Virus Evolution

Question 1

What are branch lengths an estimate of?

Answer 1

Of the time since species diverged

Question 2

What does an unrooted tree mean?

Answer 2

They are related by dont know where common ancestors sit

Question 3

What is the root

Answer 3

The oldest point in the tree i.e. the common ancestor of all the species in the tree

Question 4

What are the two ways to root a tree?

Answer 4

1. Use a known out group - an out group is a species or group of species that diverged first
2. Midpoint rooting - assume that all species are evolving at the same rate and put the root in the middle of the tree

Question 5

What is a node?

Answer 5

Where two branches join

Question 6

What is the tip?

Answer 6

The end of the branch

Question 7

What is a Clade?

Answer 7

Groups e..g A, B and D all share a common ancestor, could say they form a clade

Question 8

If there are 4 sequences how many unrooted trees are there?

Answer 8

3 unrooted trees

Question 9

If there are 4 sequences and 3 unrooted trees, how many branches and therefore rooted trees are there?

Answer 9

5 branches, 15 rooted trees. The root could be on any of the branches

Question 10

If there are 5 sequences how many rooted and unrooted trees are there?

Answer 10

15 unrooted trees
105 rooted trees

Question 11

How do distance matrices work?

Answer 11

Just count the number of differences between two sequences then convert to a percentage

Question 12

Go through creating a tree from distance matrix methods

Question 13

What does minimum evolution distance matrix methods use?

Answer 13

Simultaneous equations

Question 14

What does maximum parsimony use?

Answer 14

Informative sites

Question 15

What is an informative site?

Answer 15

When there are at least two different nucleotides at the site, and each of which is represented in at least two of the sequences under study

Question 16

Why aren’t informative sites very accurate?

Answer 16

Not taking into account some evolutionary changes, only looking at informative sites

Question 17

What is bootstrapping?

Answer 17

Produce a new sequence of alignment of the same length as the real alignment , by random sampling from the sites in the real alignment
Make a phylogenetic tree from this alignment
Repeat steps 1 and 2 many times
Record how often each partition in the ‘real’ tree occurs among the bootstrapped trees

Question 18

Why is multiple hits important?

Answer 18

Models fo sequence evolution attempt to correct for multiple hits i.e. more than on substitution occurring at the same site over evolutionary time
If we sample at time 4 and time 1 and it has changed from A to T then might say it has only changed once but at time 3 and time 2 it may have been G and C so has changed 3 times

Question 19

Are transitions or trans versions more common?

Answer 19

Transitions more frequent than trans versions usually

Question 20

What is A to G called (purine to purine)

Answer 20

Transition

Question 21

What is A to C called (purine to pyramidine)?

Answer 21

Transversion

Question 22

What does JC69 model assume?

Answer 22

One rate for transversion and transitions

Question 23

What does K90 model assume?

Answer 23

Rates of transversion and transitions are different

Question 24

What is the GTR model?

Answer 24

General time reversible - six classes of substitutions, base frequencies vary

Question 25

What is the F81 model?

Answer 25

All substitutions are equal, base frequencies can vary

Question 26

What is the K2P model?

Answer 26

Transitions and trans versions have different substitution rates, base frequencies are assumed equal

Question 27

What is the HKY85 model?

Answer 27

Trnaisiotns and trans versions have different substitution rates, base frequencies can very

Question 28

What is a molecular clock?

Answer 28

Rate of evolution of a given protein remains roughly the same over time

Question 29

What does a molecular clock not mean?

Answer 29

Does not mean that -
All proteins evolve at the same rate
All sites within a protein evolve at the same rate

Question 30

What is a synonymous change?

Answer 30

Silence change, doesn’t change underlying amino acid

Question 31

What is ds?

Answer 31

The rate of synonymous (silent) substitutions
It reflects the mutation rate and is similar for different genes in the same virus

Question 32

What is dN?

Answer 32

The rate of non synonymous amino acid replacing substitutions

Question 33

Are dN or dS values lower?

Answer 33

DN values are lower because of constraints on proteins. DN values vary between proteins because different proteins have constrained to different extents

Question 34

How do you work out the substitution rate?

Answer 34

= slope so molecular distance/time