Lec 6

Question 1

What happens to allele frequency change when we have finite (instead of infinite) population size?

Answer 1

When we talk about evolution, we often talk about natural selection in the same breath, or use the terms interchangeable - as if natural selection is the only mechanism of evolutionary change over time

Natural selection is just ONE mechanism

Question 2

The TWO most important processes that cause allele frequencies to change through time (evolution) are:

Answer 2

Natural selection and genetic drift

Question 3

Genetic Drift

Answer 3

The RANDOM change of allele frequencies in a population of FINITE size

Beetles squashed randomly for no genetic reason

If someone happened to step on green beetles more than brown beetles, the amount of brown beetles will increase

Differential survival of individuals is due to extrinsic factors, NOT to genetics or natural selection

Mendel’s law of segregation tells us that alleles are transmitted RANDOMLY to gametes

Random transmittal of alleles to offspring by heterozygotes in small populations means that the frequency of transmission of each allele may not be equal in each generation

Question 4

Genetic drift happens because Mendelian inheritance is about ____________

Answer 4

Averages

What percentage of offpring are ___________?

Is it possible that two individuals with __ genotype produce four ________________ offspring? (Concept important, details not)

Question 5

We can think about the effects of genetic drift by starting with the analogy of flipping a coin. Imagine you flip a normal coin. What’s the probability of getting heads?

Answer 5

50%

Question 6

Flip it again. What’s the probability of getting heads?

Answer 6

50%

Question 7

Flip again. What’s the probability of getting heads?

Answer 7

50%

Question 8

Even though the chance of getting heads is 50%, if you got 3 heads in a row would you think it was weird?

Answer 8

No

Question 9

How about if you flipped the coin 3000 times and got 3000 heads. Would that be weird?

Answer 9

Yes

Question 10

We can think about the effects of genetic drift by starting with the analogy of flipping a coin

Answer 10

At large sample sizes, OBSERVED frequencies are similar to EXPECTED frequencies - but this is often NOT the case at small sample sizes

At small sample sizes, we often see deviations between expectations and observations

Question 11

Wright-Fischer Model

Answer 11

Most commonly used model to describe genetic drift

Important for making predictions

Assumes a HAPLOID population

NO sexes

Discrete generations (every individual replaced each generation)

Constant size of 2N
-Simulate behavior of diploid population even though we are assuming haploid

No mating required for reproduction

No other evolutionary processes at work (no selection, mutation, migration)
-Baseline model, there WILL be other processes at work

Use this model to predict HOW allele frequencies will change under genetic drift

Discuss reasons why a population wouldn’t conform to this model

Question 12

Have allele frequencies in our population changed in generation 2?

Answer 12

Yes

Question 13

Was natural selection operating?

Answer 13

NO

We RANDOMLY picked alleles, there was no reasoning

Question 14

Genetic drift is the ______ change in allele frequencies from one generation to the next, in the ________ of natural selection

Answer 14

RANDOM; ABSENCE

Question 15

We want to come up with some sort of _______ about allele frequency changes over time due to drift

Answer 15

Prediction

Calculate EXPECTED allele frequencies in generation 2 given allele frequencies present in generation 1

Assume random sampling

Whether or not a particular allele “survives” to generation 2 DEPENDS ONLY ON ITS FREQUENCY IN GENERATION 1

Alleles at higher frequencies are more likely to be “chosen” (survive) than alleles at low frequencies

Question 16

EXPECTED changes in allele frequencies

Answer 16

Expectations are bout averages

Roll a 6-sided die 6 times, you will on average roll a 2 1/6 rolls

However, this number will vary across trials - sometimes it will be above average, sometimes below average

Question 17

If we start over with a new population with the exact same allele frequencies and do our random draws again, will we get the same result?

Answer 17

NO, we do NOT get the same outcome

Many small changes from generation to generation = big, somewhat random changes in allele frequencies over time

Question 18

Consequences of genetic drift for allele frequency change

Answer 18

Over time, ALL alleles will eventually become fixed or lost

Chance of fixation = chance that allele persists to next generation = frequency of the allele in current generation

Drift is blind to allele identify or dominance - all that matters is frequency

Question 19

If the starting frequency of the A allele in a population is 0.6, what is the probability of that allele going to fixation?

Answer 19

60%

Question 20

If an allele is at a frequency of 10% in a population, it has a _______ chance of being FIXED and a _____ chance of being LOST

Answer 20

10%; 90%

Question 21

Over time, genetic drift will purge ______ from populations

Answer 21

Variation

Question 22

How fast can allele frequencies change under genetic drift?

Answer 22

Consider a population at HWE with alleles A and a

Both alleles are at 50% in the population (equal frequencies). How fast will allele frequency change?

How fast allele frequencies change depends on starting population size

Question 23

Will alleles fix faster due to drift in large or small populations?

