Genetic Drift

Question 1

What is genetic drift/random sampling?

Answer 1

changes in relative allele frequencies due to random events (ex. disasters like hurricanes)

Question 2

Is genetic drift more influential to variation in small or large populations? why?

Answer 2

small - there’s a higher chance of losing alleles (genetic diversity) if there’s fewer individuals

Question 3

T or F: genetic drift is an important driver of evolution

Answer 3

true

Question 4

T or F: direction of genetic drift is unpredictable

Answer 4

true

Question 5

Why is the direction of genetic drift unpredictable?

Answer 5

genetic drift is a result of RANDOM events, so whether or not, and which alleles will be lost or retained and in what frequencies is totally random

Question 6

How does genetic drift effect variation within a population (increase, decrease, maintain)?

Answer 6

it reduces variation within a population because alleles can be lost

Question 7

how does genetic drift reduce variation within a population?

Answer 7

results in loss of alleles –> increases homozygosity

Question 8

What phenotypes did the 2018 (first) study by Donihue and Losos look at?

Answer 8

they measured toe pad size against body size of lizards before and after (surviving) a major hurricane (genetic drift event) to determine whether natural selection is acting on, and selecting for, larger toe pad size

Question 9

Why would increased toe pad size and shortened femurs in the island lizards result in increased fitness?

Answer 9

larger toe pads and shorter femurs compared to body size results in a better ability to grip onto branches during a hurricane = increased survival

Question 10

What did the 2018 (first) study Donihue and Losos find?

Answer 10

their figure showed a clear difference between the average toe pad size (compared to body size) of lizards before and after the two hurricanes. they found that afterwards, the lizards had larger average toe pads

Question 11

How does the 2018 (first) Donihue and Losos study provide evidence for natural selection?

Answer 11

their study shows a fitness difference between phenotypes (larger vs smaller toe pad size) by finding the average toe pad size after a hurricane event was larger than before the event (those with larger had higher fitness)

Question 12

Why does the 2018 (first) Donihue and Losos study not provide evidence for evolution?

Answer 12

even though there’s a phenotypic difference, there’s no evidence that the larger toe pad size is genetic/heritable and for evolution to occur, the phenotype with increase fitness must be heritable

Question 13

What could Donihue and Losos do to determine the heritability of the toe pad phenotype?

Answer 13

• study the same experiment in the next generation for those traits
• analyze information on the genetic basis of toe pad size

Question 14

What did Donihue and Losos do in their follow-up study to gain more evidence for evolution of toe pad size?

Answer 14

they looked at the next generation in the same lizard population and found the same results: after the hurricane in 2019, the toe pad sizes were larger

this provides evidence that there’s a connection between survival and the next generation (heritability)

Question 15

What was the overall major finding of the work by Donihue and Losos?

Answer 15

they provided strong evidence supporting that hurricanes are causing the evolution of toe pad sizes in these island lizards

= on islands where hurricanes were more frequent, the lizards had larger toe pads (across different species and in different locations)

Question 16

How does genetic drift affect the relative frequencies of genotypes?

Answer 16

it increases homozygosity and decreases heterozygosity because it causes the loss of alleles

Question 17

What is the expected result in terms of genetic drift from a pop G simulation if the population size is large (10,000 individuals), both alleles are at 0.5 frequency, over 100 generations and no mutations, migrations, or natural selection?

Answer 17

the allele frequencies exist about the same over time and hover around the zero genetic drift line, P(A) = 0.5

Question 18

How can we use pop G to simulate the effects of genetic drift?

Answer 18

by lowering the population size, keeping allele frequency at 50%, no introduced mutations, migrations, and no natural selection (relative fitness = 1 for all) to compare to the zero genetic drift line

Question 19

What happens in pop G when the population size is decreased?

Answer 19

the frequency of A and a fluctuate more and more as the population size decreases = more genetic drift occurring

some of the populations even become fixed for A or a (ie., one of the alleles is lost) = reduction in variation

Question 20

T or F: the reduction in variation (fluctuation of A and a frequency) in small populations is due to fitness differences between the alleles

Answer 20

false = when genetic drift is a strong influence (when pops are small), the loss of alleles or change in allele frequency is due to chance

Question 21

What is the evolutionary result of genetic drift (ie., across multiple populations)?

Answer 21

divergent evolution of populations (populations of the same species that have different allele frequencies)

Question 22

What is a relevant example of genetic drift in humans?

