Quiz 3 Flashcards
(131 cards)
1
Q
Total population size equation after selection
A
N(p^2wAA + 2pqwAa q^2waa)
2
Q
Frequency of genotype AA after selection
A
p^2wAA/(p^2wAA + 2pqwAa + q^2waa)
3
Q
Mean fitness (w bar) equation
A
p^2wAA + 2pqwAa q^2waa
4
Q
Genotype frequency of AA after selection
A
(wAAxp^2)/w bar
5
Q
∆p equation and interpretation
A
∆p=p’-p
When ∆p>0, A increases in frequency
When ∆p<0, A decreases in frequency
6
Q
What did the graph of allele frequency over time show? What type of selection did this show?
A
It showed that allele frequencies shift (evolve) toward fixation of either A1 or A2, depending on their initial frequency
- Disruptive selection
7
Q
If you have a graph showing only positive ∆p values for all possible p allele frequencies, what will happen over the long term and what type of selection is occurring?
A
Directional selection favouring A (no matter what the allele frequency is, A will increase over time.
8
Q
If you have a graph showing only negative ∆p values for all possible p allele frequencies, what will happen over the long term and what type of selection is occurring?
A
Directional selection for the q allele (Directional selection favouring a)
9
Q
If you have a graph showing positive ∆p values switching to negative values for the p allele frequencies, what will happen over the long term and what type of selection is occurring?
A
Heterozygote advantage (Aka balancing selection and overdominance)
- The organisms shift to a stable equilibrium point from unstable equilibria near the ends
10
Q
If you have a graph showing negative ∆p values switching to positive values for the p allele frequencies, what will happen over the long term and what type of selection is occurring?
A
Heterozygote disadvantage (aka disruptive selection, underdominance)
- Organisms shift away from an unstable equilibrium to stable equilibria near the ends
11
Q
If p=0 or p=1, then we know that the population is…
A
At equilibrium (either stable or unstable)
12
Q
In the case of underdominance (disruptive selection), selection can…
A
Cause fixation of a non-optimal allele (depending on initial conditions)
13
Q
In the case of heterozygote advantage, selection will maintain…
A
Polymorphism
14
Q
How to calculate relative fitness of a phenotype (W)
A
Pr[type x recaptured]/Pr[most fit recaptured]
15
Q
If you have a p=0.5 in a population, how would the p’ after one generation of selection in this population differ from that of a population with p=0.95?
A
p’ would be bigger in a population with p=0.5 because genetic variation is maximized when p=0.5 (lots of variance allows natural selection to make a big change)
SO MAXIMUM RATE OF CHANGE IS SEEN AT INTERMEDIATE FREQUENCIES
16
Q
True or false: The peppered moth example is a simple example of selection
A
False; there’s lots of things complicating this example, such as the fact that there’s an intermediate phenotype named insularia caused by different loci
- But it’s still a textbook example since there is clear evidence of selection against a melanic form, but more complicated than first appeared
17
Q
In a population of infinite size, natural selection causes a deterministic change in allele frequency. Over time, this will cause a favoured mutation to spread through the population. This will happen fastest when selection is (weak/strong)
A
Strong
18
Q
True or false: Even beneficial mutations don’t always establish
A
True
19
Q
In what circumstances are beneficial mutations especially vulnerable to loss?
A
When they’re rare
20
Q
How can you represent the effect of selection without talking about the three genotype fitnesses?
A
Using the selection coefficient (s) and dominance coefficient (h)
21
Q
Formula for calculating s?
A
Set the fitness of one genotype to 1 (standardize all the values) and then calculate s
WAA= 1+s
WAA/waa = 1+s
22
Q
Formula for calculating h?
A
Set the fitness of one genotype to 1 (standardize all the values) and then calculate h
WAa= 1+hs
WAa/Waa = 1+hs
23
Q
What is s?
A
Tells us the percentage increase in fitness of AA compared to aa
24
Q
What does h tell us?
A
Where heterozygotes fall in relation to AA and aa
- so h=0.75 tells us that Aa genotypes are 3/4 of the way between AA and aa.
- h tells us how much the heterozygote behaves like the dominant AA vs. the recessive aa
25
When is h=1?
When there's a dominant mutation (heterozygote acts like homozygous dominant)
26
When is h=0?
When there's a recessive mutation (heterozygote acts like homozygous recessive)
27
When is h=0.5?
When there's co-dominant alleles
28
What s value would represent that AA being 20% more fit/likely to survive than aa?
s=0.2
29
What is the probability of fixation formula for a beneficial mutation?
