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Evolution > Lec 5 > Flashcards

Lec 5 Flashcards

1
Q

Overall goal of class is to discover origin and maintenance of biodiversity

A

Biogenetics are outcomes

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2
Q

Deviations from HWE: Assumption 1 - No selection

A

Natural selection results in the differential survival of certain alleles/genotypes across generations

Trees became darker due to soot, darker moths selected for (blended better with trees)

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3
Q

Pocket mice color

A

Color in mice is controlled by a single gene, with two alleles, A (dark), a (light)

Natural selection favors individuals with coat colors that offer camouflage in their natural environment

Light-colored pocket mice living in the dark lava fields suffer higher rates of mortality

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4
Q

Viability selection

A

Ability to survive to reproduce

Higher viability = better survival

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5
Q

In lava fields, which ALLELE do you hypothesize will lead to higher viability: A or a?
Brown : AA and Aa
White: aa

a) A
b) a

A

a) A

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6
Q

Based on the phenotypes you observe below, which GENOTYPE will have the highest viability in lava fields?
Brown: AA and Aa
White: aa

a) AA
b) Aa
c) aa
d) AA and Aa will have the same fitness higher than aa

A

d) AA and Aa will have the same fitness higher than aa

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7
Q

To understand how selection causes allele frequencies to change, we need to quantify the EFFECT of each genotype of viability

A

Viability selection is an AVERAGE across lots of individuals because each individual will have other alleles at many other loci that could affect survival and reproduction

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8
Q

Viability selection is about ___________

A

Average fitness

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9
Q

Average allows you to compare to ________________

A

Other alleles

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10
Q

Example of viability

A

A mouse that has a beneficial genotype (AA) at the color locus (and thus blends in well to its environment) might have deleterious alleles at the immune system loci, and thus be prone to parasites

In this example, we need to know HOW MUCH BETTER an individual with the AA or Aa genotype does, on average, compared to an individual with the aa genotype

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11
Q

Only ________________ matters when we are measuring selection

A

Relative fitness

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12
Q

Genotypes that do better ________ will survive to the next generation

A

ON AVERAGE

ALWAYS comparing genotypes to each other

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13
Q

Selection coefficient

A

Measure of the fitness REDUCTION of a particular phenotype

ALWAYS in terms of the one with smallest viability (i.e. vaa = 0.8 means it is 80% worse than vAA, vAA is 20% better than vaa)

We define selection coefficient, s, for each genotype in terms of the ratio of its viability to the largest viability

The largest relative fitness has a selection coefficient of 1

vaa/vAA = 1-s

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14
Q

Selection Coefficient: Example

A

White mouse has 60% of the survival of the dark brown mouse on the lava fields - in other words, for every 100 brown mice that survive, only 60 white mice survive

This means that the white mouse is 40% WORSE than the brown mouse

vaa/vAA = 1-saa
60/100 = 1-saa
0.4 = saa
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15
Q

Selection coefficient is selection ____ that phenotype/genotype

A

Against

If the difference in survival between AA and aa was larger (saw aa has 50% of the survival of AA), the selection coefficient would be larger

50/100 = 1-saa
saa = 0.5
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16
Q

Predicting how ALLELE and GENOTYPE frequencies change by natural selection

A

Imagine that before selection happens, we have 100 each of AA, Aa, and aa genotypes

After selection, we have 50 aa but 60AA and Aa - we can then calculate the selection coefficient, s, to look at how the frequencies of the A vs a allele will change over time

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17
Q

Is the A1 allele favored over the A2 allele in this environment?

a) Yes
b) No
c) A1 and A2 have the same fitness

A

Here we see the frequency of one allele, A1, changing over time

a) Yes

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18
Q

Based on the curves of selection coefficients, when is the A1 allele doing the best (and A2 the worst)?

