Topic 6: Population Genetics

genetic variation in a population is maintained as a result of _______ selection

balancing 

what is the most frequent measure of genetic variation ? what is the formula ?

population heterozygosity → the number of heterozygotes divided by total number of individuals ?

define null and alternative hypothesis

null

• default assumption

• assuming nothing unusual is happening 

• no change 

alternative 

• the opposite—something is happening 

• an effect/change 

all HW principal calculations assume a _________ population

panmictic (random mating) 

a HW disequilibrium is USUALLY due to….

heterozygosity (deficit or excess))

**If AF changes, GF will follow and also change. But if GF change, AF remain the same. Explain how this is possible

If AF change, GF automatically change because genotypes contain alleles

But if GF change, AF can stay the same because alleles are simply reshuffling into the different genotypes.

list the assumptions of HW principle that will result in HW disequilibrium if violated

1. random mate selection (panmnictic) 

2. no migration 

3. no selection 

4. population reproduces sexually 

if HW is violated, there are 3 results/outcomes. what are they & explain what they mean

1. a change in allele frequencies (evolutionary force)

2. hardy weinberg disequilibrium (non evolutionary force)

3. a change in AF AND hw disequilibrium (both forces occuring)

t/f HW disequilibrium means a change in allele frequencies

f

hw diseq. means the observed GF don’t match the expected GF

what does a change in GF, but not AF mean 

A non-evolutionary force is acting on a population, causing HW diseq.

list the evolutionary forces that can change both GF and AF

1. natural selection

2. migration

t/f allele frequencies can change with traits that aren’t genetic

false

Af can ONLY change through evolution is the alleles are heritable (passed from parent to offspring)

• if trait isn’t heritable, AF cant be affected.

explain how NS causes AF to change 

1. NS occurs when individuals with a certain trait are able to survive/reproduce better than those w/o the trait 

2. If the trait favoured by NS is HERITABLE, it can be passed to their offspring 

3. this causes allele frequencies to change for the next gen 

can selection change the frequencies of alleles from one generation to the next?

yes

NS favours some alleles over others, so AF can increase in the next generation

can we still calculate GF using HW once selection occurs in a pop?

NO

hw assumes no selection in a pop, therefore once it occurs, hw is violated. observed gf wont = expected gf

in a hw pop, expected __________ = observed ___________

genotype;genotype

t/f once selection occurs in a hw pop, its effects are noticeable after one generation

f

the effects of NS are usually not that noticeable after one gen, big differences only show up after MULTIPLE gen

• actually it depends on the strength. for a recessive lethal allele, yes its obvious but for other milder case no

if GF changes and AF doesnt = __________ 

if GF changes and AF does = ___________ 

hw disequilibrium caused by NON-EVOL FORCES 

hw disequilibirum caused by EVOL forces 

does the rate of evolution (AF change) in response to selection against a particular allele depend on whether the allele is dominant or recessive?

yes

• dominant deleterious allele: natural selection can see it, even in hetero and can remove it quick

• recessive deleterious allele: stays hidden in heterozygote so NS can only remove when homo, therefore its removed slowly

recessive alleles stay in populations for much longer

if you have a population where a recessive lethal allele is very common/high frequency (95%), what happens to the AF after one gen? what about the gen after that?

after one gen

• AF will dramatically decrease

  • everyone homo for that allele dies

  • the alleles that are surviving are “hiding” in hetero

after that gen

• AF will decrease slowly because hetero are still carrying that allele and are passing it to their offspring

multiple loci also means multiple genes t/f

yes 

for quantitative traits:

• few genes —> traits look more ___________

• many genes —> traits look more ___________

discrete;continuous and bell shape curve

list the 3 modes of selection for quantitative traits

1. directional

2. stabilizing

3. disruptive

which of the 3 modes of selection is most rare 

disruptive 

in general, selection ________ (increases/decreases) variation

decreases

t/f mutations change AF

yes, its an evolutionary force

• but since mutations occur rarely, they usually change AF very slightly each generations

• over long time periods, small changes add up and drive evolution

t/f mutation causes hw disequilibrium

f

t/f any violation to HW results in HW diseq

f

• not all violations of the assumptions of the hw principle will lead to hw diseq.

mutation results in which of the following:

1. change in AF

2. hw diseq

3. change in AF & hw diseq.