Pr[fix]=2hs
30
What is the probability of fixation formula for a beneficial dominant mutation?
Pr[fix]=2s
31
True or false: even quite beneficial mutations have quite low probabilities of fixing in the population
- explain an example for this
True
- e.g. for a dominant mutation that increases fitness by 10%, Pr[fix]= 20%... 80% of beneficial mutations would never survive
32
True or false: beneficial mutations that are recessive have a lower chance of fixing
- explain why (2 reasons)
True
- because when a mutation is rare (like recessive alleles), most of the copies are present in heterozygotes usually at first so polymorphism is maintained at first
- When it's recessive, its fitness is much smaller, so the net strength of selection is weaker
33
True or false: Haldane's 2hs equation also accounts for genetic drift
False; while it represents the chance of stochastic loss, it doesn't really represent the importance of drift because there's no N present in the equation (no dependence on N)
34
What equation accounts for both the effects of drift and selection on Pr[fix]? What is the equation for diploids?
Pr[fix]=2s(Ne/N)
For diploids: Pr[fix]=2hs(Ne/N)
35
What is the formula for rate of accumulation of beneficial mutations?
Rate of accumulation = mutation rate * fixation probability
= 2Nµn * 2hsNe/N
= 4Nehsµn mutations per generation
36
Unlike drift and neutral mutations (the molecular clock), the accumulation of beneficial mutations will happen most rapidly in _____ populations
- Give an example of a population you would see this in
Large (so you would see this more often in prokaryotes and unicellular eukaryotes that have much bigger population sizes, resulting in more adaptive evolution)
37
As the population size decreases, the probability of fixation by drift becomes....
Higher than the probability of fixation by selection
38
At what relative value will selection effects on fixation dominate over drift? (don't assume co-dominance)
When 4hsNe>1
39
At what relative value will selection effects on fixation dominate over drift with co-dominant alleles?
When 2Nes>1
40
What is the drift barrier hypothesis?
Mutations that reduce mutation rate/increase error correction are very weakly selected. Species with large effective population size are most able to optimize DNA copying accuracy/reduce errors.
- Natural selection generally favours lower mutation rates because high mutation rates lead to a higher load of deleterious mutations, and since natural selection is stronger at higher Ne, then it makes sense for bigger populations to have smaller mutation rates
41
Describe the discovery of allozyme variation
Lewontin and Hubby (1996) found extensive evidence for variation in the mobility of enzymes in drosophila, indicating underlying genetic variation. 1/3 loci were polymorphic at the species level (differed between species, first time seeing variation in the genome)
42
What did Kimura claim about the variation in allozymes?
Claimed that the variation could be selectively neutral and that drift may be a more reasonable reason for the allozyme variation,as long as |2Nes|<1 (whether s was positive or deleterious and assuming h=0.5)
- Said that natural selection often explain phenotypic variation, but not necessarily variation in the genome
- Genomes are huge and there's many mutations that are either neutral or effectively neutral, that have such a small effect on fitness that they just behave as if they're under genetic drift.
43
What would happen to allele frequencies under pure selection (no drift) when p=0.5 and WAA=1?
Expect allele frequency to go up (no loss)
44
What would happen to allele frequencies under pure drift (no selection) if p=0.5 and WAA=1?
Expect 50/50 ratio of A1 to fix vs. be lost
45
What is purifying selection?
The purging of deleterious mutations that are present in the population (directional selection against a new mutations, assuming that new mutations are bad)
46
A mutation that is under purifying selection has what s value?
s<0 (deleterious mutation)
47
Natural selection will only be able to effectively purge deleterious mutations (i.e. selection will be efficient) when...
|2Nehs|>1 for deleterious mutations
or
|4Nehs|>1 for all mutations
48
What does it mean if a mutation has a deleterious selection coefficient of |s|<1/2Ne
These mutations are nearly neutral because their dynamics are more determined by drift than selection
49
True or false: many mutations are approximately neutral, deleterious and lethal, and only a small fraction of mutations are beneficial
True
50
At what s value does selection outweigh drift?
|s|>1/2Ne
51
What is the rate of accumulation for mutations that have an |s|>1/2Ne and are deleterious?
0 (getting purged)
52
What is the rate of accumulation for mutations that have an |s|>1/2Ne and are beneficial?
4Neµnhs
53
What is the rate of accumulation for mutations that have an |s|<1/2Ne and are nearly neutral?