Each colored curve on the plot shows change in allele frequency of the A1 allele at a different value of s

a) s = 0.1
b) s = 0.4
c) s = 0.7

A

c) s = 0.7

A1 is 70% better than A2

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19
Q

We (do, do not) define a selection coefficient for the favored genotype

A

Do NOT

Only the NON-FAVORED genotype

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20
Q

If we have brown and white mice, and the selection coefficient for brown mice is 0.7, that means they are doing much _______ than white mice

A

Worse

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21
Q

We can see this clearly by looking at how quickly A1 __________________ in frequency

A

Increases

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22
Q

When s = 0.1, A1 is only 10% ________ than A2

A

Better

That means it increases slowly over time

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23
Q

When s = 0.7, is is 70% ______ than A2

A

A2 individuals will die a lot more than A1 individuals, and A1 will rapidly increase over time

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24
Q

Selection coefficients vary with the environment

A

Selection coefficient shows the selection AGAINST that phenotype

Which genotype has the highest viability will differ between environments

The selection coefficient can therefore differ between environments

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25
Q

We observe a plant with white and purple flowers. The white plant produces 100 offspring and the purple plant produces 20 offspring. What can we infer?

a) There is a selection coefficient of 0.5 against purple
b) There is a selection coefficient of 0.2 against purple, and the white allele will increase in frequency
c) There is a selection coefficient of 0.8 against purple, and the white allele will increase in frequency
d) There is a selection coefficient of 0.2 against white, and the white allele will increase in frequency

A

c) There is a selection coefficient of 0.8 against purple, and the white allele will increase in frequency

vpurple/vwhite = 1-spurple
20/100 = 1 - spurple
spurple = 0.8
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26
Q

Selection and evolutionary change: If selection coefficients do not change over time, there are 3 outcomes of viability selection in terms of changes in frequencies of phenotype and genotypes in a population:

A

1) Directional selection
2) Heterozygote advantage
3) Heterozygote disadvantage

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27
Q

Directional Selection

A

Occurs when ONE allele always has higher viability than other alleles

vAA > vAa > vaa
Rate of change in fA will depend on s: how much BETTER is A than a?

Directional selection rate of change of same value of s - why can this differ?

Here we see rates of change in the frequency of A1 over time when A1 is dominant (red line), incompletely dominant (blue line), and recessive (orange line)

Don’t really need to plot both alleles because whatever A1 is doing, A2 will do the opposite

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28
Q

When does A1 increase most rapidly?

a) When A1 is dominant
b) When A1 is recessive
c) When A1 is incompletely dominant

A

c) When A1 is incompletely dominant

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29
Q

Directional selection will move the favored allele towards _________

A

Fixation

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30
Q

Fixation

A

Only on allele at a locus (NO VARIATION)

Look at gains and loss of variation

Fixation occurs when there is only 1 allele at a locus (frequency = 1.0)

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31
Q

______________ alleles will increase rapidly in the population - however, it takes a longer time for them to go to fixation

A

Favored dominant

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32
Q

___________ alleles may initially be at low frequencies, but increase rapidly once there are enough homozygotes

A

Favored recessive

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33
Q

Fixation of A1 is fastest under ___________, when heterozygotes produce a slightly inferior phenotype

A

Incomplete dominance

When heterozygotes have LOWER fitness than the dominant homozygote

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34
Q

Directional Selection: It takes a long time to get rid of recessive, unfavored alleles because they can “hide” at low frequencies in heterozygotes

A

If both the AA and Aa genotypes produce a dark brown mouse, there is no selection against the allele unless it is in an aa homozugote

If Aa phenotype is an intermediate (incomplete dominance), then you can have selection against that phenotype

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35
Q

Evolution is change in allele frequencies, but natural selection acts on _____________

A

Phenotypes

In example, a allele invisible to selection when in heterozygotes because it has no effect on phenotyep

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36
Q

Directional selection leads to a ______ of genetic variation over time

The favored allele will eventually fix, and the unfavored allele will be lost from the population

A

LOSS

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37
Q

Directional selection will result in the most rapid fixation of the dominant allele when:

a) Heterozygotes have the same fitness as dominant homozygotes
b) Both homozygotes have HIGHER fitness than heterozygotes
c) Heterozygotes have LOWER FITNESS than the dominant homozygote
d) Heterozygotes have the HIGHEST fitness

A

c) Heterozygotes have LOWER FITNESS than the dominant homozygote

38
Q

Heterozygote Advantage

A

Heterozygotes do BETTER, so vAA < vAa > vaa

AKA Overdominance

Results in a stable polymorphism

Allele frequencies will be maintained at equal proportions in the population

Stable polymorphism: allele frequencies maintainted ~ f(A) = 0.5

Heterozygote advantage MAINTAINS genetic variation in populations

There is usually one allele more common than another

Generally RARE

39
Q

Heterozygote Advantage and Mutations with Large Effects

A

Sickle-cell anemia is caused by a single mutation in the hemoglobin-Beta gene

There are major fitness consequences for sickle cell homozygotes: the blood cells become sickle-shaped, clogging blood flow