Answer 22

microcephalin - this was not due to fitness differences (no natural selection), just random chance

Question 23

Explain how bowling can be a metaphor for genetic drift

Answer 23

the width of the bowling lane can be considered the population size = the narrower the lane, the easier it is for the ball to drop into the gutter = an allele to be lost

the proximity to the edge of the lane can be considered the allele frequency = the closer the ball is to the gutter, the more likely it is to go into the gutter = the lower the frequency of an allele, the more likely it is to be lost

Question 24

What is a genetic bottleneck?

Answer 24

a reduction in population size to a small size

Question 25

T or F: genetic bottleneck events in a population increase the effects of genetic drift and founder effects

Answer 25

true

Question 26

what are founder effects?

Answer 26

when genetic variation is dependent on the allele frequencies present in surviving individuals after an event which reduced population size (ie., genetic bottlenecks)

Question 27

What can cause genetic bottlenecks?

Answer 27

population crashes due to sampling events such as environmental disasters

colonizing a new population from a small number of founder individuals

Question 28

How long can genetic drift/founder effects continue influencing variation in a population?

Answer 28

a long time, regardless of population growth rate

Question 29

Explain how elephant seals are a good example of a genetic bottleneck and resulting, persistent genetic drift/founder effects

Answer 29

Dramatic crash in population size caused by over-hunting, down to ~40 individuals in 1850

since, the population has been allowed to rebound back up to ~100,000 but the genetic variation present in that population today is all based on what alleles were present in the 40 survivors in 1850

= genetic drift and founder effects still persist hundreds of years later and regardless of rebounded pop size

Question 30

Why might we want to quantify the effects of random sampling/genetic drift?

Answer 30

in order to predict how population sizes can affect the frequency of A and a alleles

Question 31

How can we quantify the effects of random sampling/genetic drift?

Answer 31

Use Hardy Weinberg set up to determine what allele and genotype frequencies look like in a large population prior to a sampling event

then use the binomial distribution-based Wright-Fisher model of genetic drift to compare the probability of the genotype frequencies after a sampling event

Question 32

What are the steps of quantifying the effects of random sampling?

Answer 32

1. large population size with 2 alleles (A, a) with equal frequency (p = q = 0.5) and genotype frequencies = 1/4 AA, 1/2 Aa, 1/4 aa (HWE: p2, 2pq, q2)
2. random sampling event occurs causing a population crash and only a very small number of individuals survive, ex. n = 4. What is the probability that just by chance, all 4 have the AA genotype?
3. based on binomial distribution, if AA has a 1/4 frequency in the original population size and there’s 4 individuals in the population –> (1/4)^4 = 1/256 chance that the 4 surviving individuals are all AA

Question 33

Explain the Wright-Fisher model of genetic drift and binomial distribution

Answer 33

Binomial distribution assumes that each individual in the experiment has an equally likely chance of being selected = this is why the Wright-Fisher model uses this probability distribution method because individuals in a population have an equally likely chance of surviving a random sampling event

Wright-Fisher model can be used to predict the probability (frequency) of the different genotypes with the number of individuals in the population and their allele frequencies

Question 34

What was the classic genetic drift experiment that was basically a real life pop G simulation?

Answer 34

Peter Buri assessed the effects of genetic drift in 1956 - he looked at the frequency of alleles (started at 50/50) in 107 small populations (subject to genetic drift; n = 16, including both males and females) of Drosophila flies over 19 generations

Question 35

What did Peter Buri find from his Drosophila experiment?

Answer 35

even just from the initial population to the first generation, there was already spread of allele frequencies

after just 5 generations, some populations started to show a huge decrease and near losses of alleles

After 19 generations, he found that 30 populations became fixed for one allele and 30 became fixed for the other

Question 36

How did Peter Buri’s experiment compare to the Wright-Fisher model of genetic drift?

Answer 36

Buri’s results showed that over a shorter period of time, more populations lost one of the two alleles and there are fewer populations retaining both A and a (on a graph, larger bars on the ends - like the gutters)

whereas,

the WF model shows more populations retaining both A and a alleles (slower loss of variation)
lower peaks on the ends (gutters) = over 19 generations, there were less populations fixed for one allele and more populations with both

Question 37

Why are Peter Buri’s results different from the Wright-Fisher model of genetic drift? Given that they both use n = 16 and initial frequency of alleles = 0.5

Answer 37

the WF model is THEORETICAL which means it doesn’t account for the actual number of reproductively active individuals in a population and assumes all 16 individuals are contributing to reproduction

In real life, just because there’s 16 individuals, it doesn’t mean all 16 are reproducing and if there’s less reproducing individuals, the population size is EVEN SMALLER so we would see an even greater genetic drift effect (faster loss of alleles)

Question 38

How could the Wright-Fisher model of genetic drift be adjusted to more accurately match the results observed by Peter Buri?

