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BIOL2202 Genetics > Module 5--Population Genetics & Genomics > Flashcards

Module 5--Population Genetics & Genomics Flashcards

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1
Q

What causes temporal changes in the genetic makeup of a population?

A

Systematic and random evolutionary forces

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2
Q

What is the Theory of Allele Frequencies?

A

When the members of a population mate randomly, it is easy to predict the frequencies of the genotypes from the frequencies of their constituent alleles

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3
Q

How to calculate allele frequencies?

A

Frequency of an allele = number of the allele / total number of alleles

In the example, frequency of LM = (1787 x 2 + 3039) / (1787 + 3039 + 1303) x 2 = 0.53

frequency of LN = (1303 x 2 + 3039) / (1787 + 3039 + 1303) x 2 = 0.47

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4
Q

What is the probability that a homozygous dominant individual will be born?

A

p x p = p2

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5
Q

What is the probability that a carrier individual will be born?

A

p x q x 2 = 2pq

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6
Q

What is the probability that a homozygous recessive individual will be born?

A

q x q = q2

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7
Q

What assumption is made in the Hardy-Weinberg Principle (this table)?

A

Random mating between individuals in the population

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8
Q

What equation defines the frequency of the three genotypes, under random mating?

A

p2 + 2pq + q2 = 1

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9
Q

What is the Hardy-Weinberg Principle?

A

-Describes mathematical relationships between allele frequencies and genotype frequencies

p2 + 2pq + q2 = 1

-Allows the prediction of a population’s genotype frequencies form its allele frequencies

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10
Q

What is the Hardy-Weinberg equilibrium?

A

The Hardy-Weinberg genotype frequencies persist generation after generation, if mating is random and no differential survival or reproduction exists

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11
Q

How to check for agreement between observed data and predicted numbers?

A

By calculating chi-square statistic

X2 = Sum [(observed of one genotype-expected of one genotype)2/expected of one genotype]

-If X2 <0.001, population is in HW equilibrium

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12
Q

What effect does mutation have on Hardy-Weinberg equilibrium?

A

If the rate of mutation from A to a or from a to A changes, then the frequencies of A and a will change in Hardy-Weinberg equilibrium

(So HW equilibrium assumes that there is no mutation in population)

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13
Q

What are the results of non-random mating?

A

Non-random mating may lead to an excess of homozygous individuals

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14
Q

What is the result of inbreeding/consanguineous mating?

A

Homozygosity across the whole genome

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15
Q

What is the result of assortative mating/mating between alike individuals?

A

Homozygosity only in the genes associated with assortative mating, which increases linkage disequilibrium around

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16
Q

What effect does natural selection have on Hardy-Weinberg equilibrium?

A

Elimination of individuals carrying a deleterious phenotype will drive genotypic and allele frequencies away from H-W equilibrium

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17
Q

What is population subdivision?

A

When populations separate from one another, they become different

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18
Q

What effect does population subdivision have on Hardy-Weinberg principle?

A

Differences accumulated between populations violate the Hardy-Weinberg principle of uniform allele frequencies throughout the population

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19
Q

What processes play a major role in genetic differentiation?

A
  • Genetic drift
  • Migration
  • Natural selection
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20
Q

What is migration?

A

Introduction of genotypes via migration can alter allele and genotypic frequencies

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21
Q

What is the effect of population merging?

A

Reduces heterozygosity (Wahlund effect)

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22
Q

What happens if populations remain in Hardy-Weinberg equilibrium?

A

Population are not evolving

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23
Q

How natural selection changes allele frequencies?

A

Allele frequencies change systematically in populations because of differential survival and reproduction among genotypes

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24
Q

What is fitness, w?

A

Ability to survive and reproduce

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25
Q

What does the fitness value represent?

A

Each member of the population has its own fitness value

  • 0 if it dies/fails to reproduce
  • 1 if it survives and produces 1 offspring
  • 2 if it survives and produces 2 offsprings, etc.
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26
Q

How to calculate the average fitness of the population?

A

By averaging the fitness of individuals

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27
Q

What is the idea behind relative fitness?

A

Survival and/or reproductive rate of a genotype (or phenotype) is different in different environments

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28
Q

What is the relative fitness of the superior genotype(s) in each environment?

A

= 1

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29
Q

What is fitness deviation, s?

A
  • It is the selection coefficient
  • Measures the intensity of natural selection acting on the genotypes in the population
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30
Q

What is the relative fitness of the inferior genotype(s) in each environment?

