivisions in the population; complete sharing of genetic material

115
Q

What does i mean when Fst is 1

A

There is no sharing a genetic material, extreme differentiation

116
Q

What does selection do

A

Alters inheritance of allele and genotype frequencies so that it is no longer neutral

117
Q

What are the types of selection

A 
Natural selection
Balancing selection
Positive (Darwinian) selection
Negative (purifying) selection
Directional selection
Disruptive selection
Stabilising selection
118
Q

Does selection increase or decrease genetic varitation and population differentiation

A

Both- depends on the type of selection

119
Q

When can selection act

A

when there is a reproductive excess (more offspring are produced than can survive and reproduce)

120
Q

How can you calculate selection coefficients

A

you base them on differences in survival rates

121
Q

What letter is used to indicate fitness

A

W (Malthusian fitness

122
Q

Why does survival need to be associated with a genotype or allele

A

because you need to identify alleles or genotypes that covey a fitness advantage or disadvantage

123
Q

What letter is used for the dominance coeffcient

A

h

124
Q

If the dominance coefficient h is =0.5 then:

A

alleles are additive (co-dominant)

125
Q

If the dominance coefficient h is <0.5 then:

A

B is recessive (or partially recessive)

126
Q

If the dominance coefficient h is >0.5 then:

A

B is dominant (or partially dominant)

127
Q

What are the equations for working out the respective fitness values

A 
AA = 1
AB = 1-0.5s
BB = 1-s
128
Q

Why do you rarely see deleterious mutations which are dominant or co dominant in large populations

A

Deleterious dominant mutations will be selected out as soon as they arrive in their heterozygous state

129
Q

How can deleterious recessive mutations be removed from large populations

A

The recessive mutatiions first need to increase in frequency due to drift before selection canact upon them

130
Q

What are the equations for measuring selection with overdominance

A 
AA = 1-s1
AB = 1
BB = 1-s2
131
Q

Which type of selection does not reduce genetic variation

A 
balancing selection (e.g. overdominance and negative frequency dependent selection) which maintain polymorphism
It maintains both A and B alleles in a population
132
Q

What is the effect of over-dominant selection Fst

A

It reduces population differentiation as is balances the allele frequencies

133
Q

Why does overdominance favours rare alleles

A

because they are more often in a heterozygous state

134
Q

What is overdominance

A

heterozygote superiority

135
Q

What is the classic example of overdominance and what are the fitnesses W

A

beta hemoglobin in populations in west africa
AA = 0.89
AS = 1
SS = ).2

136
Q

In what two cases is there not adaptive evolution

A

when there is no genetic variation or not variation in fitness values

137
Q

What is the relationship between overdominance and Fst on spatial and temporal scales

A

At a spatial scale, overdominant selection will reduce the FST
at the temporal scale, overdominant selection increases the FST by promoting the turnover of alleles.
(Every new immigrant allele has a selective advantage, causing alleles to be replaced in rapid succession).

138
Q

What is the most common selection process

A

negative (purifying selection)

139
Q

What other factors can affect temporal Fst

A

number of alleles per locus, effective migration rate

140
Q

What is disruptive selection

A

When the extremes are positively selected

141
Q

What is pleiotropy

A

where one gene effects multiples traits

142
Q

What is genetic hitchhiking

A

When an allele changes frequency, not because it is under selection, but because it is near another gene undergoing a selective sweep.

143
Q

What is a selective sweep

A

WHEN a positively selected mutation occurs and spreads in a population by directional selection, frequency of linked allele (or weakly selected) increases.

144
Q

What is background selection

A

loss of genetic diversity at a non-deleterious locus due to negative selection against linked deleterious alleles

145
Q

What is recombination’s effect on population differentiation

A

little effect or reduces it (introgression)

146
Q

What does recombination do

A

It shuffles genetic variation, increasing genetic variation at a genotypic level

147
Q

Example of recombination

A

Homologous recombination (intra-locus recombination)
Non-homologous recombination (inter-locus recombination)
Gene conversion
Chromosomal rearrangements
Introgression (between species)
Horizontal gene transfer (deeply diverged taxa)

148
Q

Why do siblings look different

A

Because of recombination

149
Q

What does recombination happen between

A 
homologous genes (often a consequence of sex), 
gene paralogous (gene conversion) and 
between different species (introgression or horizontal gene transfer)
150
Q

Why is combination important

A

It separates the good mutations from the bad, speeding up adaptive evolution

151
Q

Example of the role recombination had in adaptive evolution

A

Hybrid speciation in Lake Malawi cichlids (Domino Joyce, Hull)

152
Q

What is introgression

A

the incorporation (usually via hybridization and backcrossing) of alleles from one entity (species) into the gene pool of a second, divergent entity (species)

153
Q

What is a fixed allele?

A

A fixed allele is an allele that is the only variant that exists for that gene in all the population

154
Q

What is the relationship between Ne and Drift

A

the magnitude of drift is inversely proportional to effective pop size

155
Q

What event can dramatically decrease the harmonic mean

A

a bottleneck event

156
Q

In terms of an ideal situation, what would the relationship between N and Ne be

A

N=Ne

157
Q

What are the requirements for Ne to equal N

A

equal no. of males and females who can all reproduce
all individuals are equally likely to reproduce
the number of offspring does not vary anymore than expected by chance
Mating is random
The no. of breeding individuals is constant from one gen to the next

158
Q

What does effective population size mean

A

it is the size of the population that would lose genetic diversity/lose heterozygosity at the same rate as the actual population

159
Q

What does different sex ratios decrease Ne

A

Because not every individual will have an eqaul chance to reproduce

160
Q

Why could Ne be smaller than N

A 
anything that increases VARIANCE among individuals in reproductive success:
unequal sex ratio
high variance in family size
inbreeding
variation in pop size over generations
overlapping generations

Conservation Genetics (6 decks)

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