TS5: Evolution Flashcards

1
Q

Which is more important: genetic stability or genetic plasticity? [Give key points for both arguments]

A

Stability:
- DNA repair
- Accurate cell division
- Passing genes to offspring
[Altruistic behaviour]

Plasticity:
- Adapt to new environments
- Survival

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2
Q

What is a hypermutator allele, and why might this impact the theory behind molecular clocks?

A

A hypermutator allele is a genetic mutation that increases the rate at which mutations occur in an organism’s DNA e.g., hitting the fidelity of DNA replication.

This means cells have increased genetic variation due to the hitchhiker hypermutator allele, and so the rate of spontaneous mutation will not be constant throughout the population.

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3
Q

What are the 4 key points in Darwin’s theory of evolution?

A
  1. Descent with modification
  2. Random variation
  3. Struggle to survival (selection pressure)
  4. Survival of the fittest
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4
Q

How did Darwin come up with the idea of descent with modification?

A

Whilst looking at pigeons, he realised there’s a tendency for offspring to resemble their parents, but not be identical to them. E.g., all pigeon variations descended from the common rock dove.

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5
Q

Define evolution.

A

Species changing over time.

[NB: there’s no reference to a mechanism of how this is achieved]

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6
Q

Define natural selection.

A

The differential survival and/or reproduction of classes of entities that differ in one or more characteristics, and this difference cannot be due to chance.

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7
Q

Describe the problem of inheritance.

A

Darwin’s theory of natural selection seemed to go against Mendel’s theory of inheritance: Darwin’s proposed small changes as the source of variation for natural selection, but Mendel argued inheritance was binary, based on the laws of dominance and recessivity.

We now know that genetic variation can produce apparently blended inheritance and continuous, small variation due to multigene traits.

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8
Q

State the Hardy-Weinberg equation and its 4 key assumptions.

Why is it still important today, despite these assumptions?

A

p^2 + 2pq + q^2 = 1

where p is the frequency of the dominant allele, and q is the frequency of the recessive allele.

Assumptions:
1. Infinite population size
2. No mutations or migration
3. Mating is random
4. No natural selection (all genotypes have an equal chance of survival and reproductive success)

It shows that recessive alleles can be maintained in a population.

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9
Q

Define the ‘fundamental theorem’ of natural selection.

Give the equation that describes this.

A

Changes in the average level of fitness in a population can be predicted by looking at the amount of genetic variation that contributes to fitness, assuming that the environment remains stable.

This genetic variation is typically referred to as the “additive genetic component of fitness,” and it refers to the genetic variation that is passed down from parents to offspring and that contributes to differences in fitness between individuals.

dM/dt= W –E – M/C

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10
Q

What was Malthus’ theory, and how did it inspire Darwin?

A

Economist Thomas Malthus explained that while population growth was exponential, resource growth was linear.

This inspired the competition for resources behind Darwin’s theory.

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11
Q

What is the Modern Synthesis? What are the 4 key pillars that it’s based on?

A

Also known as Neo-Darwinian synthesis, is a scientific theory that integrated Darwin’s and Mendel’s ideas of evolution and inheritance.

It’s based on 4 key pillars:
1. Natural selection is the primary mechanism for evolution of species.
2. Evolution occurs through changes in gene frequencies in populations over time.
3. Genetic drift causes evolution in small populations.
4. Speciation occurs through accumulation of genetic differences between populations over time.

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12
Q

Define major allele frequency (MAF).

A

The frequency at which the most common allele occurs in a population.

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13
Q

What is Hamilton’s law? Give the equation related to this theory.

A

Explains that altruistic behaviour can evolve by natural selection if the cost to the individual is outweighed by the benefit of a close relative.

rb > c

r = relatedness of the individual to the relative
b = benefit to the recipient
c = cost to the actor (individual)

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14
Q

What is inclusive fitness?

A

A measure of an individual’s overall reproductive success, including both their own direct reproductive success and the reproductive success of their close genetic relatives.

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15
Q

Describe the neutral theory of evolution.

A

Suggests that most evolutionary changes at the molecular level are due to random genetic drift rather than natural selection.

Most mutations have little or no effect on fitness, becoming fixed by random genetic drift.

  • Rate of evolution is determined by the rate of mutations occurring, not the rate of selection.
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16
Q

Define genetic drift.

A

The random fluctuation of gene frequencies over time due to chance events such as reproduction and death.

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17
Q

Define fixation (in reference to an allele).

A

When all individuals within a population have that allele, it has become fixed.

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18
Q

State the formula that describes fixation within neutral evolution i.e., heterozygosity at time t, and give its implications.