1. change in AF

t/f on its own, mutation ONLY has an impact over very long periods of time

f

define selective sweep

the rapid fixation of a beneficial allele by selection 

why can’t ns ever fully remove mutations from a population

• mutations are able to hide in heterozygotes where they can’t be seen (since hetero have same fitness as a normal homo)

• even if NS fully removes the mutation, remember mutations randomly appear in populations, so they can pop in whenever. u can never fully block them out.

define migration

the movement of alleles from one population to another, driven by ENVIRONMENTAL conditions:

• long distance dispersal (animals moving to a new location)

• transport of pollen 

whats the difference between species and populations 

species —> a group of organisms that can interbreed and produce offspring

• all share basic genetic makeup 

• eg. dogs are a species 

population —> subset of species, a group of individuals of same species that live in the same area and interbreed with people within population (way more than with other pops.) 

• eg. corgi in USA is one pop, corgi in UK is another pop.

with migration, it takes ________ (#) round of random mating to restore HW equilibrium

one

if migration increases genetic variation, how does it homogenize populations at the same time?

WITHIN one population, migration adds new alleles, increasing genetic variation

BETWEEN populations, migration makes them more similar, reducing teh genetic difference between the two

migration ________(increases/decreases) the value of Fst among populations

decreases

list whether each force is random or non-random

1. natural selection

2. mutation

3. migration

4. genetic drift

1. natural selection: non-random

2. mutation: random

3. migration: either non-random or random

4. genetic drift: random

small sample size = __________ (high/low) sampling error

large sample size = __________ (high/low) sampling error

high;low

compare sampling error to genetic drift

sampling error is the random difference between expected and actual results when taking a sample 

genetic drift is the evolutionary effect of sampling error happening over generations (causes random changes in AF) 

genetic drift = sampling error in reproduction over time 

• the smaller the population, the bigger the sample error and stronger the genetic drift 

T/F genetic drift is stronger in larger populations

F

what does it mean when:

1. Fst = 0

2. Fst = 1

1. all populations have identical allele frequencies

2. no alleles are shared among poopulations

t/f in any population, genetic drift will always cause the pop to become completely fixed.

t

• only if selection is not involved 

list and explain the 2 main types of sampling error in populations

1. founder effect

• a population started by a small group of ppl coming from a larger parental population 

• they “found” a new population 

2. population bottleneck

• a sudden sharp decline in populations size that CAN dramatically change AF (due to sampling error) 

• can be caused by natural disaster, disease, habitat loss, human activity

which is more powerful when population sizes are large: drift or ns

ns

in what situation would drift be much more powerful than ns

when population size is small 

which evolutionary force opposes genetic drift

migration

it takes ________ (little/lot) of migration to reduce the effects of drift

little

which evolutionary force opposes NS and can increase frequency of a deleterious allele in a population

migration, mutation, and genetic drift

t/f non random mating can change allele frequencies on its own

f

• it cannot

explain what it means when we say non-random mating indirectly affects evolution

1. non-random mating changes genotype frequencies, but AF stays the same

2. Only when combined with other evolutionary forces (selection, mutation, or drift) can it change AF

list the 4 types of non-random mating 

1. Inbreeding

2. Outbreeding

3. Positive Assortative mating

4. Negative Assortative mating

inbreeding causes more heterozygous or homozygous alleles

homozygous

does inbreeding change AF

no

what is inbreeding depression

a reduction in the average fitness among individuals within a population, due to inbreeding 

inbreeding/outbreed and assortative mating can both cause HW disequilibrium, but what differs between the two

hint: loci

**Inbreeding/outbreeding affect ALL loci, while assortative mating only affects specific loci tied to that trait 

what does it mean when we say populations are isolated

• pops are separated (by distance, barriers) with little to no migration or gene flow between them

• as a result, each pop evolves independently

• genetic drift or selection can make them diverge over time

explain the genetic rescue effect

→ An increase in average population fitness because of an increase in genetic diversity 

• Deliberately introducing individuals from elsewhere mitigates the negative effects of inbreeding & genetic drift in small populations 

• Basically migration done on purpose to help small, inbred populations recover genetically. 