However, heterozygotes have limited disease pathology AND are protected from malaria because the malaria parasite does not infect sickle cells

Sickle cell mutation

  • AA = All normal shaped
  • Aa = mixture of good and sickle shape
  • aa = all sickled
40
Q

Mutations with major effects: SNPs

A

There has been natural selection for the sickle cell allele in parts of Africa with high malaria incidence because of the advantage to heterozygotes

41
Q

Heterozygote Disadvantage

A

AKA Underdominance

Heterozygotes are WORSe, so vAA > vAa < vaa

Example: By river, it is good to be light in open areas, dark in closed areas, but no intermediate

Aa LEAST abundant

Very hard to detect because this is what happens in directional selection: One allele reaches fixation and the other is lost

Result in heterozygote disadvantage and directional selection the SAME; process differs

It’s VERY HARD to separate heterozygote disadvantage from directional selection

Few examples

If they start at equal frequencies, one will randomly reach fixation and the other will disappear

42
Q

What effect does heterozygote ADVANTAGE have on allele frequencies over time?

a) Causes the dominant allele to go to fixation
b) Causes the recessive allele to go to fixation
c) Creates a stable polymorphism that maintains both alleles
d) Randomly causes one allele to go to fixation

A

c) Creates a stable polymorphism that maintains both alleles

43
Q

Frequency-dependent selection

A

The examples of selection we have looked at so far (directional selection, homozygote advantage, homozygote disadvantage) are FREQUENCY INDEPENDENT - the favored phenotype of genotype does not change based on how common it is in the population

In FREQUENCY-DEPENDENT SELECTION, the fitness of a particular phenotype changes as its frequency in the population changes

Frequency dependence can be positive or negative

44
Q

Positive frequency-dependent selection

A

Here, P1 = phenotype one, P2 = phenotype 2

Positive frequency dependence: Fitness associated with a trait increases as frequency increases

Each phenotype is favored once it is common

Which phenotype fixes in the population depends on the starting frequencies
-The more common one will be fixed

Land snail shells coil to the right or to the left

In the so-called “flat” snail species, individuals mate in a face-to-face position

Mating in these species can only take place between individuals whose shells coil in the same direction
-Opposing coil directions won’t line up properly

Whichever coil is more common gets more mates, and should increase in the population

45
Q

Under negative frequency dependence, what happens to the fitness of P1 as it becomes more common in the population?

a) Fitness of P1 decreases
b) Fitness of P1 increases
c) Fitness of P1 stays the same
d) Fitness of P1 is unpredictable

A

a) Fitness of P1 decreases

46
Q

Negative frequency-dependent selection

A

When the A1 allele starts at a high frequency, phenotype P1 is common, It has low fitness, and A1 declines in frequency

A1 eventually reaches an intermediate frequency

When the A1 allele starts at a low frequency, phenotype P1 is rare. It has high fitness, and A1 increases in frequency

Fitness goes DOWN as the frequency of a phenotype increases

Phenotype is favored when it is rare

Negative frequency dependence results in intermediate frequencies of each phenotype and cyclical dynamics
-As soon as one phenotype gets too common, its fitness decreases and the other phenotype increases; cycles like this

47
Q

Butterfly wing patterns under + and - frequency dependent selection

A

Butterflies in the Amazon have bright colored wings to warn predators

The species Heliconius numata has 3 different wing color morphs

Wing pattern morph under positive frequency dependent selection from predators, because predators learn and avoid the most common phenotype
-Predators learn which morph is dangerous

However, female mate preferences are for different wing types from their own, and thus under negative frequency dependent selection
-Females want to mate with males from different morph; under NEGATIVE selection from females

The push-pull of these two processes on a trait controlled by the SAME supergene maintains variation in the population

48
Q

Under NEGATIVE frequency dependence, a particular phenotype is

a) Favored at high frequencies
b) Favored at low frequencies
c) Under constant directional selection
d) Under heterozygote advantage

