Phylogeny

Question 1

What does a phylogenetic tree show?

Answer 1

Evolutionary relatedness between species based upon genetic similarities

Question 2

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

Answer 2

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

Question 3

What is the genetic distance?

Answer 3

The proportion of nucleotides that are different between sequences

Question 4

How is genetic distance represtented in a phylogenetic tree?

Answer 4

Horizontal distance

Question 5

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

Answer 5

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

Question 6

What does the bootstrap value represent?

Answer 6

The reliability of the topology of the tree

Question 7

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

Answer 7

70% or higher

Question 8

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

Answer 8

100

Question 9

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

Answer 9

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

Question 10

What is a synonymous mutation?

Answer 10

Mutation that results in the same amino acid being present

Question 11

What is a non-synonymous mutation?

Answer 11

Mutation that results in another amino acid being present

Question 12

What is a transition?

Answer 12

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

Question 13

What is a transversion?

Answer 13

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

Question 14

What are the two purines?

Answer 14

A, G

Question 15

What are the two pyrimidines?

Answer 15

C, T

Question 16

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

Answer 16

Transversions result in amino acid substitutions more often than transitions do

Question 17

Which do occur more often: transversions or transitions?

Answer 17

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

Question 18

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

Answer 18

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

Question 19

What is the p-distance?

Answer 19

The proportion of different nucleotides between two sequences

Question 20

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

Answer 20

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

Question 21

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

Answer 21

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

Question 22

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

Answer 22

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

Question 23

What does an unrooted tree show?

Answer 23

The relationship between organisms, without showing the common ancestor

Question 24

What is the disadvantage of unrooted trees?

Answer 24

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

Question 25

What does a rooted tree show?

Answer 25

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

Question 26

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

Answer 26

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

Question 27

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

Answer 27

True

Question 28

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

Answer 28

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

Question 29

What is the flaw of the UPGMA method?

Answer 29

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

Question 30

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

Answer 30

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

Question 31

What is the advantage of a maximum likelihood tree?

Answer 31

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

Question 32

What is the disadvantage of maximum likelihood trees?

Answer 32

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

Question 33

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

Answer 33

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

Question 34

What can BLAST be used for?

Answer 34

To identify biologically related DNA sequences based on comparable biochemical properties

Question 35

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

Answer 35

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

Question 36

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

Answer 36

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

Question 37

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

Answer 37

That there is no recombination between genes

Question 38

What is BEAST software used for?

Answer 38

Analysis of viral sequences

Question 39

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

Answer 39

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

Question 40

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

Answer 40

RNA-viruses

Question 41

How is the rate of evolution expressed?

Answer 41

Nucleotide substitutions/position/year

Question 42

What is a dead end cluster?

Answer 42

A cluster that does not evolve into another dominant cluster

Question 43

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

Answer 43

1. Concatenated trees 2. Assigning clades 3. Tanglegrams

Question 44

How do concatanated trees detect reassortment?

Answer 44

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

Question 45

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

Answer 45

Segments with more mutation or larger segments affect the tree more

Question 46

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

Answer 46

Identifying unbroken lines of evolutionary descendence of genes

Question 47

What do straight vs. crossed lines in tanglegrams indicate?

Answer 47

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

Question 48

What is a bottleneck event?

Answer 48

Reduction of genetic diversity due to environmental events

Question 49

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

Answer 49

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

Question 50

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

Answer 50

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

Question 51

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

Answer 51

Sites that have to do with escaping immunity

Question 52

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?

Answer 52

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

Question 53

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?

Answer 53

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

Question 54

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?

Answer 54

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

Question 55

What does a ladder-like tree indicate?

Answer 55

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