A

= a deviation from 1

= 1 - s1

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31
Q

How to calculate the relative contributions of a genotype?

A
  • p2 x fitness of genotype (AA)
  • 2pq x fitness of genotype (Aa)
  • q2 x fitness of genotype (aa)
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32
Q

How to obtain the proportional contributions of each genotype to the next generation?

A

= Relative contribution of a genotype / Sum of all relative contributions of all genotypes

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33
Q

In the next generation, all of the alleles transmitted by aa homozygotes are a, and half the alleles transmitted by the Aa heterozygotes are a. How to calculate the frequency of a in the next generation, q’?

A

q’ = proportional contribution of aa + 1/2 x proportional contribution of Aa

  • q’ will be less than q, if natural selection against allele a
  • q’ will be larger than q, if natural selection in favor of allele a
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34
Q

How can fitness be influenced?

A
  • By different alleles of a single gene
  • By the allele of many genes that affect quantitative traits (more often)
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35
Q

How can natural selection affect the distribution of a quantitative trait?

A

Through directional selection, disruptive selection, or stabilizing selection

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36
Q

What are the 3 types of natural selection?

A
  • Directional selection favors values of a trait at one end of its distribution
  • Disruptive selection favors extreme values of a trait at the expense of intermediate values
  • Stabilising selection favours intermediate values of a trait
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37
Q

What is random genetic drift?

A

Allele frequencies change unpredictably in popluations because of uncertainties during reproduction

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38
Q

What factors contribute to random genetic drift?

A
  • The alleles of segregating genes are randomly incorporated into gametes
  • Random variation in the number of offspring that a parent produces
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39
Q

What is the effect of random genetic drift on different population size?

A
  • In large populations, the effect of genetic drift is minimal
  • In small populations, genetic drift may be the primary evolutionary force
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40
Q

How is the effect of population size on genetic drift measured?

A

By monitoring the frequency of heterozygotes of a population over time

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41
Q

What is the equation of the frequency of heterozygotes in the next generation, H’?

A

H’ = (1 - 1/2N) x H

  • N = popuation size
  • H = current frequency of heterozygotes
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42
Q

In one generation, random genetic drift causes the heterozygosity to decline by a factor of ____

A

1/2N

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43
Q

In t generation, what equation indicates declining heterozygosity?

A

Ht = (1 - 1/2N)t x H

-If Ht reaches 0, all genetic variability is lost

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44
Q

What message does this graph show?

A

-In small population, heterozygosity decades faster

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45
Q

In alleles are selectively neutral and the population mates randomly,

  • the probability that an allele will ultimately be fixed in the population is ____
  • the probabiity that the allele will be lost is ____
  • the probability of allele fixation or lost is ____
A
  • its current frequency
  • 1 minus its current frequency
  • independent of population size
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46
Q

How is dynamic equilibrium created?

A

Evolutionary forces may acit in opposing ways to create a dynamic equilibrium in which there is no net change in allele frequencies

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47
Q

What is balancing selection?

A

It occurs when there is overdominance

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48
Q

How to calculate allele frequencies at equilibrium with balancing selection?

A
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49
Q

What produces a stable equilibrium?

A

Balancing selection

50
Q

What is mutation-selection balance?

A

Continuous elimination of deleterious alleles by selection

  • Input by mutation
  • Output by selection
51
Q

Draw the relative fitness table for mutation-selection balance.

A
52
Q

In mutation-selection balance, how a dynamic equilibrium is created?

A

When selection eliminates deleterious alleles that are produced by recurrent mutation

53
Q

In mutation-selection balance, how genetic equilibrium is reached?

A

When the introduction of the allele into the population by mutation rate, u, is balanced by the elimination of the allele by selection, with intensity, s, against the recessive homozygotes

  • u = sq2
  • q = sqr(u/s)
54
Q

In mutation-selection balance, if the allele is lethal, then what is q?

A

q = u-1/2

u = sq2

q = sqr(u/s), when allele is lethal, s=1

q = sqr(u)

55
Q

What is mutation-drift balance?

A

Mutation replenishes the variability that is lost due to drift

  • Mutation increases heterozygosity
  • Drift decreases heterozygosity
56
Q

What equations represent what happens at equilibrium at mutation-drift balance?

A
57
Q

In mutation-drift balance, what is the effect of population size?

A

-In small populations, drift dominates over mutation

–> loss of heterozygosity = fast

–> fixation = fast

–> drift = strong

–> mutational target = small

-In large populations, mutation dominates over drift

–> loss of heterozygosity = slow

–> fixation = slow

–> drift = weak

–> mutational target = large

58
Q

What is linkage disequilibrium?