define gene

unit of DNA that occupies a fixed position on a chromosome

define allele

an alternative form of a gene, located a given locus

define locus

a fixed position on a chromosome where a gene + its alleles are lcoated

define haploid

having one complete set of chromosome 

define diploid

having 2 complete sets of chromosomes

define homozygous

having two copies of the same allele at a locus

define heterozygous

having two different alleles at a locus `

what are the 2 hypothesis on the early views of HOW much genetic variation exists in a natural populations 

1. classical hypothesis 

• populations dont have a lot of genetic variation 

• selection maintains only the BEST allele at any locus 

• heterozygotes are rare - only exist for rare deleterious mutations, which is usually quickly removed by NS 

• individuals look genetically similar 

2. balance hypothesis

• populations have a LOT of variation

• many individuals are heterozygous

• genetic diversity is high

term of the older method used to measure genetic variation (before dna sequencing existed)

• explain in detail 

protein electrophoresis 

• measures variation by looking at protein differences, not DNA 

• based on the fact that different alleles make different proteins 

1. run proteins on a gel (electrophoresis), the different alleles each have their own migration rates + distance (how far they travel) 

2. by comparing the protein result and their differences, you can determine which individuals have the same alleles based on the band 

• also can see which are heterozygous and homozygous

what are the 2 hypothesis scientists had on WHY HIGH genetic variability existed in population  

• which hypothesis is the correct one? 

1. selectionist hypothesis

• heterozygotes have higher fitness and are more fit for survival (favoured by NS) 

2. neutral hypothesis

• many alleles in a population are neutral and don’t affect fitness 

• gene variety is completely random, and have nothing to do with survival 

• variation exists randomly, not bc its helpful or harmful 

• correct one 

why is genetic variation considered random, but phenotypic variation in a population is not random

genetic variation exists due to chance + randomness

• but which variations (phenotypes) stay or spread is NOT random = natural selection

t/f most alleles in natural populations are neutral and do not affect fitness 

t 

define allele frequency

how common each allele is in a population

define hardy weinberg principle

a model that predicts GENOTYPE FREQUENCIES from allele frequencies 

what doe a null hypothesis assume

nothing has changed or differed

list 5 things a hw population assumes 

1. no mutation

2. no migration

3. no natural selection

4. random mating 

5. very large population 

t/f according to hw principle, if all assumptions are met, then AF and GF stay constant throughout generations

t

what is the purpose of determining whether a population is a HW population

to determine whether evolutionary forces are acting on the population

________ population —> population with random mating

panmictic

define ‘balancing selection’

any form of selection that results in the maintenance of genetic variability

• part of the balance hypothesis

explain the neutral hypothesis

explanation for why genetic variability exists in a population 

• says most alleles are neutral and do not affect fitness 

• variation isnt for survival 

• the correct hypothesis !

explain the selectionist hypothesis

explanation for why genetic variability exists in a population 

• high genetic variability bc heterozygotes  have higher fitness and can survive better 

• heterozygotes are favoured by natural selection

explain the classical hypothesis

explains HOW MUCH genetic variation exists in a population

• claims pops dont have much genetic variation

• selection only maintains the one best single allele

• heterozygosity is rare and only exists due to rare deleterious mutations (which are usually removed quickly by ns)

• most individuals look genetically similar

explain the balance hypothesis

explains HOW MUCH genetic variation exists in a population

• claims pops have much genetic variation 

• many individuals are heterozygous 

• genetic diversity is high

• the correct hypothesis (not classical)

does the rate of evolution (AF change) on an allele, depend on whether that allele is dominant or recessive

YES

dominant

• exposed to selection immediately since they are visible and NS acts on phenotypic traits

• its effect shows up even with just one allele

• NS sees it quickly right away

• spreads much faster

recessive

• with recessive lethal alleles, the frequency is high at first, drops quickly, then slows down

• ns can never completely remove them from a population bc they hide in heterozygotes

Q: Does the rate of evolution depend on whether the allele is common or rare?

Yes

• Common allele → natural selection changes its frequency faster because more copies are exposed to selection.

