Lecture 5

Question 1

What is a tree in context of phylogeny?

Answer 1

Its a graph consisting of nodes and branches without a loop

Question 2

What is an unrooted phylogenetic tree? draw one

Answer 2

a tree with two types of nodes:
* tip/leaf: node with 1 branch attached
* internal node: node with 3 branches attached

Question 3

what is a rooted phylogenetic tree? draw one

Answer 3

a tree in which one branch is subdivided by a new node

Question 4

Can unrooted trees be rooted? if yes, how so?

Answer 4

yes. with an outgroup( a distantly related individual ) which means that the branch ending in the outgroup is subdivided by the root node.
and it is chosen to be a very distantly related organism to the remaining organism in the tree

Question 5

Each branch may have a length of ?

Answer 5

> /0

Question 6

What is a pedant branch?

Answer 6

branch attached to a tip

Question 7

what is a cherry?

Answer 7

a pair of tips only separated by one internal node

Question 8

what is a caterpillar tree?

Answer 8

a tree with only one cherry

Question 9

what is a monophyletic group or clade?

Answer 9

Its all descendants of a common ancestor

Question 10

What is an ultrametric tree? show on a tree

Answer 10

Sum of all branch lengths from any tip to the root is the same

Question 11

Polytomy

Answer 11

the definition of a phylogenetic tree is extended so that internal nodes have more than 3 branches attached. this node is called polytomy

Question 12

What is the string representation of this tree? refer to slide 8

Answer 12

((B:1, C:1):1, A:2):1,D:3)

Question 13

What is the string representation of this tree? refer to slide 9

Answer 13

((A:2, D:4) :1, B:1, C:1)

Question 14

Can a tree have multiple newick representations?

Answer 14

yes but they are all equivalent

Question 15

only? contributes to branch lengths

Answer 15

vertical distances along the evolutionally time axes

Question 16

In Charles Darwin’s representation what are the tips and what are the branches?

Answer 16

tips are the species, and the branches are the ancestry

Question 17

In a pylogeny of species of simians what are the branching events and branch length?

Answer 17

branch events are speciation events
branch lengths are time between speciation events

Question 18

In a pathogen phylogeny of HIV epidemic, what are the tips, branching events and branch lengths?

Answer 18

• different infected hosts
• transmutation events
• time between transmission events

Question 19

What was the data used for measuring similarity between species previously and currently?

Answer 19

previously: morphology
currently: typically sequencing data for species or pathogens or B-cells, etc

Question 20

Name 3 ways of defining similar between species

Answer 20

Phenetic, cladistic, mechanistic

Question 21

What is phonetic based on?

Answer 21

• its based on over all similarity
• pairwise distance based

Question 22

what methods does phonetic use?

Answer 22

UPGMA, least square algorithm

Question 23

What is cladistic based on?

Answer 23

shared characteristics
character based

Question 24

what methods does cladistic use?

Answer 24

parsimony

Question 25

What is mechanistic based on?

Answer 25

-evolutionary model -character-based

Question 26

what methods does mechanistic use?

Answer 26

maximum likelihood, Bayesian inference

Question 27

In an alignment each site is a ?

Answer 27

homolog

Question 28

How is each alignment obtained?

Answer 28

from raw sequencing reads by putting reads such that number of mutations, insertions and deletions are minimised

Question 29

What is the basic idea of distance based methods?

Answer 29

1-we define how to measure distance between sequences (JC69,etc) 2- Calculate the distance between all pairs of sequences 3- find a tree where the distances follow the sequence distance matrix most closely

Question 30

What are two strategies of distance based methods?

Answer 30

algorithmic and optimality

Question 31

How does the algorithmic method work?

Answer 31

its a sequence of steps where iteraretively smallest distances are clustered in a tree

Question 32

How does the optimality approach work?

Answer 32

Using a cost function, it minimises the difference of the sequence distance matrix to the inferred tree distances

Question 33

UPGMA assumes evolution according to what?

Answer 33

a strict molecular clock in which the rate of DNA/RNA/ Protein sequence evolution is constant over time

Question 34

What is the output and input of the UPGMA?

Answer 34

input is the distance matrix, output is the ultrametric phylogenetic tree

Question 35

Find the UPGMA tree for sequences below based on the hamming distance matrix for : s1:TCACACCT s2:ACAGACTT s3: AAAGACTT s4: ACACACCC

Answer 35

Slide 28

Question 36

How does the least square method work?

Answer 36

It defined a cost function which minimised the sum of differences between the distance matrix and the tree distance matrix for a proposed tree

Question 37

What is the runtime of UPGMA? How did you find that?

Answer 37

O(n^3) for n sequences. n: for pruning nodes (replacing a cherry with a new node) n^2 : for creating the distance matrix therefore n^3 in total

Question 38

How many trees can n=1,2,3 tips make?

Answer 38

n=1,2 both 1 for n=3, 3

Question 39

For runtime of least square methods what shall we do?

Answer 39

we need to optimise the cost function and therefore we need to visit each tree in the space of trees, therefore we need to find how many trees on n tips exist: number of rooted and unrooted trees on n tips

Question 40

if we have n tips, how many branches do we have?

Answer 40

2n-3

Question 41

How many unrooted trees with n tips exist?

Answer 41

(2n-5)!!

Question 42

How many rooted trees on n tips exist?

Answer 42

(2n-3)!!

Question 43

The least square decision problem is an --- problem, thus there is no --- time algorithm unless --, so we have to check --- trees with ---.

Answer 43

NP-complete, polynomial, P=NP, all, n tips

Question 44

Is UPGMA consistent? Explain further

Answer 44

yes, it is. The distance matrix tends towards the tree distances, therefore we cover the true tree

Question 45

IS Least square method consistent? Explain further

Answer 45

Yes, the squared difference between the calculated matrix and the tree distance tends towards 0, therefore the true tree is a least squares tree.

Question 46

UPGA and neighbour joining algorithms have a running time of :

Answer 46

polynomial time

Question 47

running time of least square methods is ?

Answer 47

NP complete

Question 48

What are two problems of phenetic approaches?

Answer 48

- they disregard information beyond pairwise distances - large distances come with large variances which are typically ignored.

Question 49

What is the minimal and maximum number of cherries in a phylogenetic tree with 99 tips ?

Answer 49

49 cherries and one left over

Question 50

In how many ways can you write a network string for a rooted tree with species A,B,C? In how many ways can you write it for n species?

Answer 50

4 ways, answer in slides, 2^(n-1)

Question 51

Consider the least square method, why would we use weights wi,j which aren't equal to 1?

Answer 51

we don't have infinite amounts of sequence data, we need to down weight the contribution of weights for distance matrix with a lot of noise wij=1/Dij( the estimated pairwise distance matrix)