Phylogenetic Trees

Aidan Budd, EMBL Heidelberg

April 2nd 2008, Cambridge

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 Prior Experiences?

• Have you read papers containing phylogenetic

trees?
• Have you estimated trees yourselves?
• What kinds of questions were the trees being
used to answer?

2
Trees in Publications:
Camel heavy-chain Ig

PMID: 11861879, Su et al. MBE 2002

3
Some Terminology

4
Some Terminology

Internal Branches
4
Some Terminology

4
 Some Terminology

External/Terminal Branches (leaves)

4
Some Terminology

4
 Some Terminology
Internal Nodes

4
Some Terminology

4
Some Terminology
External Nodes (OTUs)

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 “Relatedness” and
“Similarity”
C
B
A 0.1
B is more closely related to C than to A
B and C share a more recent common ancestor than
either does with A
A is equally distantly related to C as to B
A shares the same most recent common ancestor with C
as it does with B
B is more similar to A than to C
The combined branch-length from B to A is less than
from B to C
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 Which of these four
statements is incorrect?
C
(i) D is most similar to B B
(ii) D is most closely related to E F
E
(ii) A is most closely related to C

(iv) B is most closely related to F

A
D

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 Exercises
• Create a text file with this tree in parentheses format
0.1

a
b
c
d
e

• Load and examine in tree visualisation software

• Try to adjust the representation of the tree to bring:
• the a and e branch labels adjacent to each other

• the c and d branch labels as far apart as possible

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 Exercises
Draw the following tree by hand on paper

(((a,b),f),(c,(d,e)));
How many terminal branches does it have?
Can branches be rotated so that labels a and e are
adjacent?

Try the same for the tree below if you have time:

(((a,b),f),(c,(d,e)),((g,(h,i)),(j,k)));
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 Applications
Which question(s) best answered by
estimating a phylogeny?

A. Are two sequences related to each other?

B. How similar are a pair of sequences to each
other?
C. Which organism is my newly-discovered
animal most closely related to?

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 Applications
For 2 minutes, list (with your partner) possible
applications of phylogenetic trees
Example:
Is an influenza outbreak in Cambridge due one or
several different external sources?
(i.e. are some external sequences more closely
related to Cambridge sequences than others are?)
Non-Cambridge
Cambridge

(NB - PMID: 17140286 uses trees in this way)

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 Quiz
Which sequence is d most closely related to?
a
b
c

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 a
A b
c
d
e
f
g
i
B
E
h
Modified
5.0 from Imported tree 0
4.0 3.0 2.0 1.0 0.0

Which of A B C
and D is NOT
equivalent to E?

C D
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 Statistical Models of
Evolution
• Mesquite Demo
• Aims to illustrate
• concept of branch lengths
• that different trees (topology +
branchlengths), with a given model of
evolution, make different alignments
differently likely

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 Which tree is most
likely, given the data?
A
B
C
D
A D
A
iii
0.3 D
2.5
0.16 0.1 3.0
1.5
0.3 0.1 2.5
i C
D
5.0 C
B A A
2.5 B
3.0 D
1.5 0.3
2.5 0.16 0.1
5.0 C
0.3 0.1
ii iv
B
B C
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 Rooting Trees
B
MouseX

HumanY

A HumanZ

RabbitW
Chick
Chick
HumanY
Frog
MouseX
RabbitV
RabbitV
Default symmetrical+
2.0 1.0 0.0
HumanZ

RabbitW

Frog
Default symmetrical+
2.0 1.0 0.0 HumanZ

HumanY

All the same unrooted tree MouseX

C RabbitV

Chick

Which rooted tree has the root Frog

in the most plausible position?

RabbitW
Default symmetrical+
1.40 1.30 1.20 1.10 1.0 0.90 0.80 0.70 0.60 0.50 0.40 0.30 0.20 0.10 0.0

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 Estimating Phylogenies
Choose
appropriate set
of sequences Set of related
Question MSA
sequences

Remove
potentially
mis-aligned
regions
Choose model and
estimation method.
Phylogeny Estimate phylogeny
Estimate Filtered MSA
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 Published Trees
PMID: 17244599 PMID: 18205905
Figures 1 and 4 Figure 2
Yuan et al. (2007) MBE Moreira et al. (2008) BMC Evol Biol
For each tree think about
• What question are they trying to address
with the phylogenetic tree. Is it appropriate?
• How did they prepare their alignments?
• How did they choose sequences to analyse?
• How do they root the tree?
Compare the papers in these regards
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 Final Quiz
Each group devise one or more quiz
questions for the others

Examples:
• How many internal branches on a bifurcating
6-taxa unrooted tree?
• What is the minimum and maximum number
of gene duplications needed to explain the
evolution of a three-member gene family?

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 Software
• Tree Viewing: Dendroscope, NJPLOT
• Tree Viewing and Editing: Mesquite
• Evolving simulated data sets: Mesquite
• Link to lots of software: http://
evolution.genetics.washington.edu/phylip/
software.html (Google with “joe phylogeny
software”)

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