Lecture 7 - Inbreeding, Molecular Evolution and the Neutral Theory

Question 1

What are the main importance’s of the bottleneck/founder effect?

Answer 1

Reduction in heterozygosity (H) influences fitness immediately after bottleneck
-reduced heterosis, exposure of deleterious alleles
-small initial impact
-influenced by subsequent rate of increase
Reduction in allelic diversity influences ability to respond to long-term selection
-reduced ability to respond to stochastic events
-larger inital impact (on rare alleles)
-less influenced by subsequent rate of increase

Question 2

What is inbreeding?

Answer 2

Mating between two related individuals

Question 3

What is inbreeding depression?

Answer 3

Loss of fitness due to loss of genetic diversity

Question 4

What are the features of inbreeding

Answer 4

• inbreeding depression
• homozygosity of 2 alleles by desend
• increase in homozygosity in a population
• genetic subdivision of a population

Question 5

Where is inbreeding inevitable and why?

Answer 5

Inbreeding is inevitable in small populations
-every individual becomes related quickly becuase it is impossible to find a completely unrelated partner
-

Question 6

What is the formula for the increase in inbreeding in a certain population size?

Answer 6

Increase in inbreeding in a random mating population of size Ne is proportional to 1/(2Ne) per generation

Question 7

How does genetic drift affect homozygosity?

Answer 7

Increased homozygosity through loss of alleles

Question 8

How does inbreeding affect homozygosity?

Answer 8

Increased homozygosity due to change in genotype frequencies

-no change in allele frequencies

Question 9

What two events are likely in a small population?

Answer 9

• Genetic drift

- Inbreeding

Question 10

What two explanations are there for inbreeding depression (loss of fitness due to loss of genetic diversity)?

Answer 10

Dominance hypothesis

Overdominance hypothesis

Question 11

What is the dominance hypothesis of inbreeding depression?

Answer 11

• Assumes (partially) recessive deleterious alleles

- Increased number of homozygotes lead to more expressed deleterious alleles

Question 12

What is the Overdominance hypothesis of inbreeding depression?

Answer 12

• Assumes heterozygote advantage/heterosis

- Reduced number of heterozygotes leads to reduced fitness (hybrid vigour)

Question 13

How might inbreeding depression change over time under the dominance hypothesis?

Answer 13

Purging the genetic load

• deleterious recessive alleles will be expressed
• selection can act
• this leads to allele frequency changes and removes deleterious alleles from the population
• increased fitness after successive generations of inbred matings

Question 14

What evidence is there for purging?

Answer 14

Mice
-continued inbreeding in mice shows fitness improvement consistent with the dominance hypothesis
Drosophila
-Base population 1250
-30 lineages derived from base population
-maintained a n=20 for 19 generations
-6 purged populations, each maintained n =250 for 3 generations
-Each of the 6 had 15 full-sibling lines
-inbreeding depression decreased in the purged population compared to the base population

Question 15

What are the three formulae involved in loss and fixation due to drift?

Answer 15

Frequency of a new mutation: (1/(2Ne))
Chnace of getting fixed = frequency: (1/(2Ne))
Chance of getting lose: 1-(1/(2Ne))

Question 16

What is a mutation (in terms of fixation)?

Answer 16

A change that may or may not go to fixation

Mutation rate = μ

Question 17

What is a substitution (in terms of fixation)?

Answer 17

A mutation that has gone to fixation and replaced all other alleles at that locus
Substituation rate = k

Question 18

What is the formula for rate of substitution?

Answer 18

μ
(Probability of new mutations in a population X probability of fixation of a new mutation)
=> Substituation rate = mutation rate and does not depend on population size

Question 19

What are the features of DNA substitution rates?

Answer 19

• Rates are variable among organisms
• Rates are variable among chromosomes (and regions within chromosomes) within species (e.g humans and chimpanzees, Y chromosome especially different)
• rates are variable depending on the type of substitution

Question 20

What are the features of the rate of evolution of the α-Globin gene?

Answer 20

• present in sharks, cats, newt, chicken, echnidna, kangeroo, dog, human etc. (very wide spread)
• the amino acid substituations over time are a good fit to a straight line
• this indicates that the rate of α-globin evolution has been relatively constant over the past 450 million years
• k = 0.9 X 10^-9 amino acid replacements per year

Question 21

What is the molecular clock?

Answer 21

When the rate of substitution k = constant

Question 22

What can the molecular clock be used for?

Answer 22

-to estimate divergence events, if some divergence events can be dated independently (e.g. fossil record)

Question 23

Give an example of the use of the molecular clock

Answer 23

Speciation and the molecular clock on Hawaii

• Hawaiian islands have been formed in succession
• Kauai (5.1 Mya), Oahu (3.7Mya), Maui-Nui (1.9/1.6 Mya), Hawaii (0.43 Mya)
• Mean Cytd distance between the different islands birds’ are a good fit to a straight line against the time since separation
• Mean Yp1 distance between the different islands drosophila are a good fit to a straight line against the time since separation

Question 24

What are the features of evolutionary rates in different proteins?

Answer 24

Data taken from Fibrinopeptides, Hemoglobin, Cytochrome c proteins across species with different divergence times

• linear lines siggest that rates have not changed over time
• rates constant among species but differ among proteins

Question 25

Why are the evolutionary rates in different proteins constant among species but differ among proteins?

Answer 25

Selection as the main driving force
-more important molecules evolve more rapidly as they are being constantly fine tuned
Neutral theory
-Less important molecules evolve more rapidly because they have fewer selection constraints

Question 26

What expectations are there from the genetic code about the evolution of sites in chromosomes?

Answer 26

• most synonymous changes are in third position, some in first
• more substituations per nucleotide over a long divergence time at synonymous sites
• less substitutions per nucleotide over a long divergence time at nonsynonymous sites
• sites with fewer selection constraints evolve faster

Question 27

What is the neutral theory?

Answer 27

The neutral theory argues that the most genetic variation at the molecular level is selectively neutral and is therefore maintained by mutation and genetic drift

Question 28

What type of model is the neutral theory and how?

Answer 28

A null model

• does not deny that all deleterious alleles are selected against
• does not suggest that all morphological, behavioural or physiological differences are the result of drift

Question 29

What is the likely fate of new mutations?

Answer 29

Lost from the population