R23 Phylogenetics (building trees)

Question 1

What does ‘Taxonomic ranks are arbitrary” mean ?

Answer 1

Made by one person

Molecular phylogeny is much more resolved rather than arbitrary

Question 2

What do these components of a tree mean:
- Direction arrow
- branches
- nodes
- clades

Answer 2

Direction arrow shows time, from older to modern species

branches are the edges

root node are the most recent common ancestors and leaf nodes are the tips, the modern species we are sampling

clade: everything stemming from one node

Question 3

How many types of trees are there to show the exact same phylogenies ?

Answer 3

4

Question 4

What data can phylogenies show ?

Answer 4

trait data, morphological data, molecular data

Question 5

What is an example of clustering algorithms ?

Answer 5

UPGMA (unweighted pair group method with arithmetic mean)

Clustering using pair wise similarities, then the difference between the other cluster is the distance in the branch

Question 6

What is the problem with parsimony reconstructions ?

Answer 6

Not all changes are equally likely, different mutation rates and substitution rates

We need to check a large number of trees to be sure we found the best one

Question 7

What are the solutions to parsimony reconstruction?

Answer 7

A substitution model shows the maximum likelihood tress using probability

Only look at plausible trees, use efficient algorithms, subtree prune and regrafts

Question 8

What do trees do ?

Answer 8

Trees reflect inheritance, flow of genes through time, allow a model for evolutionary changes through time

Question 9

What is parsimony ?

Answer 9

The easiest, most simplest hypothesis is correct

Question 10

How can we root an unrooted tree ?

Answer 10

Place the line in different locations and make that the root

Multiple trees may be correct

Question 11

UPGMA will give a different topology to than rooting an unrooted tree. How ?

Answer 11

Species that are closest together will be placed on the tree with the most recent common ancestor

The path with lowest mutations is taken as the shortest branch

Question 12

What is midpoint rooting ?

Answer 12

When we place the root at the centre of the unrooted tree

Question 13

What is a tree called when the branch length information is not present ?

Answer 13

Cladograms

Question 14

If two species diverted but have different length branches with different number of mutation events how do we work out how long ago they diverted?

Answer 14

Work out an average between both branches

Question 15

Why do phylogenetic branches differ in length ?

Answer 15

• Substitution rates vary between branches
• Samples differ in age
• Mutations are random, so some branches accumulate more by chance.

Question 16

What is the use of a molecular clock ?

Answer 16

allow substitution rates to differ between branches

Question 17

What is topology ?

Answer 17

The branching pattern of a tree, what it looks like

Question 18

How do you fill in a pairwise distance matrix to build a tree?

Answer 18

find the smallest distance, those 2 species are now a cluster in the following matrix

find out the distance from that cluster to the other species and fill in a new matrix. Distance to the other species is calculated by: d(A,B)= d(A,X)+d(B,X) / 2
A and B are the newly merged cluster and X is another specie

then repeat with the next smallest distance and another matrix until all species are clustered

The last specie to be clustered is the one that diverts first, then the second last to be clustered diverts second and so on, the branch length they diverted by will be in the matrix

Question 19

What assumptions is UPGMA making ?

Answer 19

rate of evolution is constant across all lineages

pairwise distance is additive, no evidence of unequal mutations or horizontal gene transfer

Question 20

What determines the steepness of a lineage through time plot, which measures the (log) number of species against time?

the ratio of the speciation and extinction rate S/E

the carrying capacity for the clade

the difference between the rate of speciation and the rate of extinction, i.e. S -E

the amount of incomplete lineage sorting for the clade

Answer 20

the difference between the rate of speciation and the rate of extinction, i.e. S -E

Question 21

What is the the “pull of the present”?

a speed-up in the recent past in the rate of lineage diversification inferred from a dated phylogeny

the expected increase in the (log) number of lineages for a clade with non-zero extinction rate

the artefactual upturn in the (log) number of lineages in the recent past if we include both extinct and extant taxa

the effect of niche filling on the change of the (log) number of lineages in the recent past

Answer 21

the expected increase in the (log) number of lineages for a clade with non-zero extinction rate

Question 22

When might a phylogeny reconstructed using UPGMA be incorrect?

the principle of maximum parsimony is violated

we have specified the wrong root

we have assumed the wrong substitution model

rates of evolution vary drastically between taxa

Answer 22

rates of evolution vary drastically between taxa