A

Ht = H0 x (1-1/2N)^t

where H0 is the starting heterozygosity.

  1. As t gets bigger, the eventual result is that Ht = 0, so the probability of fixation is equal to initial frequency…
  2. BUT, the large the population size N, the longer the time that is will take for 1. to occur.
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19
Q

What does the equation derived from the neutral theory of evolution, accounting for mutation and fixation, show?

A

The larger the population, the slower heterozygosity occurs.

Mutation ADDs variation into the population (not dependent on population size).

20
Q

Define each of the terms that are used to define the equation relating mutation and fixation to the neutral theory of evolution:
- G
- H
- u

A

G = the probability that 2 alleles drawn at random are equivalent
H = the probability that the alleles are different (1-G)
u = mutation rate

21
Q

State the Gillepsie formula.

A

G = 1/(1+4Nu)

G = probability the two alleles drawn are the same i.e., small G is high heterozygosity.

N = effective population

u = mutation rate

22
Q

What is the selection coefficient of an allele?

A

The difference between the mean relative fitness of individuals of a given genotype and that of a reference genotype.

23
Q

State the equation for the probability of fixation of a beneficial allele.

How does this prove Darwinian natural selection predictions?

A

(1 - e^-s) / (1 - e^-2Ns)

If Ns is large, e^-2Ns is very small, so 1-e^-2Ns is close to 1. Therefore the probability of fixation depends on s i.e., a high selection coefficient gives a high probability of fixation, which is exactly what natural selection predicts.

NB: for fixation of deleterious allele, flip everything:

(e^s - 1) / (e^2Ns - 1)

24
Q

Explain how the population size affects the probability that a deleterious allele goes to fixation in a population.

A

A deleterious allele that appears in the population at low frequency could go to fixation.

The probability of this happening is determined by the value 2Ns, where N is population size and s is the selection coefficient. A high value of Ns means the probability of fixation is low for a detrimental allele.

However, is Ns is small, the probability of fixation is quite large. This means that the probability of fixation for a detrimental allele is higher when the population size is small.

25
Q

Describe mutation accumulation experiments and explain why these are useful for studying evolution.

A

MA experiments use population bottlenecking at consistent intervals to create a situation in which organisms can evolve with practically no natural selection occurring i.e., close to pure genetic drift.

This allows for the rates of mutations to be studied without the influence of natural selection, as well as determining if certain characteristics are influenced by types of selection (e.g., purifying selection) or not, and studying non-genetic variation such as from epigenetics.

26
Q

What is coalescent theory?

A

A model of how alleles sampled from a population may have originated from a common ancestor (MRCA).

27
Q

Define purifying selection.

A

When variation is eliminated from the population, so fewer mutations will be observed than expected by chance.

[Also known as negative selection]

28
Q

Define positive selection.

A

When changes within a region of the genome are beneficial and so go to fixation more rapidly than the neutral expectation i.e., low N or high s.

29
Q

Explain the dN/dS ratio test.

Why is it not sufficient?

A

It is a statistical method used in molecular evolution to compare the rates of non-synonymous (dN) and synonymous (dS) substitutions in protein-coding DNA sequences.

The dN/dS ratio is a measure of the selective pressure acting on a gene, with values greater than 1 indicating positive selection, values equal to 1 indicating neutral evolution, and values less than 1 indicating purifying selection.

Most sites are under purifying selection, so this method isn’t sufficient.

30
Q

Describe the McDonald-Kreitman test and its assumptions.

A

The test compares the number of synonymous and non-synonymous mutations within and between species.

The basic idea of the test is that under neutrality, the ratio of synonymous to non-synonymous polymorphisms within species should be the same as the ratio of synonymous to non-synonymous substitutions between species. However, if there has been positive selection on a protein-coding gene, then the ratio of non-synonymous substitutions to synonymous substitutions should be higher between species than within species.

  1. Synonymous mutations are neutral.
  2. Population sizes are similar between the two species.
31
Q

What is a selective sweep?

A

When a beneficial mutation arises and becomes quickly fixated, taking with it the surrounding genomic region.

This can lead to a loss of genetic diversity in the surrounding region due to linkage disequilibrium.

32
Q

Why can’t we do an MK test for cancer?

A

MK tests require analyzing both within-species and between-species ratios. As there is no ‘other cancer species’, this cannot be done and so a dN/dS ratio must be used (not too bad as most mutations are under positive selection).

33
Q

Define Hill-Robertson interference. Give two examples of Hill-Robertson processes.

A

This occurs when the fixation of a beneficial allele also results in a high prevalence of a deleterious allele that was situated close to the beneficial allele, due to the inheritance of both mutations together.