Answer 38

if the population size was decreased to less than 16, it might resemble Buri’s results more due to the effective population size (number of individuals contributing to reproduction) usually being smaller than the actual population size in real life populations

Question 39

What is the effective population size?

Answer 39

Ne

the amount of individuals within a population contributing to reproduction - not every individual within a population is contributing to reproduction

it is the size corresponding to genetic drift (not the actual population size)

Question 40

Will Ne be smaller or larger than N?

Answer 40

smaller

Question 41

How does the effective population size effect genetic variation within a population?

Answer 41

the Ne will always be smaller than the population size, sometimes it can be much smaller

genetic drift has a stronger effect on smaller populations, and since the effective population size is the true representation of the population size, if that value is small, alleles will be lost at a faster rate = genetic variation will be reduced

Question 42

How can bottleneck/random sampling events affect the effective population size?

Answer 42

after a population crash/in a small population, the ratio of male to female individuals and the proportion of individuals capable of reproducing is RANDOM and likely not equal

ex. a population may now only consist of males in which case there’s no possibility of reproduction

ex. there may be no or very few reproductively mature individuals = alleles not present in the reproducing individuals will be lost

Question 43

Explain how elephant seals are a good example of effective population size effecting genetic variation

Answer 43

after their numbers were dramatically reduced to ~40, there was asymmetry in the number of males present and the number of males able to contribute to reproduction

only the reproducing males would have been able to pass on their genes, and alleles in non-reproducing males would have been lost

so the founder effects are even stronger in this population = the current ~100,000 individuals have alleles based on probably even less than 40 individuals

results in very low genetic variation

Question 44

What is another example of effective population size contributing to genetic variation?

Answer 44

In bee colonies, only the Queen bee (a single female) contributes to reproduction = very small effective population size compared to actual population size

Question 45

What is the effective population size in humans? how does it compare to the actual population size?

Answer 45

Ne = 10,400 (estimated)
N = ~8 billion (estimated)

Question 46

Effective population size is difficult to measure, so how do we do it?

Answer 46

we estimate it using the Wright-Fisher model

Question 47

What happens in a small population when a new neutral (no effect to fitness = no natural selection) mutation arises?

Answer 47

the smaller the population, the higher probability that the new neutral mutation will become fixed

= the new mutation will replace other alleles just by chance because of the small pop size

Question 48

How does a small population size affect the probability of a new neutral mutation becoming fixed?

Answer 48

the smaller the pop, the more likely a new neutral mutation will become fixed

Question 49

What happens in pop G when:

pop size = 100
pop number = 100
generation = 500
neutral mutation = fitnesses = 1
new mutation introduced, frequency of A = 0.99

Answer 49

just by chance, at least one population (ex. 99 of the 100 populations) becomes fixed for the new neutral mutation (A allele)

= the introduced neutral mutation (A allele), not at all due to fitness differences (no natural selection), is expected to replace the a allele in at least one (ex. 99 of the 100) populations

Question 50

What happens in pop G when:

pop number = 100
generation = 500
neutral mutation = fitnesses = 1
new mutation introduced, frequency of A = 0.99

but you increase the population size?

Answer 50

As population size increases, less populations become fixed for the new mutation = the new mutation is less likely to replace the a allele just by chance

ex. at N = 10,000, only 50 of the 100 populations were fixed (compared to the 99 fixed when N = 100)

Question 51

What happens in a small population when a deleterious mutation arises?

Answer 51

it is more likely to become fixed

Question 52

What happens in pop G when:

population size is small (10-100)
pop number = 100
generation = 500
deleterious mutation: fitness of AA = 0.75, Aa and aa = 1
new mutation introduced: frequency of A = 0.99

Answer 52

When the population is small and the new mutation causes decreased relative fitness (AA = 0.75), more populations become fixed for the A allele and few lose it

ex. N = 10, 89 of 100 populations become fixed for the deleterious mutation A

ex. N = 100, 47 of 100 pops become fixed for A

Question 53

will genetic drift or natural selection have a stronger effect on allele frequencies?

Answer 53

it depends on how strongly the processes are acting on a population

Question 54

How can we determine the strength of genetic drift and natural selection to compare them?

