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Population Dynamics > Phylogeny > Flashcards

Phylogeny Flashcards

1
Q

What does a phylogenetic tree show?

A

Evolutionary relatedness between species based upon genetic similarities

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2
Q

What is implied when species are clustered together in a phylogenetic tree?

A

That they have a common ancestor (note: implication, not fact!)

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3
Q

What is the genetic distance?

A

The proportion of nucleotides that are different between sequences

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4
Q

How is genetic distance represtented in a phylogenetic tree?

A

Horizontal distance

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5
Q

Why does genetic distance between species stemming from a common ancestor increase over time? (4)

A
  1. Adaptation to immune system of hosts -> changing of epitopes
  2. Adaptation to therapies (resistance mechanisms)
  3. Random changes
  4. Bottleneck events
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6
Q

What does the bootstrap value represent?

A

The reliability of the topology of the tree

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7
Q

From which bootstrap value onwards is the reliability of the topology of the tree sufficient for typing?

A

70% or higher

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8
Q

At which bootstrap value is the reliability of the topology of the tree such that we can speak of perfect clustering?

A

100

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9
Q

Which variable do we need to know in order to estimate when a certain variant split off from the most recent common ancestor?

A

Rate of genetic change over time (often nucleotides/position/year)

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10
Q

What is a synonymous mutation?

A

Mutation that results in the same amino acid being present

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11
Q

What is a non-synonymous mutation?

A

Mutation that results in another amino acid being present

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12
Q

What is a transition?

A

A swap from purine->purine (A <–> G) or pyrimidine->pyrimidine (C <–> T)

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13
Q

What is a transversion?

A

A swap from purine->pyrimidine or pyrimidine->purine

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14
Q

What are the two purines?

A

A, G

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15
Q

What are the two pyrimidines?

A

C, T

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16
Q

What is the difference in biological effect between a transversion and a transition?

A

Transversions result in amino acid substitutions more often than transitions do

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17
Q

Which do occur more often: transversions or transitions?

A

Although there are more possibilities for transversion, the molecular mechanisms that generate transitions occur much more frequently, making them more common

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18
Q

Why is a higher GC-content associated with a higher melting temperature of genetic material?

A

CG-combinations have two hydrogen bonds, making them more stable than AT-combinations, which have one hydrogen bond

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19
Q

What is the p-distance?

A

The proportion of different nucleotides between two sequences

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20
Q

What does the horizontal distance in a phylogenetic tree represent? (2)

A

Because genetic distance is linearly proportional to time passed, it represents both:
1. Genetic distance to most recent common ancestor
2. Time since most recent common ancestor

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21
Q

What are the flaws of using p-distance to measure relatedness of sequences?

A

Does not recognize the difference in the biological effect of transitions (small) vs. transversions (high) -> it only expresses homology

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22
Q

What are the working assumptions for the Jukes Cantor (JC69) method to calculate genetic distance? (2) Are these assumptions correct?

A
  1. All nucleotides occur equally frequently
  2. Any nucleotide has a probability of 25% to be replaced by another nucleotide

Assumption 1 is incorrect -> in reality, this is never the case
Assumption 2 is incorrect -> the theoretical possibilities of transversions:transitions = 2:1, in reality, transitions occur more frequently

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23
Q

What does an unrooted tree show?

A

The relationship between organisms, without showing the common ancestor

24
Q

What is the disadvantage of unrooted trees?

A

No root = no possibility to estimate a most recent common ancestor -> does not allow to talk about ancestor-descendant relationships

25
Q

What does a rooted tree show?

A

Shows the last common ancestor of the groups in the tree -> allows to talk about ancestor-descendant relationships

26
Q

What is an outgroup and why is it included in a phylogenetic tree?

A

An organism that is related, but not completely related -> it is a way of forcing distinction into the tree

27
Q

True or false: genetic distance within a phylogenetic tree is additive

A

True

28
Q

What are (examples of) three different methods to construct a phylogenetic tree?

A
  1. UPGMA
  2. Neighbour-joining (NJ)
  3. Maximum likelihood
29
Q

What is the flaw of the UPGMA method?

