Lecture 22

Question 1

Define population genetics

Answer 1

population genetics: a mathematical description of evolution constrained by laws of Mendelian inheritance

Question 2

Why is it untrue to say that dominant alleles will tend to spread in populations simply because they
are dominant? Who posited this idea and who showed that it was flawed?

Answer 2

Udny Yule argued that dominant alleles of polydactyl would spread in populations.

However hardy Weinberg disproved this idea as proved that there is no variation in genotypic frequencies when there are no evolutionary pressure

Question 3

What are the 5 assumptions of HWE? Provide an example of a deviation from each assumption
and how it would change allele or genotype frequencies in a population.

Answer 3

1. Population is infinite (no genetic drift)
   - deviation
2. population is hermaphoditic
3. No selection
4. No mutations within the idealized population
5. No migration in or out (gene flow)

Question 4

If p = 0.45, determine 2pq

Answer 4

q= 1-0.45 = 0.55
2pq= (2.45.55)= .495

Question 5

If a population has 500 AA, 257 AB, and 505 BB individuals, what are the frequencies of both
alleles? Is this population approximating HWE? If not, provide a potential explanation for the
deviation.

Answer 5

(AA)= (500/1262)=0.396

(AB)= (257/1262)=0.204

(qq)= 505/1262 =0.400

expected count under HWE:
q= 2(AA)+AB/2Total= 2(500+257)/2*1262=0.498
1-q=0.502

AA: p^2* total= (0.498^2)1262 =313
AB: (20.498.502)1262= 631
BB: q^21262= (.502^2)1262=318

Since heterozygosity is much lower than what is expected under HWE it is not approaching hwe likely due to inbreeding resulting in 50% loss of heterozygosity in each generation.

Question 6

If the equilibrium value of p is 0.6 for two alleles that display heterozygote advantage, would delta p
be positive or negative if q = 0.75?

Answer 6

If q is 0.75, p= 0.25.

since p is less than the equilibrium delta p will be positive to push the p value back towards the equilibrium

Selection acts to maintain both alele frequencies and prevent fixation of either p or q.

heterozygote advantage in humans: sickle cell anemia if you are heterozygous you don’t have disease and resistant to malaria

Question 7

What is the main genetic consequence of inbreeding? Why does this often result in inbreeding
depression? Define inbreeding depression in your answer.

Answer 7

selfing/inbreeding reduces heterozygosity by 50% in each generation.

This exposes deleterious receive mutations that would otherwise be masked by heterozygosity.

This results in inbreeding depression which is a loss of fitness due to exposure of deleterious receive mutations as a result of inbreeding.

Question 8

If the frequency of a neutral allele (one that does not affect fitness) in a finite population is 0.85,
what is the probability that allele will fix?

Answer 8

The probability that it will fix is equal to its frequency of 0.85.

Question 9

Why is it true to say that genetic drift reduces genetic diversity in a population?

Answer 9

eventually one of the alleles will fix and one will be lost resulting in the population all having that allele past this point and thus reducing genetic diversity.

Question 10

How does gene flow change allele frequencies in populations? What is gene flow’s main effect on
speciation?

Answer 10

When an individual in one population migrates to another population it can mate with individuals of that population and introduce new alleles into the population.

Gene flow allows the changing of alleles between populations preventing reproductive isolation as differences are not accumulating between the populations.

Question 11

11. Explain the concept of Bateson-Dobzhansky-Muller incompatibilities and how they provide a
    genetic explanation for reproductive isolation

Answer 11

A population is split into two subpopulations in which two different alleles are fixed in each subpopulation by either selection or drift.

E.g:
- parental generation with aabb genotype and a speciation event occurs in the f2 where you get
- AAbb in one population
- aaBB in the other population

therefore: Big A is compatible with little B and little a is compatible with big B

it is also known that little a is compatible with big A as the presence of the AA in the genotypes of the f1s after fixation indicates that individuals were once heterozygous for Aa until some selective pressure caused the big A allele to fix.

if you cross the f1 –>the offspring (AaBb) will be sterile as there is no previous history of the Big A allele and Big B allele being compatible

as a result, there is reproductive isolation as the f2 generation cannot reproduce.

Question 12

What are the two main takeaways from Orr’s snowball?

Answer 12

as populations diverge incompatibilities between alleles accumulate.

later/substitutions of alleles have more potential incompatibilities than earlier ones.

in an ancestral genotype abcde ; substitution of the D allele would lead to more incompatibilities than substitution of the b allele

derived alleles( subsituted/fixed alleles) have more potential incompatibilities than ancestral( no fixed/original alleles)

so the uppercase alleles would have more incompatibilities than the lower case alleles from the ancestral genotype

Question 13

What is the two-fold cost of sex?

Answer 13

If both asexual and sexual females ar producing two offspring per generation.

Since asexual population contain only “females” all offspring will reproduce. In sexual populations half of the offspring will be males meaning only half of the offspring can reproduce. Asexual populations thus grow twice as fast.