Answer 54

by calculating s vs Ne as measures

s= strength of natural selection (fitness & differential fitness)

1/Ne = strength of genetic drift (pop & Ne size)

Question 55

What does it mean if s > 1/Ne?

Answer 55

natural selection will have a stronger influence on the allele frequencies

Question 56

What does it mean if s < 1/Ne?

Answer 56

genetic drift will have a stronger influence on the allele frequencies

Question 57

If s > 1/Ne, will Ne be large or small?
If s < 1/Ne, will Ne be large or small?

Answer 57

s > 1/Ne = Ne will be large (larger pop size, less genetic drift)

s < 1/Ne = Ne will be small (smaller pop size, more genetic drift)

Question 58

T or F: if genetic drift is the prevailing force, natural selection cannot also be occurring

Answer 58

false, natural selection can still be acting, it just won’t be as strong as the effects of genetic drift

Question 59

in what population sizes are new slightly advantageous mutations (ex. fitness of AA = 0.99, Aa and aa = 1) more likely to become fixed? what does this show?

Answer 59

large populations where there’s no genetic drift

this takes a VERY long time (ex. Pop G = 500,000 generations) and very large Ne

this shows the balance between chance and fitness (ie., genetic drift and natural selection)

Question 60

in what population sizes are new neutral mutations more likely to become fixed?

Answer 60

small populations where genetic drift is strong

Question 61

in what population sizes are new deleterious mutations more likely to become fixed?

Answer 61

small populations where genetic drift is strong

Question 62

Describe the study about inbred wolves on Isle Royale

Answer 62

the population was colonized on Isle Royale (an island) in 1950

population size remained small - fluctuated around ~25, max was ~50 but eventually dwindled down to 2 wolves

small population and isolation led to strong genetic drift effects and inbreeding = decreased fitness –> losing variation and mating with each other caused deformities and population crash

genetic rescue was proposed to introduce gene flow from mainland wolves

Question 63

What were the major results of the Isle Royale wolf study?

Answer 63

the population size has increased due to new individuals but also, more importantly, due to higher survival rates in offspring (less inbreeding = more diversity in alleles = higher fitness)

Question 64

What is gene flow?

Answer 64

movement of individuals (or gametes) between populations

Question 65

How can gene flow effect population structure?

Answer 65

the introduction of new genes into a population can change the genetic composition (the allele frequencies) into the population = increases genetic diversity

Question 66

What is the major benefit of gene flow?

Answer 66

it increases genetic diversity in a population

Question 67

What evolutionary effect does gene flow have on multiple populations?

Answer 67

by introducing genetic diversity within populations, it counteracts divergent evolution, caused by genetic drift, of populations = homogeneity across populations

Question 68

How are gene flow and genetic structure measured?

Answer 68

using F statistics - developed by Sewall Wright

Question 69

What are F statistics?

Answer 69

F = Fixed

a way to measure variation between populations by comparing the ratio of heterozygosity to homozygosity - specifically measures the loss of heterozygosity

Question 70

What was Sewall Wright’s major study organism?

Answer 70

guinea pigs

Question 71

What is FST?

Answer 71

a measure of population differentiation = the different allele composition in different populations of a species = a measure for how genetic variation is organized between populations

Question 72

What is the range of FST values? What are the basic interpretations of the value?

Answer 72

0 to 1

where <0.05 is very little structure and >0.25 is a lot of structure

Question 73

What does it mean for a population to have little structure? How much gene flow is there?

Answer 73

there’s a lot of gene flow and the distribution of A and a alleles between populations is similar = both populations have similar composition

Question 74

What does it mean for a population to have a lot of structure? How much gene flow is there?

Answer 74

there’s not much gene flow and the distribution of A and a alleles between populations is very different = the populations look very different

Question 75

What does it mean when FST = 0?

Answer 75

populations have the same alleles in the same frequencies

lots of gene flow

Question 76

What does it mean when FST = 1?

Answer 76

populations are fixed for different alleles = there is only homozygosity

no gene flow

Question 77

What is the formula used in F Statistics?

Answer 77

F = (expected H - observed H) / expected H

where H = heterozygosity

Question 78

What is the formula used to calculate FST?

Answer 78

FST = (total H - subpopulation H) / total H

where H = heterozygosity

Question 79

What are the challenges for F statistics?