A

Can only provide a correct result when genetic distances are equal, which is rarely the case

30
Q

In which cases is neighbour-joing a good method? (3)

A

Situations in which a quick analysis is required, such as:
1. Preliminary analysis
2. Quick evaluations of contaminations in a lab
3. Typing

31
Q

What is the advantage of a maximum likelihood tree?

A

It evaluates all possible tree topologies, which makes it more reliable than NJ trees

32
Q

What is the disadvantage of maximum likelihood trees?

A

Takes a long time to be constructed because all possible trees have to be evaluated

33
Q

Why are some amino acid substitutions more prevalent than others? (2)

A
  1. They are advantageous to the virus
  2. They do not disturb biological function and are not harmful

Conclusion: amino acid substitutions that are disadvantageous are selected against and are thus uncommon

34
Q

What can BLAST be used for?

A

To identify biologically related DNA sequences based on comparable biochemical properties

35
Q

When does BLAST consider sequences of nucleotides/amino acids to be similar?

A

Based on a similarity score of nucleotides/amino acids
When a threshold for similarity is met, BLAST considers these sequences to be similar

36
Q

What is the effect of setting the threshold of similarity in BLAST higher/lower?

A

Threshold too low: slows down search -> BLAST identifies too many similar sequences
Threshold too high: may lead to missing relevant sequences

37
Q

What does a similar tree topology for different genes of the same virus indicate?

A

That there is no recombination between genes

38
Q

What is BEAST software used for?

A

Analysis of viral sequences

39
Q

Which information can BEAST estimate when sample dates and sample locations are known? (5)

A
  1. Rates of evolution
  2. Location of evolution
  3. Date of evolution
  4. Most recent common ancestor
  5. Coalescent events = branching events
40
Q

Do DNA or RNA viruses typically have a higher rate of evolution?

A

RNA-viruses

41
Q

How is the rate of evolution expressed?

A

Nucleotide substitutions/position/year

42
Q

What is a dead end cluster?

A

A cluster that does not evolve into another dominant cluster

43
Q

What are the three methods to detect reassortment in phylogenetic analysis?

A
  1. Concatenated trees
  2. Assigning clades
  3. Tanglegrams
44
Q

How do concatanated trees detect reassortment?

A

By using multiple marker genes of the same virus -> if there is a dissimilar tree topology for multiple genes of the same virus, this indicates reassortment

45
Q

What is the weakness in using concatenated trees for detecting reassortment?

A

Segments with more mutation or larger segments affect the tree more

46
Q

How does the method of assigning clades for detecting reassortment work?

A

Identifying unbroken lines of evolutionary descendence of genes

47
Q

What do straight vs. crossed lines in tanglegrams indicate?

A

Straight line = similar tree topology -> no reassortment
Crossed line = dissimilar tree topology -> reassortment

48
Q

What is a bottleneck event?

A

Reduction of genetic diversity due to environmental events

49
Q

What is the effect of bottleneck events on the genetic diversity of segmented viruses?

A

Loss of genetic diversity in some or all of their segments -> causes a new antigenic cluster to become dominant

50
Q

What is the effect of bottleneck events on the genetic diversity of non-segmented viruses?

A

Genome-wide genetic sweeps -> virus will be replaced by another variant of the virus

51
Q

Which sites in the genome are under an especially high genetic pressure?

A

Sites that have to do with escaping immunity

52
Q

The ratio of synonymous vs. non-synonymous substitutions can indicate whether it is advantageous for a virus to have a specific site mutate. What does a ratio of non-synonymous/synonymous of < 1.0 indicate?

A

Purifying selection -> virus wants to keep the site the same, mutations at the site are disadvantageous

53
Q

The ratio of synonymous vs. non-synonymous substitutions can indicate whether it is advantageous for a virus to have a specific site mutate. What does a ratio of non-synonymous/synonymous of ~ 1.0 indicate?

A

Neutral evolution -> mutations at this site are neither advantageous nor disadvantageous

54
Q

The ratio of synonymous vs. non-synonymous substitutions can indicate whether it is advantageous for a virus to have a specific site mutate. What does a ratio of non-synonymous/synonymous of > 1.0 indicate?

A

Positive slelection -> mutation at this site is beneficial for the virus

55
Q

What does a ladder-like tree indicate?

A

Higher genetic pressures, in which variants constanly get swapped out for newer variants

56
Q
A

Population Dynamics (5 decks)

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