Phylogeny

2

Trees and their terms

3

4

Tree terminology

edge (branch)

leaf (terminal node)

internal node (hypothetical ancestor)

root

5

6

Rooting a tree

7

Order doesn’t matter(trees are like mobiles)

A B C D ABCD

=

AB C D

=

8

Tree description

,)(

,)(

( A( , B )), C

A CB

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

Types of substitution

A G

C T transitions

transitions

transversions

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 THasegawa et al.

A

C

G

T

A C G T

•More parameters = better fit•but, don’t want too many parameters

Probability is different from likelihood

You hear a noise in the ceiling…

Could be elves bowling in the attic

The probability that you have bowling elves is very low…

…but if you did have them, the probability that you would hear them

is very high (=likelihood)

Bayesian methods

• 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

Bayesian posterior probabilities

1.0

0.8

0.5

A

E

B

C

D

Open problems

Visualisation

There are few constraints on how we can draw trees

X

A

BC

D

Y

X

B

AD

C

Y

We can reorder Y

@broadinstitute

X

B

AD

C

Y

X is a partial order

X

B

AD

C

Y

X is a partial order

X: evolutionary distance

B

AD

C

Y

X: time

B

AD

C

Y

Y

X

Z?

What would third dimension represent?

Paloverde

@wellcometrust

Touching the tree

@dr_pi

Big trees

add

@rdmpage

@rdmpage

Where are the trees?

http://www.treebase.org/

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

Why aren’t we archiving these trees?

How can we find the trees that we have?

TreeBASE interface

TreeBASE interface

Browser

The End