A

b) Favored at low frequencies

49
Q

Deviations from HWE: Assumption 2 - No mutations

A

Mutation BY DEFINITION changes allele frequencies by creating new alleles

Mutation = the introduction of new genetic variation into a population

We ASSUME a di-allelic model, so there can only be 2 alleles, a and A, at any locus, although in reality this is NOT true

mew = mutation rate paramenter
-The probability that ONE allele in each individual randomly mutates to the other in each generation

50
Q

A model of mutation: Rate of change to the alternative allele

A

If these two rates are the SAME, allele frequencies will NOT change

If one rate is faster, then allele frequencies will change in that direction

51
Q

Mutation equilibrium

A

With no genetic drift or selection, a mutation equilibrium will be reached where there are no changes in allele frequencies

If mutation is equally likely in both directions, then equilibrium is reached when fA = 0.5

How quickly equilibrium is reached will depend on mutation rates

52
Q

How long does it take to reach mutational equilibrium?

A

The importance of mutations in driving allele frequency changes (in the absence of selection) varies depending on the taxon

53
Q

If mew A->a = mew a->A and mew = 10^-8, it takes a very ____ time to reach equilibrium from a starting fA = 0 (A novel mutation)

A

LONG

54
Q

Mutation-selection balance

A

We have looked at these processes in isolation, but they occur together

Imagine that A is beneficial and a is deleterious

Over time, selection should increase the frequency of A

How should A change over time under just mutation?
-Not enough information; some A alleles will randomly turn into a, and some a into A

This process explains why it is very hard to completely purge deleterious alleles from a population
-Under SELECTION + MUTATION, A will increase in frequency according to s, the selection coefficient (how strongly favored A is)

However, a will remain at low frequencies due to mutations at rate mew from A -> a

The population will eventually reach a stable equilibrium between mutation and selection

55
Q

How should selection change the frequency of A over time? (assuming A beneficial, a deleterious)

a) Increase the frequency of A
b) Decrease the frequency of A
c) No change in A

A

a) Increase the frequency of A

56
Q

How should A change over time under just mutation?

a) Increase the frequency of A
b) Decrease the frequency of A
c) No change in A
d) Not enough information to predict direction of change

A

d) Not enough information to predict direction of change

Mutation is RANDOM, plus we don’t know rates of mutation in either direction

57
Q

Does mutation seem like a major force shaping allele frequency change?

A

Mutation rates are typically quite LOW

We can usually safely ignore recurrent mutations when modeling changes in allele frequencies: natural selection and drift are more important

58
Q

Mutation is a WEAK force of evolution because:

A

Only over LONG periods of time mutation can produce appreciative changes in allele frequencies

Only when mutation is PAIRED with selection it can change allele frequencies rapidly - we need a mutation + positive selection on that mutation to produce rapid increase in frequency

59
Q

When would you expect the frequency of allele A to increase in frequency most rapidly?

a) When saa = 0.8 and u from A -> a is high
b) When saa = 0.5 and u from A -> a is high
c) When sAA = 0.8 and the u from A -> a is low
d) When saa = 0.8 and the u from A -> a is low

A

d) When saa = 0.8 and the u from A -> a is low

60
Q

Deviations from HWE: Assumption 3 - Random mating

A

Assortative mating: More SIMILAR individuals mate preferentially

61
Q

Non-random (assortative) mating

A

One of the HWE assumptions is that individuals choose their mates randomly with respect to their own genotypes

If individuals tend to mate with those of the same genotype or phenotype, we call this ASSORTATIVE MATING

When individuals tend to mate with those of different genotypes or phenotypes, we call this DISassortative mating
-NOT random, just a preference in the opposite direction

62
Q

What are the consequences of assortative mating for genotype and allele frequencies?

