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.

1. Phylogeny

2. 2
Trees and their terms

3. 3

4. 4
Tree terminology
edge (branch)
leaf (terminal node)
internal node
(hypothetical ancestor)
root

5. 5

6. 6
Rooting a tree

7. 7
Order doesn’t matter
(trees are like mobiles)
A B C D ABCD
=
AB C D
=

8. 8
Tree description
,
)(
,
)(
( A( ,B )), C
A CB

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)

11. 11
Types of substitution
A G
C T transitions
transitions
transversions

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

13. Probability is different from
likelihood

14. You hear a noise in the ceiling…

15. Could be elves bowling in the attic

16. The probability that you have bowling
elves is very low…

17. …but if you did have them, the
probability that you would hear them
is very high (=likelihood)

18. Bayesian methods

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

23. Bayesian posterior probabilities
1.0
0.8
0.5
A
E
B
C
D

24. Open problems

25. Visualisation

26. There are few constraints on
how we can draw trees

27. X
A
B
C
D
Y

28. X
B
A
D
C
Y
We can reorder Y

29. @broadinstitute

30. X
B
A
D
C
Y
X is a partial order

31. X
B
A
D
C
Y
X is a partial order

32. X: evolutionary distance
B
A
D
C
Y

33. X: time
B
A
D
C
Y

34. Y
X
Z?
What would third dimension represent?

35. Paloverde

36. @wellcometrust

37. Touching the tree

38. @dr_pi

39. Big trees

40. add

43. @rdmpage

44. @rdmpage

45. Where are the trees?

46. http://www.treebase.org/

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

48. Why aren’t we archiving these
trees?

49. How can we find the trees that
we have?

50. TreeBASE interface

51. TreeBASE interface

52. Browser

53. The End