Topic 3: Neutral Theory and DNA variation

Question 1

What is the neutral theory?

Answer 1

Motoo Kimura proposed that most variation is neutral, otherwise deleterious mutations would be removed by selection and beneficial ones would be rare and quickly fixed.
This came about because high levels of polymorphism observed are not consistent with strong selection at all loci.
New variants arise through mutation and allele frequencies are due to an equilibrium between mutation and genetic drift

Question 2

What is genetic drift?

Answer 2

Random change in allele frequency that occur from generation to generation as a result of sampling effects. Is much more extreme in small populations were alleles are fixed and lost at much more random rates

Question 3

What are the four forces of evolutionary change?

Answer 3

Genetic drift
Gene flow
Mutation
Selection

Question 4

What 5 things can we predict based on the principles of the neutral theory (variation is a consequence of the balance between genetic drift and mutation)?

Answer 4

Probability of fixation of an allele
Rate of fixation of an allele
Time between fixation of an allele
Time is takes for a new allele to become fixes
Amount of diversity on a population

Question 5

All of the things we can predict from the principles of Neutral theory can be predicted from what two simple functions?

Answer 5

Population size and mutation rate (if we ignore selection and migration)

Question 6

What is the probability of fixation of a new allele?

Answer 6

The probability that a neutral allele will reach fixation is equal to its frequency at the time of consideration, p.

Question 7

What is the probability that a new mutation will reach fixation? (an allele that arose via mutation)

Answer 7

There are 2N alleles in a population, thus the new allele has a frequency of 1/(2N) therefore the probability of a new mutation becoming fixed is 1/2N where N is the number of individuals in the population

Question 8

What is the rate of fixation of new mutations?

Answer 8

The rate at which new mutations are fixed in the population is μ. This results from the fact that the rate of new mutations per bp/ gene and per generation is μ . The probability of fixation for each new mutation is 1/2N, and there are 2N μ new mutations each generation. Combining these two formulas you get 2N μ /2N and this is just μ . This means that the rate of new mutations per bp/ gene per generation is the same thing as the rate of fixation of new alleles.

Question 9

What is the average time between the fixation of new alleles?

Answer 9

1/ μ (reciprocal the rate of fixation)

Question 10

What is the average time to fixation and time to loss of a new allele?

Answer 10

Mutations that are destined to become fixed, do so in 4Ne generations, and mutations that are destined to be lost are gone in (2Ne/N) ln (2N) generations

Question 11

What is Ne?

Answer 11

This is the effective population size, it is an idealized number that is usually smaller than the actual population size (N) because it only includes successful breeders.

Question 12

Why is genetic drift stronger in small populations?

Answer 12

It is stronger in small populations because there is greater sampling error between generations. In other words, allele frequencies fluctuate more widely in smaller populations in the same amount of time.

Question 13

Are mutations lost or fixed more quickly in populations? What does this explain?

Answer 13

They are lost much faster than they are fixed, but both processes take time in larger populations. This explains why larger populations are more genetically diverse; because they stay polymorphic for longer.

Question 14

What is the usual mutation rate for a population?

Answer 14

1 x 10^-6

Question 15

How do you calculate predicted gene diversity (expected heterozygosity) as a function of population size and mutation rate?

Answer 15

He = 4Ne μ / 4Ne μ +1

Question 16

What are the shortcomings of studying genetic variation using allozyme electrophoresis?

Answer 16

Not all proteins are enzymes
Enzymes have variable functional constraints on their sequence characteristics (more likely to be under selection)
Not all amino acid changes are detectable by electrophoresis (silent, those that do not result in shape or charge changes)
Proteins are more unstable and more difficult to work with than DNA

Question 17

What is the role of ADH in Drosophila? What is its distribution and alleles?

Answer 17

ADH is an enzyme that helps to break down alcohols, and there is a fast allele (more common in colder areas, higher activity), and a slow allele (more common in warmer areas, more stable). 11 copies of ADH (5 fast and 6 slow) from 5 populations were cloned and sequences to look for hidden variation.
The ADH gene has 4 exons and three introns and they are expressed differently in larva and adults

Question 18

What was the result on the study of the 11 ADH genes that were sequenced?

Answer 18

There were 9 unique alleles, and 43 variable DNA sites, BUT only one amino acid change was seen which caused to slow to fast polymorphism(Lys to Arg). This means that all other variations/polymorphisms found were either silent substitutions in exons, introns, or untranslates 5’ and 3’ UTR
This means that there was MUCH more DNA variation than protein variation, but unlike any other gene, there was no hidden variation.

Question 19

How do you quantify variation at the level of the nucleotide?

Answer 19

You calculate to proportion of nucleotide sites that differ in a sample of genes:
Pn= S/N where S is the number of variable sites and N is the total sites compared

Question 20

What factor does Pn not account for? How do we fix this?

Answer 20

Pn does not account for the number of sequences that were observed in the sample. We account for this by using the unbiased estimate of the polymorphisms per site.
THETA = Pn/a
a is the sum of 1/i, where i is up until number of sequences-1

Question 21

What issue does theta correct? What issue does theta have? How do we correct this?

Answer 21

theta corrects for the bias caused by sampling (the more sites you compare the higher the Pn), BUT it is imperfect because it does not account for different frequency of the polymorphisms, because sites are simply counted as being polymorphic or not
We correct this by using nucleotide diversity, which is a measure that accounts for the frequency of polymorphisms in a way similar to heterozygosity

Question 22

What is pi?

Answer 22

Nucleotide diversity
The proportion of sites that differ between pairs of sequences.
In other words it is heterozygosity at the nucleotide level.