µn
54
The s values for which mutations act as nearly neutral has a (smaller/bigger) range at bigger population sizes
Smaller
55
What is one way of finding measuring selection (or its absence) in sequence data?
Compare the proportion of non-synonymous vs synonymous changes in a protein (assume that synonymous mutations are neutral)
- And then using this, find the dN/dS ratio
56
What is happening when dN/ds>>1?
For every synonymous mutation that is fixing, there are more non-synonymous mutations that are fixing.
Cause: Positive selection causing many non-synonymous mutations to fix (beneficial mutations are occurring and spreading rapidly though the species)
57
What is happening when dN/ds<<1
For every synonymous mutation that is fixing, there are less non-synonymous mutations that are fixing
Cause: Strong purifying selection preventing the fixation of non-synonymous mutations
58
If dN=dS (aka dN/ds = 1), what is happening in the population?
Non-synonymous sites are behaving about the same as synonymous sites (drift model)
59
In general, if you compared two species, on that had Ne=1000 and one that had Ne=1,000,000, how would you expect values of dN/dS to differ?
Theoretically: With Ne=1000, purifying selection would be less efficient, so more deleterious non-synonymous mutations would accumulate, but fewer beneficial non-synonymous mutations would accumulate too.
- But typically, most mutations are deleterious, so a smaller dN/dS would likely mean a larger Ne
60
Why do primates have a higher dN/ds than bacteria and fungi?
Humans have a smaller Ne than bacteria and fungi, so bacteria and fungi probably have more efficient purifying selection, increasing the proportion of beneficial non-synonymous mutations
61
True or false: the dN/ds ratio is not a very sensitive test
True
62
In general, how do we study adaptation?
Search for statistical patterns that could only be shaped by natural selection (recall that certain features are the by-product of other functions and aren't necessarily an adaptation), and give some insight into the fit between phenotype and environment
63
What are 3 ways we can compare fitness, phenotype or genotype to study adaptation?
1. Among populations in different environments
2. Among species in different environments
3. Within population, changing over time
64
True or false: repeated patterns of adaptation can give strong evidence of selection (unlikely due to drift). But it's hard to detect adaptation if it's different each time
True
65
Define adaptation
The "fit" of an organism to its environment
66
Explain local adaptation
Genotype x Environment interaction for fitness (i.e. better fit to home environment than away environment)
Trade-off in genotype performance between habitats
67
How does local adaptation relate to directional selection?
Local adaptation is termed divergent selection or spatially heterogeneous selection, meaning that selection is directional in one way in an environment, but directional in the opposite way in a different environment
68
Describe the 3 conclusions taken from the meta-analysis on the extent of local adaptation
1. Some very extreme cases of local adaptation
2. Lots of cases of little to no local adaptation
3. Few cases of the inverse pattern expected
69
Why do we see local adaptation at all? Why doesn't one genotype just dominate everywhere?
Describe the example of Sitka spruce planted in Vancouver
Due to biological constraints, it's sometimes impossible to be the best at everything because of limited resources
Alaska spruce have shorter growing times but are more cold-tolerant while california spruce have longer growing times and aren't cold tolerant; it's not physically possible to be both cold tolerant (required bud set) and long-growing
70
What are four reasons why we don't see local adaptation in some populations? What is the most important one?
1. Weak statistical power
2. Poor study design
3. No differences in the environment or no significant constraints
4. MAIN: Differences in fitness not strong enough to overcome gene flow
- e.g. fitness of specialist that evolves due to local adaptation can decrease at high migration rates due to being in the wrong environment a lot (so it's better to be a generalist in these scenarios)
71
True or false: the fitness of specialists can decrease relative to the generalists above a certain critical rate of migration
True; because specialists would be spending too much time in unfavourable environments
72
FST is (low/high) under local adaptation in different environments
High
73
When looking at the FST for an allele associated with diverged patterns between two populations in different environments undergoing local adaptation, why is the FST seen in more than just the one allele?
Due to linkage disequilibrium
74
What information can FST scans provide for measuring local adaptation within populations?
FST scans are used to see which regions of the genome are under divergent selection between populations in different environments
75
True or false: Divergent selection due to local adaptation is detectable by looking at allele frequencies
True
76
How do phylogenetic studies of repeated trait evolution help us understand what makes species adaptive to different environments? Provide an example
Different toxic and brightly coloured frogs evolved numerous times independently (convergent selection for both toxicity and being brightly coloured, so these features co-evolved)
- This suggests that similar environmental pressures in different regions have led to the repeated evolution of this adaptation
77
How can comparing dN/dS between the same species in different environments help us study adaptation?