A

Over time, assortative mating will REDUCE heterozygosity at the wing color locus, but it will NOT change allele frequencies

63
Q

Assortative mating: ________ heterozygous individuals than predicted by HWE (locus-specific)

____ Change in allele frequencies, ________ change in genotype frequencies

A

FEWER

No, just a

64
Q

Inbreeding

A

When individuals mate with genetic relatives

Form of ASSORTATIVE mating because gametes are not paired at random - they are preferentially paired with gametes from their relatives

Results in REDUCTION of heterozygosity

Fewer heterozygous individuals than predicted by HWE across the WHOLE GENOME

The aa individual has inherited both a alleles from the same individual grandparent

Relatives will have more similar genotypes

Inbreeding INCREASES the frequencies of HOMOZYGOUS genotypes across ALL loci

Deleterious recessive alleles are then more likely to become “visible” in recessive homozygotes (inbreeding depression)

65
Q

Self fertilization

A

Most extreme case of inbreeding

Alters genotype frequencies but does NOT change allele frequencies

66
Q

Deviations from HWE: Nonrandom mating ______ heterozygosity, (does, does not) change allele frequencies

A

DECREASES, DOES NOT

67
Q

Inbreeding reduces heterozygosity ___________________

A

Across the whole genome

68
Q

Assortative mating reduces heterozgosity at _______________________

A

loci responsible for phenotypes

69
Q

Disassortative mating

A

Occurs when individuals mate with partners that differ from themselves with respect to a given trait

Disassortative mating tends to generate an excess of heterozygotes
-INCREASES heterozygosity

For example, many mammals prefer mates that differ from themselves at the MHC loci - a highly polymorphic set of loci involved in the immune response
-Gives offspring a better immune system

70
Q

What effect does ASSORTATIVE mating have on allele frequencies?

a) Increase
b) Decrease
c) No effect

A

c) No effect

71
Q

What effect does ASSORTATIVE mating have on genotype frequencies?

a) Increase heterozygotes
b) Decrease heterozygotes
c) No change in homozygotes

A

b) Decrease heterozygotes

72
Q

Migration or Gene Flow

A

Migration, from an evolutionary perspective, is the movement of alleles in or out of populations

It does NOT necessarily involve the movement of adult individuals

For example, migration can include movement of pollen, eggs, and sperms of aquatic organisms, seeds dispersed by wing
-ANY process that moves alleles between populations

Also includes individuals or groups accidentally transported by floods, floating debris, plate tectonics, or humans

73
Q

Mainland-Island model of migration

A

We can build a simple model for predicting the effect of migration on allele frequencies

Assumptions:

  • Continent is large: Large populations, many alleles (genetic diversity)
  • Island is SMALL: small populations, little genetic diversity
  • No other processes operating (no selection, mutation, etc.)
  • What constitutes a “continent” and an “island” is variable

Migration from mainland have large impact on island allele frequencies

Migration from island has little impact on mainland allele frequencies, so we IGNORE migration from island to mainland

Under this model, continued migration will eventually drive the island and continental frequencies to be the SAME

This is the equilibrium state

74
Q

What effect will migration from the mainland have on allele frequencies on the island in this model?

a) Make the island and mainland frequencies more similar
b) Make the island and mainland allele frequencies more different
c) Increase variation on the mainland
d) Decrease variation on the island

A

a) Make the island and mainland frequencies more similar

75
Q

Migration results in a(n) _________ in genetic variation WITHIN populations, and a ____________ in variation BETWEEN populations

A

INCREASE (within), DECREASE (between)

76
Q

Migration + Natural Selection

A

Migration can oppose/counteract natural selection

Migration can INCREASE genetic variation within a population, while selection decreases genetic variation

Migration can swamp out local adaptation, slowing adaptation to a new environment, and DECREASING variation between populations over time

77
Q

Why is genetic variation important?

A

Genetic variation is the substrate on which selection acts: If there is no variation, there can be no adaptive evolutionary change

If there is NO genetic variation, there can be NO adaptation
-If there is no variation to act on, you cannot adapt

Different evolutionary processes act to increase or decrease genetic variation

We differentiate how processes affect variation within populations and between populations

Quantifying genetic variation is a crucial component of population genetics

This is not just important for understanding evolution - it has critical conservation applications

We have been assuming infinitely large population sizes in all of our models so far

78
Q

Effects of Evolutionary Processes on Genetic Variation

A

Ev. Process: Natural selection
Variation WITHIN: Decreases (except in cases of balancing selection)
Variation BETWEEN: Increases if selective conditions differ; decreases if conditions are the same

Ev. Process: Mutation
Variation WITHIN: Increases
Variation BETWEEN: Increases

Ev. Process: Nonrandom mating
Variation WITHIN: No effect on allele freq. ( in absence of sexual selection)
Variation BETWEEN: No effect on allele freq.