Answer 23

Small

Question 24

Allele frequencies change due to drift MUCH MORE QUICKLy in small populations

Answer 24

Remember how averages work

At large sample sizes, observed frequencies are similar to expected frequencies - but this is often not the case at small sample sizes

If we have 10 individuals and are randomly drawing A and a alleles for the next generation, can we pretty easily draw 9A and 1a alleles?
-We can! There is then a high chance that we draw 10As and 0as in the next generation, leading to the loss of a and the fixation of A

With a population of 1000 individuals, if we are randomly drawing A and a alleles for the next generation, are we likely to get 999A and 1a>
-NO - we expect we will get close to 500As and 500as

So - drift is a much more powerful evolutionary force in SMALL populations

Question 25

Based on these figures showing allele frequency change over time, which population would you hypothesize is the smallest?

Answer 25

Population A

Question 26

Heterozygosity

Answer 26

The presence of different alleles at one or more loci on homologous chromosomes

This is our key measure of the genetic variation in a population
-There can be NO adaptation/natural selection without variation

Question 27

Observed heterozygosity

Answer 27

H0

The fraction of individuals that are heterozygous at a given locus in our population
-What we actually observe

Question 28

Expected heterozygosity

Answer 28

He

The fraction of heterozygotes EXPECTED under Hardy-Weinberg equilibrium
-What we EXPECT to see

Question 29

Departures of observed heterozygosity from expectations suggest other processes are removing genetic variation

Answer 29

Often find FEWER heterozygotes than expected

Question 30

What effect does genetic drift have on heterozygosity (genetic variation) in populations?

Answer 30

Decrease heterozygosity

Question 31

What effect does genetic drift have on genetic variation in populations?

Answer 31

Genetic drift removes variation from populations - over time all alleles will either be fixed or lost

Loss of variation by drift is random - which allele is fixed or lost only depends on its frequency in the population

Genetic drift is always operating in the “background” of populations, regardless of what is going on with selection/migration/assortative mating

Thus all populations are constantly losing genetic variation over time due to drift

Question 32

Drift, variation, and population size

Answer 32

Small populations experience stronger genetic drift

Small populations therefore lose genetic variation (heterozygosity) more rapidly than large populations

Question 33

Why is genetic drift stronger in small populations?

Answer 33

The chances of a large change in allele frequency due to drift are greater when population size is small

Question 34

Genetic bottlenecks

Answer 34

Population experiences a REDUCTION in size
-Much LESS variation after being restricted

Bottlenecks lead to a loss of genetic variation

Question 35

Bottlenecks and allele frequency change

Answer 35

This figure shows 10 simulated populations

We start at the same allele frequency (A = a = 0.5)

Populations experience a bottleneck in size during the period indicated by the shaded region and return to the original size of 1000 individuals afterward

Allele frequencies fluctuate much more during the bottleneck than before or after

When population experiences a reduction in size, we observe LARGE and UNPREDICTABLE changes in allele frequencies among populations

The bottleneck causes divergence between populations. Before the bottleneck, allele frequencies are similar in all populations. After the bottleneck, allele frequencies differ greatly from one population to the next

Question 36

Look at the highlighted section of this figure. What happens to variation in allele frequencies across generations?

Answer 36

Allele frequency variation increases in magnitude

Question 37

Bottlenecks are _________ in nature

Answer 37

COMMON

Question 38

Island Diversity

Answer 38

An order of magnitude lower than mainland diversity

Why did foxes undergo a bottleneck?

• Populations of golden eagles migrated to Channel islands
• Bald eagles LEFT (previously kept golden eagles away)
• Golden eagles eat foxes

Question 39

Nucleotide diversity

Answer 39

Average proportion of nucleotide differences between sequences

Question 40

If there are differences between observed and expected heterozygosity at a locus, that likely means:

Answer 40

The conditions of Hardy-Weinberg Equilibrium are not met in the population

Question 41

Founder effects also reduce genetic diversity

Answer 41

Lost some alleles by colonizing new population

Leads to a decrease in genetic diversity

New populations are colonized by a small number of individuals

Question 42

Serial founder effects in humans

Answer 42

Humans evolved in Africa

This migration is known as the Great Human Expansion

Founder effects can result in DECREASED heterozygosity/variation

The vast majority of human genetic variation originated in Africa

Question 43

In which scenario would you expect to find the lowest heterozygosity?

Answer 43

An island population that has recently recovered from intensive hunting

Question 44

Genetic drift can be deceptive…

Answer 44

Snappers are thought to be a relatively healthy fishery

However, large effects of genetic drift were observed in snapper populations despite large population size - over 3 million individuals

Why might this be?

In a snapper, only a few large individuals in each generation produce most of the offspring - this is common in pelagic fish

Without understanding the biology and geography of a system, we may mistakenly predict the effects of genetic drift

Question 45

Why might we see low heterozygostiy in a population with millions of individuals?

a) This population was started by a founder event
b) This population has recovered from a bottleneck
c) All of the above

Answer 45

c) All of the above

Question 46

Genetic drift leads to loss of heterozygosity during population bottlenecks

Answer 46

We see a larger effect of genetic drift in populations that have experienced bottlenecks or founder effects in the past

Even though population size is large, genetic variation is low due to past bottlenecks

Question 47

Effective population size

Answer 47

Langurs live on steep cliffs, used to be joined by jungle; now separated by rice paddies

Hardy-Weinberg equilibrium assumes random mating

Can all the adult Delacour’s langurs mate with each other?

