Lec 5 Flashcards
Overall goal of class is to discover origin and maintenance of biodiversity
Biogenetics are outcomes
Deviations from HWE: Assumption 1 - No selection
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)
Pocket mice color
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
Viability selection
Ability to survive to reproduce
Higher viability = better survival
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
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
d) AA and Aa will have the same fitness higher than aa
To understand how selection causes allele frequencies to change, we need to quantify the EFFECT of each genotype of viability
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
Viability selection is about ___________
Average fitness
Average allows you to compare to ________________
Other alleles
Example of viability
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
Only ________________ matters when we are measuring selection
Relative fitness
Genotypes that do better ________ will survive to the next generation
ON AVERAGE
ALWAYS comparing genotypes to each other
Selection coefficient
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
Selection Coefficient: Example
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
Selection coefficient is selection ____ that phenotype/genotype
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
Predicting how ALLELE and GENOTYPE frequencies change by natural selection
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
Is the A1 allele favored over the A2 allele in this environment?
a) Yes
b) No
c) A1 and A2 have the same fitness
Here we see the frequency of one allele, A1, changing over time
a) Yes
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
c) s = 0.7
A1 is 70% better than A2
We (do, do not) define a selection coefficient for the favored genotype
Do NOT
Only the NON-FAVORED genotype
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
Worse
We can see this clearly by looking at how quickly A1 __________________ in frequency
Increases
When s = 0.1, A1 is only 10% ________ than A2
Better
That means it increases slowly over time
When s = 0.7, is is 70% ______ than A2
A2 individuals will die a lot more than A1 individuals, and A1 will rapidly increase over time
Selection coefficients vary with the environment
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
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
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
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:
1) Directional selection
2) Heterozygote advantage
3) Heterozygote disadvantage
Directional Selection
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
When does A1 increase most rapidly?
a) When A1 is dominant
b) When A1 is recessive
c) When A1 is incompletely dominant
c) When A1 is incompletely dominant
Directional selection will move the favored allele towards _________
Fixation
Fixation
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)
______________ alleles will increase rapidly in the population - however, it takes a longer time for them to go to fixation
Favored dominant
___________ alleles may initially be at low frequencies, but increase rapidly once there are enough homozygotes
Favored recessive
Fixation of A1 is fastest under ___________, when heterozygotes produce a slightly inferior phenotype
Incomplete dominance
When heterozygotes have LOWER fitness than the dominant homozygote
Directional Selection: It takes a long time to get rid of recessive, unfavored alleles because they can “hide” at low frequencies in heterozygotes
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
Evolution is change in allele frequencies, but natural selection acts on _____________
Phenotypes
In example, a allele invisible to selection when in heterozygotes because it has no effect on phenotyep
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
LOSS
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
c) Heterozygotes have LOWER FITNESS than the dominant homozygote
Heterozygote Advantage
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
Heterozygote Advantage and Mutations with Large Effects
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
Mutations with major effects: SNPs
There has been natural selection for the sickle cell allele in parts of Africa with high malaria incidence because of the advantage to heterozygotes
Heterozygote Disadvantage
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
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
c) Creates a stable polymorphism that maintains both alleles
Frequency-dependent selection
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
Positive frequency-dependent selection
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
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) Fitness of P1 decreases
Negative frequency-dependent selection
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
Butterfly wing patterns under + and - frequency dependent selection
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
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
b) Favored at low frequencies
Deviations from HWE: Assumption 2 - No mutations
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
A model of mutation: Rate of change to the alternative allele
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
Mutation equilibrium
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
How long does it take to reach mutational equilibrium?
The importance of mutations in driving allele frequency changes (in the absence of selection) varies depending on the taxon
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)
LONG
Mutation-selection balance
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
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) Increase the frequency of A
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
d) Not enough information to predict direction of change
Mutation is RANDOM, plus we don’t know rates of mutation in either direction
Does mutation seem like a major force shaping allele frequency change?
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
Mutation is a WEAK force of evolution because:
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
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
d) When saa = 0.8 and the u from A -> a is low
Deviations from HWE: Assumption 3 - Random mating
Assortative mating: More SIMILAR individuals mate preferentially
Non-random (assortative) mating
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
What are the consequences of assortative mating for genotype and allele frequencies?
Over time, assortative mating will REDUCE heterozygosity at the wing color locus, but it will NOT change allele frequencies
Assortative mating: ________ heterozygous individuals than predicted by HWE (locus-specific)
____ Change in allele frequencies, ________ change in genotype frequencies
FEWER
No, just a
Inbreeding
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)
Self fertilization
Most extreme case of inbreeding
Alters genotype frequencies but does NOT change allele frequencies
Deviations from HWE: Nonrandom mating ______ heterozygosity, (does, does not) change allele frequencies
DECREASES, DOES NOT
Inbreeding reduces heterozygosity ___________________
Across the whole genome
Assortative mating reduces heterozgosity at _______________________
loci responsible for phenotypes
Disassortative mating
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
What effect does ASSORTATIVE mating have on allele frequencies?
a) Increase
b) Decrease
c) No effect
c) No effect
What effect does ASSORTATIVE mating have on genotype frequencies?
a) Increase heterozygotes
b) Decrease heterozygotes
c) No change in homozygotes
b) Decrease heterozygotes
Migration or Gene Flow
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
Mainland-Island model of migration
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
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) Make the island and mainland frequencies more similar
Migration results in a(n) _________ in genetic variation WITHIN populations, and a ____________ in variation BETWEEN populations
INCREASE (within), DECREASE (between)
Migration + Natural Selection
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
Why is genetic variation important?
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
Effects of Evolutionary Processes on Genetic Variation
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
Conservation applications of population genetics
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
Genetic Restoration Ex.
Introduced NEW, unrelated panthers into Florida population = increased heterozygosity
-REDUCED recessive homozygotes; INCREASED heterozygotes
Survivorship and reproduction also increased
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
d) The allele that fixes is whichever allele starts at a higher frequency in the population
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) 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
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
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
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
c) When Aa and aa have lower fitness than AA
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) The fitness reduction of a particular phenotype
Positive frequency dependent selection
Fitness of P1 increases as it becomes more common
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
d) Reduces variation within populations, increases variation between populations
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
c) Increase in heterozygosity and survivorship after introduction of Texas panthers
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) Decrease heterozygosity at all loci across the genome
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
c) These are all conclusions of the Hardy-Weinberg model