While sexual females produce offspring less rapidly than asexual females it has a large advantage in easy removal of accumulated deleterious mutations

Question 14

14. Why is Muller’s ratchet potentially problematic for small asexual populations?

Answer 14

Muller ratchet is the idea that small asexual populations can not reconstitute the least loaded class( those within the population with the fewest deleterious mutations) if they do not reproduce as asexual populations are clonal so offspring will have the same amount of mutations as parents.

In sexual populations, there can be crossover events that produce offspring with fewer mutations than parent thus creating a variance of mutations.

Similar to a ratchet the inheritance of mutations can only move in one direction (accumulation ) in asexual populations opposed to selecting deleterious mutations out of the population.

result of genetic drift.

Question 15

15. Explain how the idea of Kondrashov’s hatchet argues for an evolutionary advantage of sex.

Answer 15

through sexual reproduction, deleterious mutations are inherited synergetically

so every generation produces a wide variance of these mutations (similar to the boom in phenotypic variance found in the f2 generation)

this results in mutations being concentrated in low-fitness individuals which allows natural selection to select these individuals out of the population much faster as opposed to asexual populations

In sexual populations if two individuals with 3 deleterious mutations mate due to genetic liability there will be a distribution between 0-6 of the amount of mutations offspring will have… the lower fitness individuals with 6 mutations will be selected out my NS.

Question 16

When a new beneficial mutation arises, what are its two possible fates? Which is more likely if s =
0.15? Explain.

Answer 16

the new beneficial mutation will either :
1. fix within the population
2. undergo scholastic loss as beneficial mutations are initially rate presenting in only one individual at first

due to individuals with these beneficial mutations either not reproducing or not passing the beneficial mutation to offspring with there being a 50% chance of offspring inheriting it (law of segregation)

Question 17

7. Explain how Haldane’s sieve argues that dominant mutations should be the “stuff of adaptation”
   much more often than recessive mutations

Answer 17

recessive benefits have a greater risk of stochastic loss as the benefits of the mutation will not be seen until there is a high enough frequency of homozygous individuals.

The only way to increase q^2 frequency is through genetic drift.

As a result, the bulk of adaptation is dominant beneficial mutations.

Question 18

Explain the general logic of Fisher’s geometric model. What is the optimum? What do mutations
do in the model? What makes a mutation beneficial versus deleterious?

Answer 18

There is a spectrum of possible phenotypes with the phenotype best fit for survival being the optimum phenotype. NS will push populations to this optimum phenotype.

mutation placing the population closer to the optimum is beneficial

mutation displacing the population further from optimum is deleterious

the effect size of a mutation is the length of the vector from A, the population mean ( how far the mutation is from the optimum)

r1,r3 are deleterious mutations that place population further from optimum

r2 is beneficial mutation placing population closer to optimum

Question 19

How did Fisher interpret the model?

Answer 19

As effect size increases the probability of the mutation being beneficial sharply decreases.

–> The longer the vector further from the optimum

microscope analogy: if a microscope is out of focuz making a small change will result in the microscope focusing far more than making a large change

fixation of Mutations of small effect are the bulk of adaptation

However, fisher missed that smaller effect mutations experience stochastic lost as a result of genetic drift or individual is not reproducing

tweaked this interpretation bc
although small effect mutations are much more likely to be beneficial according to FGM, they have a much smaller chance of fixing due to 98% chance of stochastic loss.

Question 20

How did Kimura extend Fisher’s interpretation?

Answer 20

Kimura concluded that there is a “goldilocks zone” of effect sizes that have a reasonable probability of being beneficial while also having a larger probability of fixing given that they are beneficial.

*mutation of intermediate effect opposed to small effect are the “stuff” of adaption”

Question 21

How did Orr extend Kimura’s interpretation?

Answer 21

An adaptive walk is a population getting closer to its optimum phenotype by selecting for multiple beneficial mutations over time

However, the intermediate effects that would allow for fixation vary.

Orr thus showed that as an adaptive walk occurs there will be an exponential distribution of effect sizes that will fix. This distribution will have very few large-effect mutations in the beginning and an accumulation of small-effect mutations closer to the optimum.

Question 22

What is the cost of complexity in FGM?

Answer 22

The number of phenotypic dimensions could be greater than 2, as the complexity of the organism increases.

The cost is that as the complexity of the phenotypic dimension increases the beneficiality of the mutation decreases.
–> Mutations in more complex organisms have a higher chance of being deleterious than in simpler organisms

Question 23

Do you think that humans have more “dimensions of conformity” than do mice or Drosophila? In
other words, do you think that humans may suffer from a cost of complexity relative to these species?
Defend your position with 2-3 sentences

Answer 23

it depends on whether humans are thought to be more complex than mice and drospophila. If humans are thoguht to be more complex considering our neuronal capabilities it could be arugues that we would suffer from a cost of complexity more than drosophila/mice as more complex organisms have greater phenotypic dimensions and thus have a greater propensity to accumulate deleterious mutations. However if we look at genome size, humans could be argued to be less complex and thus suffer less form cost of complexity.