This phenomenon is particularly relevant in small populations, where the strength of genetic drift is greater, and can lead to a reduction in the rate of adaptation and an increase in the rate of fixation of deleterious mutations.

  1. Genetic hitchhiking
  2. Muller’s ratchet
34
Q

Define genetic hitchhiking

A

Deleterious mutations that happen to be close to a beneficial mutation get ‘pulled along’ with it. This means that the theoretically ‘fittest’ allele is limited by the deleterious mutations alongside it.

35
Q

Define Muller’s Ratchet.

A

The presence of genetic drift means that even the fittest of alleles has the possibility of being lost. This means that the overall fitness of the population decreases to the next fittest allele.

36
Q

How might epimutations contribute to evolution?

A

Epigenetic alterations (epimutations) can be transmitted through transgenerational meiosis, and thus could contribute to heritable variation within populations.

This was tested in C. elegans using the transgenerational inheritance of RNAi or piRNA.

37
Q

How has evolutionary thinking aided in gaining mechanistic understanding of RuBisCo? Give the 3 hypotheses and use evidence to show which one seems more likely.

A

RuBisCo catalyzes the fixation of carbon dioxide in the Calvin Cycle, but has highly wasteful oxygenase activity. This may be because:
1. There’s a physical limitation/trade-off between carbon fixation and oxygenase activity e.g., the catalytic efficiency for carbon fixation and oxygenase activity is very similar, and we have shown that RuBisCo has evolved improved activity.
2. Neutral hypothesis: RuBisCo could be better, but there’s insufficient selective pressure to drive this change e.g., there was high carbon dioxide and low oxygen when RuBisCo evolved.
3. Adaptive hypothesis: oxygenase activity is useful and hence the function has been preserved

38
Q

How has evolutionary thinking aided in gaining mechanistic understanding of piRNA biogenesis in C. elegans?

A

Unlike in most other organisms, C. elegans synthesizes piRNAs from individual sequences with Ruby motifs. This motif is highly conserved, and originally also had an upstream motif.

Ancestral sequencing showed that the origin of this motif came from snRNA biogenesis, which are involved in pre-mRNA processing (spliceosome).

We also know now that piRNAs are rapidly evolving, likely to keep up with the constantly evolving transposable elements and viruses (Red Queen Hypothesis).

39
Q

Compare eukaryotic and archaeal histones.

A

Similarities:
- Conserved fold
- Conserved dimer architecture
- Similar sequence preferences

Differences:
- Archaea have no tails
- Archaea have few PTMs
- Archaea have no dedicated remodelling system
- Archaea can form oligomers and stacked spirals

40
Q

How can we test if mutations in cis-regulatory DNA are the most important?

A

Alter a gene’s expression without messing up its other roles e.g., altered time or place of expression OR altered protein function.

41
Q

What are the main two types of gene duplications?

A
  1. Tandem duplication
  2. Whole genome duplication
42
Q

Explain the principle of DCC.

A

The DCC (Duplication, Co-option, and Complementation) model is a widely accepted model for understanding the evolution of gene duplications. The model proposes that after a gene duplication event, one of the duplicated genes can undergo functional divergence or neofunctionalization, in which it acquires a new function or a subset of the original function. Meanwhile, the other duplicated gene may maintain the original function or undergo subfunctionalization, in which it retains only a subset of the original function.

43
Q

Describe the use of lab breeding (GWAS) to study mutations in evolution.

A

In GWAS, the aim is to identify genetic variations associated with a particular phenotype by analyzing the DNA of a population. To minimize the inherent genetic variation of a population, researchers often use laboratory animals that have been selectively bred to control for this genetic variability.

44
Q

Describe trait mapping.

A

Trait mapping is the process of identifying the genetic variants that are associated with a particular trait, such as a disease.

This is commonly done using GWAS and lab breeding to compare the genomes of those with and without the trait to identify SNPs.

45
Q

Compare the pros and cons of the following to study evolutionary traits:
- Lab breeds
- Domesticated species
- Wild populations

A

Lab breeds:
- Easy to manipulate in controlled conditions
- Easily inbred to create genetic homogeneity
x Not reflective of the complexity of natural populations
x May have undergone genetic drift that’s not representative of natural populations
x May be prone to deleterious genetic effects due to inbreeding

Domesticated:
- More readily available than wild populations
- Can be useful for studying selection pressures on the evolution of particular traits
x May have been bred for traits that aren’t representative of the selective pressures found in natural populations
x May have been subject to genetic bottlenecks that limit diversity

Wild:
- Reflects the natural diversity of populations
- Can be studied in a more ecologically realistic setting
x Difficult to study due to logistical or ethical constraints
x May be impacted by human-induced environmental changes