6 - Phylogenetic Inference: Trees and Distances

Question 1

List four things that HMMs can do in bioinformatics

Answer 1

1. Build and refine multiple alignments or profiles in a mathematically rigorous way
2. Assess the probability that a sequence belongs to a given family of sequences used to train the HMM
3. Gene finding/annotation in genome sequences
4. Regulatory region (promotor0 finding in genomes

Question 2

Give four terms used in trees

Answer 2

• Root
• Branch
• internal node (eg. branch point/hypothetical ancestor)
• Terminal node

Question 3

Draw the tree for the following Newick tree file format

((A,B),C),(D,E)

Answer 3

Each comma is a node, the comma between brackets is the root.

Question 4

What are cladograms and phylograms?

Answer 4

Cladogram: a branching diagram showing the cladistic relationship between a number of species.

Eg. the branchlengths don’t mean anything.

Phylogram: Scaled branch lengths indicate divergence. Ultrametric trees are often called ‘strict molecular clock trees’ because their branchlengths are directly proportional to time

Question 5

How can you tell if a tree is rooted or not?

Answer 5

Ask yourself where is the root (must come to a point) and how was it determined?

Most tree building methods will not explicitly root the tree unless you tell it to.

Question 6

Give three ways for rooting a tree

Answer 6

Ad hoc: Historical precedent or other knowledge. You decide placement of root in the tree

Intrinsic: Eg. parsimony methods, likelihood, UPGMA etc. Midpoint rooting is where you find the point of the tree that is equidistant from all the tips (in an ultrametric tree) or some approximation to this.

Outgroup rooting: Add species/sequences to your analysis that you know based on some other criteria (fossil data, morphological phylogeny, previous molecular phylogenetic results etc)

Question 7

What are monophyletic groups?

Answer 7

A clade on a tree. Clades are subtrees of larger trees. The set of all clades in a tree can be expressed by the cladogram.

Question 8

What is polyphyly and paraphyly?

Answer 8

Polyphyly: Multiple origins for the groups, the group does not contain the common ancestor

Paraphyly: SIngle origin for the group, but the group does not contain all the descendents of the common ancestor

A paraphyletic group often represents a grade on the tree (ie. a kind of morphological organization in a paraphyletic group).

Question 9

What are three broad reasons for gene trees not necessarily being species trees?

Answer 9

• Coalescence of alleles within species
• Paralogy and orthology
• Lateral gene transfer (xenology)

Eg. paralogs result from gene duplication and orthologs result from speciation.