Lecture 33

Question 1

Phylogenetic trees:

Answer 1

• Used for many reasons

- Provide a representation of the relationship between species

Question 2

Linnean taxonomy:

Answer 2

• Classifying organisms into various ranks: phylum, kingdom, class, order, genus, species

Question 3

Phenetics:

Answer 3

• Classifying organisms on how similar they are

Question 4

Cladists:

Answer 4

• Classifying organisms on their evolutionary history

Question 5

Molecular phylogenetics:

Answer 5

• Protein electrophoresis
• DNA:DNA hybridisation
• Sequences

Question 6

How is phylogeny determined?

Answer 6

• Identify homologous characters (derived from a common ancestor)
• We must ensure a good alignment of sequences

Question 7

Terminal branch:

Answer 7

• The group of organisms at the end of of a branch

Question 8

Clade:

Answer 8

• A group of sequences that share a common internal branch

Question 9

Terminal node:

Answer 9

• The point where the line stops (present)

Question 10

Internal node:

Answer 10

• The points where the tree branches

Question 11

Root:

Answer 11

• Ancestral sequences for all the other taxa
• By asserting a root we are putting a time axis on the tree
• Without a root we just have a topology
• Changing the root can change the interpretation of the topology
• Either assert an out group OR invoke a molecular clock

Question 12

Trees:

Answer 12

• Networks without cycles
• Usually bifurcating (splitting into two)
• Occasionally polytomies, or star phylogenies indicatin failures to resolve the nodes into bifurcations

Question 13

Clagogram

Answer 13

• Shows which groups are related to each other

Question 14

Ultrametric tree:

Answer 14

• Terminal branches line up at the end
• We have a root
• We have a time axis allow determination of divergence points

Question 15

Phylogram:

Answer 15

• Branch length is proportional to the number of changes or the distance between different organisms

Question 16

The parsimony principle:

Answer 16

• When consider all pssible evolutionary scenarios, the one that takes the fewest steps is most likely to be the real scenario

Question 17

Homoplasy:

Answer 17

• You have to invoke multiple changes for a single character on a phlyogenetic tree

Question 18

Small parsimony problem:

Answer 18

• For a given tree, what is the minimal number of steps required to explain the data

Question 19

The large parsimony problem:

Answer 19

• For a given tree which of all possible trees has the smallest minimum number of steps?
• Increasing number of taxa and increasing number of topologies (2N-5)!

Question 20

Searching tree space:

Answer 20

• ‘Branch and bound’

- An exact method will find the shortest trees, some data sets will be too complex for it

Question 21

Heuristics method:

Answer 21

• Branch swapping
• Remember the metaphor.. Find the highest point on a map, so walk uphill, if you’re lucky enough you may find the highest point and find the global optimum, but you will more likely walk up a local optimum

Question 22

Tree bisection and reconnection:

Answer 22

• All possible bisections and re-attachment points are evaluated
• Cut point is not necessarily the reattachment point

Question 23

Subtree pruning and re-grafting:

Answer 23

• All possible subtree removals and re-attachment points are evaluated but the cut point is the re-attachment point

Question 24

Nearest neighbour interchange:

Answer 24

• There are two rearrangements per interior branch

Question 25

Does evolution always work in the most parsimonious way?!

Answer 25

• Not sure
• But can form consensus trees to show the majority rule consensus (70% show this branch) or the strict consensus (all trees show this branch)

Question 26

Distance methods:

Answer 26

• Lose info by reducing the data set to the distance matrix
• Compare every sequence to every other sequence and summarise the number of differences as a matrix
• Group the ones together will the smallest differences,

Question 27

Bootstrap approach

Answer 27

• Sample from the original dataset, and generate a pseudo replicate (some characters are represented twice, and some are not represented at all)
• Do this 1000 times, draw a consensus of the pseudo replicates and figure out how often certain ends are grouped together
• A measure of confidence of grouping, below 70% is less confident
• Consensus tree, so branch lengths will be distorted

Question 28

Assumptions:

Answer 28

• Sites evolve independently

- All changes are equally likely