Ev. Process: Migration
Variation WITHIN: Increases
Variation BETWEEN: Decreases

79
Q

Conservation applications of population genetics

A

Species don’t like to inbreed; there is usually strong selection against it (deleterious to fitness)

Inbreeding typically occurs when population size gets small and migration is cut off, and leads to rapid loss of genetic variation

80
Q

Genetic Restoration Ex.

A

Introduced NEW, unrelated panthers into Florida population = increased heterozygosity
-REDUCED recessive homozygotes; INCREASED heterozygotes

Survivorship and reproduction also increased

81
Q

What effect does heterozygote disadvantage have on allele frequencies over time?

a) The rare allele goes to fixation
b) both alleles are maintained at intermediate frequencies in the population
c) The favored allele goes to fixation
d) The allele that fixes is whichever allele starts at a higher frequency in the population

A

d) The allele that fixes is whichever allele starts at a higher frequency in the population

82
Q

We observe a plant with red and blue flowers. The red plant produces 1000 offspring and the blue plant produces 400 offspring. What can we infer?

a) There is a selection coefficient of 0.6 against blue, and the red allele will increase over time
b) There is a selection coefficient of 0.6 against red, and the blue allele will increase over time
c) There is a selection coefficient of 0.4 against blue, and the red allele will increase over tie
d) There is a selection coefficient of 0.4 against red, and the red allele will increase over time

A

a) There is a selection coefficient of 0.6 against blue, and the red allele will increase over time

vblue/vred = 1 - sblue
sblue = 1-(400/1000)
sblue = 0.6
83
Q

When would you expect the frequency of allele A to increase in frequency most rapidly?

a) When sAA = 0.7 and u from A->a is low
b) When saa = 0.02 and u from A->a is high
c) When saa = 0.2 and the u from A->a is high
d) When saa = 0.7 and u from A->a is low

A

d) When saa = 0.7 and u from A->a is low

Means a is 70% worse than A; A is 70% better than a

84
Q

When do we expect the most rapid increase in the frequency of the dominant A allele?

a) When aa and AA have the same fitness, and Aa has the lowest fitness
b) When Aa has the highest fitness
c) When Aa and aa have lower fitness than AA
d) When Aa and AA have the same fitness, and aa has the lowest fitness

A

c) When Aa and aa have lower fitness than AA

85
Q

What does a selection coefficient measure?

a) The fitness reduction of a particular phenotype
b) The fitness increase of a particular phenotype
c) The fitness increase of a particular allele
d) The heterozygosity of a particular phenotype

A

a) The fitness reduction of a particular phenotype

86
Q

Positive frequency dependent selection

A

Fitness of P1 increases as it becomes more common

87
Q

What effect does directional selection have on genetic variation within and between populations in different environments?

a) Reduces variation within and between populations
b) Increases variation within and between populations
c) Increases variation within populations, decreases variation between populations
d) Reduces variation within populations, increases variation between populations

A

d) Reduces variation within populations, increases variation between populations

88
Q

This figure shows changes in heterozygosity and survivorship in Florida panther populations after the introduction of individuals from Texas. What pattern was observed?

a) Decrease in heterozygosity and survivorship after introduction of Texas panthers
b) Increase in heterozygosity and decrease in survivorship after introduction of Texas panthers
c) Increase in heterozygosity and survivorship after introduction of Texas panthers
d) Decrease in heterozygosity and increase in survivorship after introduction of Texas panthers

A

c) Increase in heterozygosity and survivorship after introduction of Texas panthers

89
Q

What effect does inbreeding have on genotype frequencies?

a) Decrease heterozygosity at all loci across the genome
b) Increase heterozygosity at all loci across the genome
c) Decrease heterozygosity only at loci involved in assortative mating
d) Increase heterozygosity at loci involved in assortative mating

A

a) Decrease heterozygosity at all loci across the genome

90
Q

Which of these is a conclusion of the Hardy-Weinberg Model?

a) If the allele frequencies in a population are given by A1 and A1, the genotype frequencies will be given by A1^2, 2A1A2, and A2^2
b) If no other processes are operating, populations will reach Hardy-Weinberg Equilibrium in one generation
c) These are all conclusions of the Hardy-Weinberg model
d) Allele frequencies in a population will not change over time if the assumption of random mating is met

A

c) These are all conclusions of the Hardy-Weinberg model

Evolution (15 decks)

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