A

Non-random association of alleles at two or more loci in a general population

(2nd Law of Mendel does not apply)

59
Q

How can linkage disequilibrium be measured from observed frequency and expected frequency?

A

D = observed frequency - expected frequency

D = x11 - p1 x q1

D = p1q1 x p2q2 - p1q2 x p2q1

60
Q

What is the equation for D’ parameter?

A

D’ = D/Dmax

61
Q

What is the range of D?

A

0-1

62
Q

What is the range of D’?

A

-1 to 1

63
Q

How to measure linkage disequilibrium using r2?

A

r2 = D2 / (p1 x p2 x q1 x q2)

64
Q

What is the relationship between linkage disequilibrium and distance?

A

Linkage disequilibrium decays over distance

-closer markers have greater linkage disequilibrium than distant markers

65
Q

What is the relationship between linkage disequilibrium and time?

A

Linkage disequilibrium decays over time

-young new mutations exist in long haplotypes

66
Q

What is genetic hitchhiking?

A

When an allele changes frequency not because it itself is under natural selection, but because it is near another gene that is undergoing a selective sweep and that is on the same DNA chain

67
Q

What is background selection?

A

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

68
Q

How to measure linkage disequilibrium from parental and recombinant gametes?

A

LD = p1q1 p2q2 - p1q2 p2q1

LD = x11x12 - x12x21

69
Q

Where is the equilibrium point at linkage equilibrium?

A

When the fraction of parental gametes equals the fraction of recombinant gametes

p1q1 x p2q2 = p1q2 x p2q1

p1q1 x p2q2 - p1q2 x p2q1 = 0

70
Q

What is the value of linkage disequilibrium if recombinant gametes are not produced?

A

LD > 0

71
Q

What is the value of linkage disequilibrium if parental gametes are not produced?

A

LD < 0

72
Q

Why linkage disequilibrium decays with distance?

A

Because close (linked) loci in chromosome produce few recombinants, whereas farther apart loci produce many recombinants

73
Q

Why linkage disequilibrium decays with time?

A

Every generation, a round of recombination between two genes will reduce their genetic association

74
Q

How will happen to linkage disequilibrium if a new mutation arises?

A

Alleles will be in linkage disequilibrium with that new mutation

They will form a haplotype

75
Q

What is the selection coefficient of deleterious or slightly deleterious mutations?

A

s > 1

76
Q

What is the selection coefficient of neutral mutations?

A

s = 0

77
Q

What is the selection coefficient of advantageous mutations?

A

s < 1

78
Q

Why molecules with fewer functional constraints evolve faster?

A

Because the number of effectively neutral substitutions is higher

79
Q

What does the Neutral Theory assume?

A

It assumes that favourable mutations are rare

80
Q

Would most silent (synonymous) mutations be neutral, favourable, or deleterious?

A

Neutral

81
Q

Would most replacement mutations be neutral, favourable, or deleterious?

A

Deleterious

82
Q

What will happen to most new neutral mutations in a population initially (first 20 generations): fixation, loss, or polymorphism?

A

Loss

83
Q

What will happen to most new deleterious mutations in a population initially (first 20 generations): fixation, loss, or polymorphism?

A

Loss

84
Q

How does the size of the population change the number of new mutations that occur at a locus each generation?

A

The larger the population size is, the more new mutations occur

85
Q

How does the size of the population change the probability that a new neutral mutation will fix in a population?

A

Probability of fixation increases in small populations

86
Q

On average, will it take longer to fix a new neutral mutation in a small or large population?

A

The larger the population is, the longer it takes

87
Q

How does the size of the population change the level of polymorphism expected (= number of different alleles at a locus, assuming that all of them are neutral)?

A

The larger the population is, the higher the level of polymorphism is

88
Q

Overall, out of all the polymorphisms at a locus in a population, would you expect more of them to be replacement or silent mutations?

A

Same

89
Q

How to calculate the number of mutations per generation?

A

μ0 = 2Nμ

2N = number of mutant copies

μ = mutation rate

90
Q

How to calculate the probability of fixation?

A

p0 = 1/2N

91
Q

What is the result of multiplying the number of mutations per generation and probability of fixation?

A

substitution rate = mutation rate

92
Q

What does the Neutral Theory hypothesise?

A

Most substitutions are neutral across species

93
Q

What is the relationship between the rate of evolution, the rate of substitution, and the mutation rate when evolution proceeds by genetic drift?

