This document discusses phylogenetic trees and their terminology. It covers topics like tree building methods, types of nucleotide substitutions used in models of evolution, likelihood and Bayesian approaches, and some open problems in visualizing and archiving phylogenetic trees. The document uses examples of phylogenetic trees to illustrate concepts like rooting trees, tree topology not depending on node ordering, and different dimensions that could be used to visualize trees.
9. Building trees
• Maximum parsimony
(which tree can explain data with least
amount of evolutionary change)
• Maximum likelihood
(which tree has highest probability of
generating observed data)
• Bayesian analysis
(probability distribution of trees based on
prior knowledge and current data)
12. Likelihood
12
A
C
G
T
A C G T
Observed
A
C
G
T
A C G T
Jukes-Cantor
human
chimp
Predicted by models
Kimura 2 parameter
A
C
G
T
A C G T
Hasegawa et al.
A
C
G
T
A C G T
•More parameters = better fit
•but, don’t want too many
parameters
19. • Probability of having bowling elves is low (prior
probability)
• If you have bowling elves, probability that they
would make a noise is high (likelihood)
• Bayesian methods combine prior probability with
likelihood to get posterior probability
47. 47
0
1000
2000
3000
4000
5000
6000
7000
1975 1980 1985 1990 1995 2000 2005
Year
Cumulative number
Rate of growth of phylogenetic knowledge
Number of papers with
“molecular” and
“phylogeny” in Web of
Science
Number of
studies in
TreeBASE
Petra Isenberg, see “Interactive tree comparison for co-located collaborative information visualization” http://www.ncbi.nlm.nih.gov/pubmed/17968069 and http://innovis.cpsc.ucalgary.ca/Research/CollaborativeTreeComparison
Image from Mike Sanderson’s Lab (http://loco.biosci.arizona.edu/)