• Rare allele → changes slower, especially if recessive, because most copies are hidden in heterozygotes.

list the 4 ways of fitness for heterozygotes 

1. same as one homozygote - acts like dominant/recessive

2. codominant - in between homozygotes 

3. heterozygote superiority/advantage/dominance - better than both homo 

4. heterozygote disadvantage/underdominance - worse than both homo

define quantitative traits

a phenotypic trait that varies continuously and involves multiple loci

• trait that shows a range of values

• eg. height, skin colour, weight

• varies continuously bc the trait is controlled by multiple loci with MULTIPLE alleles

t/f quantitative traits are controlled by one gene at one loci 

f 

• variation in quantitative traits is bc multiple genes are involved w multiple alleles and multiple loci 

• the more loci (genes) involved, the smoother and more continuous the trait distribution becomes 

what happens to the mean for all 3 modes of selection on quantitative traits 

1. directional - mean either increases or decreases

2. stabilizing - mean remains the same 

3. disruptive - mean remains the same 

for the 3 modes of selection on quantitative traits, list whether the variation increases, decreases, or remains the same.

1. directional - decreases

2. stabilizing - decreases

3. disruptive - increases

directional and stabilizing selection are the most common modes of selection on quantitative traits & both reduce phenotypic variation

if that’s the case, how come we can still observe lots of variation within natural populations (3 reasons)

1. populations are not in equilibrium

• selection hasn’t had enough time to remove all variation

2. mutation selection balance

• new mutations keep adding variation, while selection is removing it

3. disruptive selection MAY be more common

• since this selection increases variation, it could maintain it better than we thought

why doesn’t mutation cause HW disequilibrium (aka change GF)

• when mutation first enters into a pop, it exists at such a low frequency + rate that the effect is SUPER tiny on allele frequencies

• remember GF only changes if AF change

• so if the effect is tiny + there is random mating within the pop, HW can quickly restore the expected GF and bring back balance

explain what it means when we say random mating can restore hw equilibrium in just one generation

• random mating = everyone mates by chance, not based on preferred traits 

• even if something disrupts HW and changes the HW, as long as there is random mating, HW can quickly restore the expected genotype frequencies (hw is all about gf) and bring back hw equilibrium 

•  HW will reshuffle alleles so that GF match proportions predicted by the CURRENT (recently changed) allele frequencies after one gen 

define ‘selective sweep’

the rapid fixation of a beneficial allele by selection

• occurs whenever a beneficial allele rises rapidly in frequency (not just w mutations)

are mutations mostly neutral, beneficial, or deleterious. rank them

1. neutral 

2. deleterious

3. beneficial 

what is mutation-selection balance

when mutations are introduced into a population, they will get removed by NS but as its removing them, mutants re-introduce them

• both are happening simultaneously

• crates a repeating cycle

• the rate at which deleterious alleles are appearing through mutation = same rate at which selection is removing them

  • keeps the deleterious allele within the population, but at a low frequency

define selection coefficient. what do the #s mean 

→ a measure of the strength of NS (fitness) acting against a genotype 

• how strongly the allele affects survival/reproduction

• S = 0 → no selection (genotype has the same fitness as the best one) 

• S = 0.1 → genotype is 10% less fit than the most fit one 

• S = 1 → completely lethal (organisms w this genotype do not survive/reproduce) 

  • allele causes 100% fitness LOSS

is mutation-selection balance the reason why cystic fibrosis alleles still exist in a populations. if not, explain why. mention the selection coefficient. 

selection coefficient for CF is S=1 (very lethal) 

• its AF in a population is 2% which is considered high 

if MS balance is the reason CF alleles are still present, the CF mutation rate has to be high enough to keep up w the rate that NS is removing the allele 

• according to our calculations 🤓👆the mutation rate must be 4 × 10⁻⁴ (for MS balance to be the reason)

• the actual mutation rate = 6.7 × 10⁻⁷ (wayy lower) 

• this means the mutation is too rare for MS balance to occur

• given this rate, NS is easily able to remove the harmful allele or put it at a lower frequency 

so the ACTUAL REASON is: heterozygote superiority 

• heterozygotes with one cf allele do not have the disease & are healthy, keeping the CF allele in the population 

• heterozygotes for CF exist at a high frequency in areas with high malaria bc being heterozygous protects them from getting malaria 

which evolutionary forces can introduce new alleles into a population

migration and mutation

define homogenization

when migration acts to reduce differences in allele frequencies between populations

• makes pops more similar in terms of AF

explain the process of homogenization + 2 assumptions 

process: 

1. 2+ populations exchange migrants at equal rates

2. over time, AF in all populations become equal = homogenization

assumptions:

1. assumes no evolutionary forces are influencing AF 

2. population size of all populations’ are equal