Answer 79

it’s difficult to describe what defines a population or subpopulation

it can be difficult to describe what may be preventing gene flow or if gene flow is even being prevented

Question 80

Calculate FST for this example:

2 alleles that determine coat colour in wolves, A and a. Sample 5 subpopulations and find the following frequencies of the A allele (p):

0.2, 0.25, 0.6, 0.8, 0.00

interpret the FST value

Answer 80

1. calculate heterozygosity (2pq) for each subpopulation
2. take the average of the 2pq values to find the subtotal expected heterozygosity value (HS)

HS = [2(0.2)(0.8) + 2(0.25)(0.75) + 2(0.6)(0.4) + 2(0.8)(0.2) + 2(0)(1)] / 5 = 0.299

3. find overall frequency of A allele from the average frequencies:

overall p = (0.2 + 0.25 + 0.6 + 0.8 + 0)/5 = 0.37

4. use total p to calculate total expected heterozygosity HT (2pq)

HT = 2pq = 2(0.37)(0.63) = 0.4662

5. calculate FST with formula:

FST = HT - HS / HT

FST = (0.4662 - 0.299) / 0.4662 = 0.3586

interpretation: FST is relatively high (>0.25) - more reduction in heterozygosity = populations have very different frequencies of A and a alleles = lots of structure, more homozygosity in populations –> less gene flow and pops look different

Question 81

Can FST be high for some genes and also low for others in the same organism or population? why?

Answer 81

yes

When the FST is very different for one allele (ex. c allele found in 1 population out of 4, but A found in all 4), it is not being transferred into the other populations via gene flow even if gene flow is occurring between populations because

maybe there’s some ecological niche difference between the populations where that allele is favoured by natural selection in one environment but not the other - it is not as advantageous in the other pop so it will be selected against

basically because positive selection does not effect genomes in the same way in all populations because there’s other factors contributing to what is advantageous (ex. melanic moths in polluted vs. non polluted environments)

Question 82

How is gene flow effected by positive natural selection?

Answer 82

positive natural selection will act differently on the genomes of individuals in different populations because there are other contributing factors influencing fitness

Question 83

How are melanic moths a good example of how gene flow is effected by natural selection and how FST can vary?

Answer 83

the melanic A allele is favoured in polluted environments whereas in non-polluted, the wild type a allele is favoured

gene flow could still be occurring between these populations but the transfer of the A or a allele into the opposite population is not advantageous

Question 84

How would genetic drift be expected to act across different populations of the same size? how does this compare to gene flow?

Answer 84

genetic drift would be expected to act in the same random way in all small populations of a species

whereas

gene flow does not act randomly because it is influenced by natural selection not random events

Question 85

What can genes with outlier FST values (when compared to the rest of the genome) tell us?

Answer 85

these outlier FST values can indicate strong positive selection (and adaptation)

where the other genes in the genome show the baseline amount of genetic structure and gene flow to use as a comparison for any deviations

Question 86

How does artificial selection affect gene flow?

Answer 86

it prevents gene flow by artificially selecting for traits to get the same product every time (ex. dog breeds)

Question 87

What was the goal of the study by Akey et al., about artificial selection in the dog genome?

Answer 87

they were looking for any significant deviations of FST values in the dog genome across different breeds to determine signs of positive selection (ie., mutations associated with particular dog breeds)

Question 88

What did Akey et al. do in their study of the dog genome?

Answer 88

they genotyped ~21,000 autosomal SNPS in 10 dog breeds such as sharpeis, german shepherds, poodles

Question 89

When looking specifically at the Shar-pei genome, what did Akey et al. find?

Answer 89

there were 9 regions within the genome that had FST outlier values

Question 90

When looking at the dog genomes, what does di mean?

Answer 90

FST deviation for breed i (compared to the average FST value for the entire genome)

Question 91

Looking at a graphical representation of the Shar-pei genome, how can we tell which regions had FST values that were outliers?

Answer 91

they reached above the dashed red line

Question 92

Why did we look more closely at a section of chromosome 13 from the Sharpei genome?

Answer 92

it had an FST value with significant deviation from the baseline for the rest of the genome

Question 93

What 3 genes are in chromosome 13 of the sharpei genome? which one did we look at in more detail?

Answer 93

HAS2, SNTB1, FTSJ1

HAS2 = Hyaluronan synthase

Question 94

What is hyaluronan?

Answer 94

aka hyaluronic acid

found throughout the body (ex. joints, eyes, skin)

produced by hyaluronin synthases, including and especially HAS2

function: stretches skin, increases wound healing

Question 95

How is hyaluronan related to Sharpeis?

