Bioinformatics 9: Phylogeny 1

Question 1

Examples of what can be learnt from phylogenetic analysis?

Answer 1

When did specific episodes of positive Darwinian selection occur?

Which genetic changes are unique to the human lineage?

What was the most likely geographical location of the common ancestor of the African apes and humans?

Question 2

What is a phylogenetic tree?

Answer 2

A mathematical structure which represents a model of an actual evolutionary history of a group of sequences or organisms

i.e. an evolutionary hypothesis

Question 3

What are the terminal nodes on trees referred to as?

Answer 3

Operational Taxonomical Unit (OTU)

Question 4

What assumption is made about speciation in bifurcating trees?

Answer 4

It is rare and occurs only once (at a given node)

Question 5

3 different kinds of trees?

Answer 5

1) Cladogram -> simply shows relative order of ancestral history
2) Additive Trees (phylogram) -> Cladogram with given branch lengths
3) Ultrametric Tree (dendogram) -> type of additive tree where tips of the tree are all equidistant from the root

Question 6

2 types of data (methods) used in phylogenetic inference / tree contruction?

Answer 6

Character-based: Use aligned characters e.g. in protein, DNA sequences directly

Distance-based: Transform the sequence data into pairwise distances (dissimilarities), then use matrix during tree building

(also probabilistic method, but complicated)

Question 7

Common method used in distance-based construction? When does it fail?

Answer 7

Unweighted Pair Group Method with Arithmetic Mean (UPGMA)

Method fails when rates of evolution are not constant

Question 8

Purpose of neighbour joining?

Answer 8

Systematically pair more closely related nodes to sort a group of nodes which have no hierarchical structure