High dN/dS ratios in specific branches of a phylogeny suggest adaptive evolution in response to local environmental pressures.
If one species or population shows an elevated dN/dS in certain genes, it suggests selection for local environmental conditions (dN/dS>>1 means positive selection for a trait, results in faster evolution; dN/dS<<1 means purging selection of deleterious mutations, so slower evolution because the genes function is critical, so changes are rare)
- If two species have a high dN/dS in the same environment, this is suggestive that both species are showing signs of adapting to that environment (in the same way)
78
How does looking at linkage disequilibrium helps us make inferences about local adaptation happening within populations
If directional selection is happening on a few different loci (here, 4 genes), then it's "pulling" on the allele frequencies at each of those genes. This "pulling" by selection causes the buildup of associations. So if you see the buildup of associations, this is a hint that local adaptation is happening
79
What pattern were the scientists searching for when detecting genes that evolved slowly?
dN/dS<<1
80
Does a gene's position in a protein-protein interaction network affect its rate of evolution?
Yes; hub genes are more strongly under purifying selection than peripheral genes (since hubs are more essential and need to be more conserved)
81
When examining the evolution of Drosophila throughout the seasons, what was observed? What conclusion can we draw from this?
Rapid evolution of phenotypes in similar patterns across 10 populations. These highly repeated patterns are indicative of selection, rather than drift (not as many fluctuations)
- Drift is still operating, but selection is also operating (which is known due to the repeated patterns)
82
What is a permutation/randomization approach and how was it applied to the Drosophila study?
Involves making a null distribution as a "standard" for genes in the genome (background SNPs)
- Compared allele frequency change at a locus of interest to the average and then scan for peaks that show genomic regions driving the change
83
True or false: adaptation from new mutations and from standing genetic variation both show an increase in mean trait value
True
84
What is standing variation?
No new mutations occurring, adaptation just occurs because some selection pressure changes and selects for variation already present within the genome
85
Which is harder to detect at the genome level: adaptation due to new mutations or adaptation due to standing variation?
Adaptation due to standing variation
86
How does adaptation due to new mutations differ with adaptation due to standing variation?
In adaptation due to standing variation, see lots of slight changes in the alleles over time and adaptation is more subtle
87
In adaptation from new mutations, evolution will happen fastest in _____ populations, but still need to...
Large, wait for a new mutation
88
Adaptation can happen much more rapidly from _______, but may not...
standing variation, may not have suitable mutations present in a population (not enough VG)
89
Heritability is more important for adaptation due to...
Standing variation
90
What is a selective sweep?
When a chromosome with an adaptive mutation increases in frequency, reducing the genetic diversity near the adaptive mutation but maintaining the genetic diversity further from the mutation due to recombination (the process where a beneficial mutation rapidly increases in frequency within a population, leading to a reduction or elimination of genetic variation in nearby DNA regions)
- Adaptive mutation is fixed; all variation is eliminated
91
True or false: selective sweeps acting on a single adaptive mutation don't affect distant alleles as much
True
92
Hard selective sweeps cause a (small/big) loss of genetic diversity
Big
93
Soft selective sweeps cause a (small/big) loss of genetic diversity
Small
94
Difference between a hard selective sweep and a soft selective sweep?
Hard selective sweep happens due to de novo advantageous mutations and results in a big loss of diversity. A soft selective sweep occurs due to standing variation (or multiple mutations, standing variation allows for lots of time for recombination causing multiple mutations) which increases the frequency of many different alleles and causes a small loss in diversity
95
Define the biological species concept
Species are groups of interbreeding natural populations that are reproductively isolated from other such groups
96
True or false: there's many definitions of a species
True
97
What 2 things are required to make a species?
1. Some mechanism to reduce interbreeding
2. Accumulation of enough genetic differences that interbreeding becomes impossible
98
What 3 things in general might prevent interbreeding?
1. Vicariance
2. Colonizing a new host
3. Polyploidization
99
Describe how geography (vicariance) prevents interbreeding
Physical separation of individuals
100
Describe how colonizing a new host prevents interbreeding
New host (similar to previous host) is introduced and some species start colonizing that one instead, start interbreeding with other species on new host
101
Describe how polyploidization prevents interbreeding
If diploid gametes are unreduced (diploid) and mate, this forms a tetraploid which is viable but if it crosses with a 2n, offspring will be 3n which tend to be infertile
102
Define allopatry
Total geographic isolation leading to speciation
103
Define parapatry
Individuals still able to encounter each other, less often
104
Define sympatry
Species encounter each other but when they try to mate, it just doesn't work
105
Vicariance is an example of what type of speciation?
