Bioinformatics 10: Phylogeny 2

Question 1

Strengths and weaknesses of evolutionary distance-based tree construction?

Answer 1

Strengths:
Computationally simple and quick
Distance correction

Weaknesses:
No insight about actual evolutionary changes
UPGMA (but not NJ) assumes a molecular clock
At longer times, distance are non-linear (require correction)

Question 2

Occam’s razor - relation to character-based methods?

Answer 2

simple hypotheses are preferable to more complicated ones

• smallest number of evolutionary changes in a tree = most favourable i.e. Maximum Parsimony

Question 3

Informative vs Non-informative base changes / SNPs between sequences?

Answer 3

Informative = 1 type of change at a given point (2 variable bases)
Non-informative = more than 1 type of change at a given point  (3 or more variable bases)

Question 4

Strengths and weaknesses of Maximum Parsimony (character-based) trees?

Answer 4

Strengths:

• does not reduce sequence information to a single number
• tries to provide information on the ancestral sequenes
• evaluates different trees

Weaknesses:

• computationally expensive (large no. of trees to consider)
• does not correct for multiple mutations (does not imply a model of evolution)
• evolution is not necessarily parsimonious (Occam’s razor not necessarily correct)
• no info on branch lengths/distances

Question 5

Statistical technique used to compare trees and find the ‘best’ one?

Answer 5

Bootstrapping

% of the time a given tree is ‘better’ than other compared trees