A

All same

94
Q

Under drift, how does population size affect the generation and maintenance of genetic diversity?

A

Larger population generate and carry more variability than in small populations

95
Q

What is the main difference between the Neutral Theory and the Nearly Neutral Theory?

A

Population size only has effect in the Nearly Neutral Theory

96
Q

In Nearly Neutral Theory, what factor is considered?

A

Probability of fixation for slightly deleterious mutations

97
Q

In Nearly Neutral Theory, _____ overpowers _____ in large populations

A

Selection overpowers drift in large population

98
Q

In Nearly Neutral Theory, _____ overpowers _____ in small populations

A

Drift overpowers selection in small populations

99
Q

What are the types of selection at the molecular level?

A
  • Purifying, or
  • Directional
100
Q

What tests can detect an excess of favourable mutations in the genome?

A
  • Tajima’s D
  • Fst Based Tests
  • HKA Test
  • dN/dS ratio tests
  • Macdonald-Kreitman test
101
Q

What is the time to fixation, for neutral mutations?

A

4N

102
Q

What is the effect of population size on neutral mutations?

A

Neutral mutations are highly sensitive to population size

103
Q

What is the time between new mutations that fix, for neutral mutations?

A

u-1

104
Q

What is a neutrality test?

A

A statistical method aimed at rejecting a model of neutral evolution

105
Q

What is the neutrality hypothesis?

A
  • Strongly deleterious mutations are immediately eliminated from the population
  • If this is the only type of selection, then the only mutations that segregate in the population are neutral
106
Q

What are the other assumptions of the neutrality hypothesis?

A
  • The efficacy of selection depends both on s and on the effective population size Ne
  • Selection efficacy is reduced when multiple selected alleles segregate in the population: Interference
107
Q

What is selective sweep?

A

A new beneficial mutation will rise in frequency (prevalence) in a population

108
Q

As selected mutations increase in frequency, they tend to _____ _____ in the neighboring region where neutral variants are segregating.

A

Reduce variation

109
Q

What is fixation?

A

Allele rise to 100% frequency

110
Q

What is the signature of a selective sweep?

A

Reduced genetic variability around the selected gene

111
Q

What is a frequency spectrum?

A

A count of the number of mutations that exist in a frequency of xi = i/n; for i = n - 1, in a sample of size n

112
Q

What is Tajima’s D?

A

Difference between two measures of nucleotide diversity,

  • Average number of polymorphic mutations, pi
  • Number of segregating mutations, Theta
113
Q

How to get the average number of polymorphic mutations, pi?

A

Sum the totals from tables and divide the number of comparisons

e.g. (10+6+3+1)/10 = 2

114
Q

How to get the number of segregating mutations, theta, (number of polymorphic sites)?

A

Number of sites where differences are found

e.g. 4

115
Q

How to calculate Tajima’s D?

A

-Substract average number of polymorphic mutations (pi) with number of segregating mutations (Theta)

d = pi - theta

-Divide d by the standard deviation to get D

116
Q

How to interpret the value of Tajima’s D?

A
  • Negative Tajima’s D: excess of low frequency polymorphisms
  • Neutral expectation is that pi = Theta; D = 0
  • Balancing selection is expected to give a positive D value
117
Q

_____ _____ tend to produce significantly negative values of Tajima’s D

A

Population expansions

118
Q

_____ _____ tend to produce significantly positive values of Tajima’s D.

A

Population bottlenecks

119
Q

What is dN/dS ratio test?

A

dN = rate of nonsynonymous substitution per nonsynonymour site

dS = rate of synonymous substitution per synonymous site

dN/dS < 1: deleterious replacements

dN/dS = 1: neutral replacements

dN/dS > 1: beneficial replacements

120
Q

What is the hypothesis for McDonald-Kreitman test?

A

All mutations are neutral

All dN/dS polymorphic sites should equal for dN/dS fixed differences

121
Q

What is the alternate hypothesis of McDonals-Kreitman test?

A

Replacements are favoured

Favoured mutations fixed quickly, so dN/dS polymorphic < dN/dS fixed

122
Q

What is McDonald-Kreitman test about?

A
  • If evoultion of protein is neutral, the percentage of mutations that alter amino acids should be the same in all lineages being compared
  • If all mutations are neutral, all should have the same probability of persisting
  • So, dN/dS among polymorphisms should be the same as within fixed differences

BIOL2202 Genetics (6 decks)

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