Allopatric
106
Colonization of a new host is an example of what type of speciation?
Parapatric
107
Polyploidization is an example of what type of speciation?
Sympatric
108
Prezygotic isolating mechanisms are characterized by which two things?
1. Occur before the union of gametes (sometime during the mating of the parents)
or
2. Prevent potential parents of different species from mating
109
Postzygotic isolating mechanisms are characterized by which two things?
1. Occur following the union of gametes
or
2. Prevent hybrid offspring from surviving or reproducing
110
What are 5 examples of prezygotic isolating mechanisms?
1. Mating behaviour and courtship
2. Differences in flowering time
3. Different pollinators
4. Physical morphology
5. Encounter rates (different habitats? geography?)
111
What are 6 genetic isolating mechanisms?
1. Intrinsic postzygotic inviability
2. Intrinsic postzygotic infertility
3. Bateson-Dobzhansky-Muller model
4. The adaptive landscape
5. "Holey" adaptive landscape
6. Extrinsic post-zygotic isolation
112
What is intrinsic postzygotic inviability?
Offspring is inviable simply due to the combination of gametes, this is independent of the environment
113
What is intrinsic postzygotic infertility?
Offspring is viable but infertile simply due to the combination of gametes, this is independent of the environment
114
Describe the Bateson-Dobzhansky-Muller (BDM) model
Ancestral genotype acquires different mutations that fix in their own populations. When these fixed alleles then mate again, the fitness of the hybrid is low for some reason
- Epistasis: interaction between loci, here it causes low fitness when in hybrids
115
Describe the adaptive landscape model
Species adapting to different peaks in an adaptive landscape (emphasis on selection), so when species at peaks come to mate, the hybrid falls into the fitness valley
116
Describe the "holey" adaptive landscape model
Populations become geographically separated and diverge by genetic drift. Hybrid offspring has low fitness and falls in hole
117
Describe extrinsic post-zygotic isolation
Offspring has decreased fitness due to environment (e.g. predation)
- e.g. Mullerian mimic hybrids are viable but aren't recognized by predators as poisonous and are therefore eaten more often
118
What 3 things causes differences between individuals to evolve and result in speciation?
1. Drift
2. Selection
3. Reinforcement
119
Why would differences between individuals evolve from a genetic drift perspective? (3)
1. Gradual accumulation of different mutations in different populations with no migration
2. BDM incompatibilities (fix due to drift) or "holey landscape" model
3. Speciation is a slow process: builds up at rate of neutral molecular clock
120
Why would differences between individuals evolve from a natural selection perspective? (4)
1. Differences in ecology between populations
2. Selection favours different mutations
3. Isolation by BDM incompatibilities as side-effects of adaptation and low hybrid fitness between differently adapted parents (adaptive landscape model)
4. Accumulates more rapidly than drift
121
(Selection/drift) cause speciation more rapidly
Selection
122
What is reinforcement?
A reason why differences evolve causing speciation, populations evolve separately and then when they come back into contact competition between similar individuals pushes the proto-species further apart
123
Why do recessive beneficial mutations have a lower probability of fixation compare to dominant ones?
When rare, they are mostly heterozygotes where they have little fitness effects
124
What are the two fixed equilibrium p values?
p=0, p=1
125
What formula allows you to predict the polymorphic equilibrium on delta p over p graphs?
p= (wAa-waa)/(2wAa-waa-wAA)
126
What is an exaptation?
A term used to describe how traits that were previously spandrels can take on new functions over time
127
The further the dN/dS is from 1, the (smaller/larger) the effective population size
Larger (bc dN/dS near 1 indicates drift is at play which has a greater impact in smaller populations)
128
What are two factors that contribute to variation in phenotype?
Vg (variation in genetics) and Ve (variation in environment)
129
What is a reciprocal transplant experiment?
involves moving organisms from one environment to another, and then observing their performance in their new, foreign environment, and vice versa, to assess the role of local adaptation and environmental influence on fitness.
130
True or false: BDM incompatibilities require vicariance in order to fix
True
131
True or false: In the holey landscape, two geographically isolated populations diverge genetically but show similar fitness in their respective environments.
True