Answer 95

sharpeis have unique skin morphology that is super stretchy = hyaluronan functions in helping skin stretch

Question 96

What did Akey et al. find in relation to sharpeis and the HAS2 gene?

Answer 96

that HAS2 amount was increased and expression was elevated in the Sharpei genome

Question 97

How does the HAS2 gene in sharpeis compare to that in other dog breeds?

Answer 97

All dogs have hyaluronan and the HAS2 gene, and it is not a different type of hyaluronan being produced, but there’s just a higher baseline in the sharpei genome than in other dog breeds

which makes sense because they have way stretchier skin than other dog breeds

Question 98

What other animal examples are there of increased HAS2 gene expression?

Answer 98

naked mole rats: produce very high levels of hyaluronan
- they have a nonsynonymous mutation in their HAS2 gene (so it is slightly different than sharpei’s)

humans:
rare disease, cutaneous mucinosis, caused by very high levels of hyaluronan production

Question 99

without isolation experiments, and using only sequence analysis, how could you determine whether a gene (or part of a genome) is essential?

Answer 99

look at population samples or across species to see whether the gene or genome section is present in all of them = if it’s highly conserved it’s a strong indicator that it’s essential

ie., look at genetic variation across different groups = low variation means strong purifying selection is acting to conserve the gene or segment

also can compare amount of nonsynonymous vs synonymous mutations

Question 100

What does it mean if a gene or section of a genome is highly conserved across populations or species?

Answer 100

it is most likely essential

and there’s strong purifying selection acting to keep it

Question 101

What is an example of two divergent lineages sharing highly conserved genes?

Answer 101

Human and yeast ubiquitin proteins

the amino acid sequence is 96% similar

the nucleotide sequence is 75% similar

Question 102

How can we determine the amount of variation in a species?

Answer 102

use dN and dS to compare the amont of nonsynonymous and synonymous mutations

Question 103

What is dN?
What is dS?

Answer 103

dN = a measure of nonsynonymous mutations within a species

dS = a measure of synonymous mutations within a species

Question 104

In general, is dS > dN? or dN > dS?

Answer 104

dS > dN = there’s more synonymous mutations than nonsynonymous

Question 105

How can we determine the amount of variation between species?

Answer 105

use KA and KS to describe nonsynonymous and synonymous divergence

Question 106

What is KA? What is KS?

Answer 106

KA = a measure of amino acid changes in the amino acid sequence caused by nonsynonymous mutations

KS = a measure of substitutions in the nucleotide sequence caused by synonymous mutations

Question 107

When there is strong functional constraint (strong purifying selection), what is the ratio of KA to KS? dS and dN?

Answer 107

KA / KS = close to 0

dS > dN

there’s more synonymous mutations present and purifying selection is acting to remove the nonsynonymous mutations

Question 108

What did the study by Kachroo et al. about humanization of yeast genes do?

Answer 108

they replaced 414 essential yeast genes with their human orthologs (the human version of the same gene) to determine how many could be replaced and have the culture still survive

using a temperature-sensitive allele inactivation assay

Question 109

When did humans and yeast diverge from a common ancestor?

Answer 109

~1 billion ya

Question 110

What are orthologous genes?

Answer 110

genes with a shared ancestry (found in both lineages from a shared ancestor)

Question 111

How many orthologous genes do humans and yeast share?

Answer 111

thousands (~1/3 of the genes in the yeast genome are shared with humans)

Question 112

What did the study by Kachroo et al. about humanization of yeast genes find?

Answer 112

they found that ~half (47%) of the yeast genes could be ‘humanized’ (replaced) by the human ortholog and the yeast culture would still survive

Question 113

What can be interpreted from the results of Kachroo et al.?

Answer 113

the orthologous genes and their functions are highly conserved across both the human and yeast genome

Question 114

What selection can we expect when KA/KS or dN/dS < 1 (~0)?

Answer 114

strong purifying selection is acting on to remove the synonymous mutations

ex. ubiquitin in humans and yeast

Question 115

What selection can we expect when KA/KS or dN/dS = ~1?

Answer 115

no strong purifying selection

there’s not much fitness differences so not much selection action = neutral evolution

ex. pseudogene (nonsense mutations) or recent gene duplication

Question 116

What selection can we expect when KA/KS or dN/dS > 1?

Answer 116

strong positive selection

lots of nonsynonymous mutations and few synonymous

NS is favouring more mutations that cause AA changes or nonsynonymous mutations = more variation

ex. MHC
genes involved in immunity will have more variation to increase effectivity