The total population surviving in the above region is estimated to be between 200 and 250 individuals, surviving in 19 isolated subpopulations; the species is believed to be extirpated form 3 additional sites, and some important populations, including those in Cuc Phuong National Park and Pu Luong Nature Reserve, have decreased by 20% in the last 5 years

Question 48

Say we measured heterozygosity in the langurs and compared it to expectations under a Wright-Fisher model with population size = 250. Would we expect H0 to be higher or lower than He?

Answer 48

Lower

Question 49

Effective population size (Ne)

Answer 49

Say we measured heterozygosity in the langurs and compared it to expectations under a W-F model with N = 250. Would we expect H0 to be higher or lower than He?
-Probably pretty low! Because the populations are isolated, drift is playing a larger role than would be expected for a population of 250 individuals. We might instead see the amount of drift expected from a population of 10 individuals

Ne is the number of individuals in a Wright-Fisher model that would produce the amount of genetic drift observed in the real population

Question 50

Other factors can affect Ne

Answer 50

1) Change in actual population size
2) UNEQUAL SEX RATIOS: All offspring need to inherit one allele from each parent. If there are many males and few females, the population will ACT smaller because the probability of drawing alleles from the same mother is large. A population with 100 males and 10 females will act like a population of N = 36, not N = 110 (has the same heterozygosity as a population of 36)
3) Variance in offspring number: If some individuals have 10,000 offspring and others have none, the population will ACT like a small population even if there are large numbers of individuals

Question 51

Wright-Fisher Expectation

Answer 51

Unequal offspring
-Effect on heterozygosity will be similar to a much smaller population

Mating disproportionately with one individual instead of equal mating between all individuals

Question 52

Variation, drift, and risk of extinction

Answer 52

Reduced heterozygosity is often associated with reduced ability to adapt - small isolated populations are more at risk and often considered “threatened”

The smaller the populations, the less the genetic diversity, the less heterozygosity, the less allelic and phenotypic polymorphism

Small populations are more vulnerable to chance events

Question 53

Extinction vortex

Answer 53

Populations are reduced and fragmented by habitat loss and hunting

Heterozygosity declines in small populations due to genetic drift - alleles become fixed or lost

Small population size increases inbreeding, which leads to inbreeding depression (recessive alleles exposed to selection)

Genetic diversity is irreversibly lost
-Loss is much more rapid than introduction of new variation by breeding

Populations are more vulnerable to chance events

Populations go extinct

From a conservation perspective, intervening only when populations are already small means its often too late

Small population -> inbreeding or random genetic drift -> loss of genetic variability -> Reduction in individual fitness and population adaptability -> lower reproduction and high mortality -> Smaller population

When population sizes get so small that they resort to inbreeding, they are usually beyond saving

Question 54

Drift can also cause population divergence and (perhaps) the formation of new species

Answer 54

Imagine we have a group of islands that can each sustain 10 individuals

No migration, selection, or mutation - just drift operating

We seed each island with 10 Aa heterozygotes

We then look at how alleles are distributed across islands over time

Eventually, each island will fix for a different allele

Divergence = different allele frequencies among populations

If allele frequencies are different enough across many loci, we end up with new species

Question 55

Isolation and drift: The Galapagos lava lizard

Answer 55

Lava lizards are poor dispersers

They maintain small populations on dry rocky areas in Santa Cruz and surrounding islets

Question 56

Drift in Lava Lizards

Answer 56

During the Late Pleistocene glacial event sea levels were substantially lower, allowing lava lizards to disperse between islands

Sea level rose, cutting lizards on different islands off from each other

As predicted by theory, there are now allele frequency differences at the same loci in lizards on different islands

Lizards on smaller islands also had less genetic variation, again as predicted

Question 57

Effective population size is reduced when populations are fragmented and can lead to an extinction vortex because:

Answer 57

Individuals are not able to mate with each other due to isolation, making the potentially breeding population smaller than total population size

Question 58

Interactions between selection, drift, and mutation

Answer 58

If drift alone was at work, all populations would become homozygous at all loci over time

In reality, mutation introduces new mutations

Selection, drift, and mutation are always operating simultaneously in populations

Question 59

How important are selection vs. drift to allele frequency change (and thus evolution)?

Answer 59

The effectiveness of natural selection at fixing alleles depends on population size and strength of selection

At small population sizes, drift is a stronger evolutionary force

At larger population sizes, selection is stronger than genetic drift

Figure shows probability that a novel mutation fixes in the population at different selection coefficients

Note that here the selection coefficients give selection against the other allele, so s = 0.5 means the new mutation is 50% better

We see that at small population sizes, the only way for a new mutation to fix is if it is very, very strongly selected

When population size is larger, the chance of fixation increases even if selection is weaker

Allele is less likely to be lost when population size is large; if population size is small, alleles with low frequencies are likely to be LOST unless there is very strong selection for it

At low frequencies much MORE likely to be LOST