Phylogeny reconstruction

1
Phylogeny reconstruction
How do we reconstruct the tree of
life? Outline Terminology Methods distance
parsimony maximum likelihood bootstrapping P
roblems homoplasy hybridisation
Dr. Sean Graham, UBC.
2
Phylogenetic reconstruction
3
Phylogenetic reconstruction

• Rooted trees

4
Phylogenetic reconstruction

• Rooted trees
• Outgroup

5
Phylogenetic reconstruction
Introduction
6
Understanding Trees
7
Do these phylogenies agree?
Figure 14.17
8
Branch lengths
A
B
C
D
A
B
C
D
1 nt change
9
Understanding Trees

• Trees can be used to describe taxonomic groups

Monophyletic
Paraphyletic
Polyphyletic
10
What is the relationship between taxonomic names
and phylogenetic groups?
11
What is the relationship between taxonomic names
and phylogenetic groups?
12
What is the relationship between taxonomic names
and phylogenetic groups?
13
Polyphyletic example Amentiferae
14
Polyphyletic example Amentiferae
Oaks
Walnuts
Willows
Evolution of catkins
Ancestor with separate flowers
15
Vertebrate Phylogeny
Are these groups monophyletic, paraphyletic or
polyphyletic? fish? tetrapods? ( four
limbed) amphibians? mammals? ectotherms (
warm blooded)?
16
Constructing Trees
Methods distance (UPGMA, Neighbor
joining) parsimony maximum likelihood (Bayesian)
17
Distance Methods (phenetics)
18
Distance methods rely on clustering algorithms
(e.g. UPGMA)
D
B
A
Example 1 morphology
Trait 2
C
Distance matrix
A B C D
A 1.0 3.0 4.9
B 3.3 3.0
C 3.0
D
Trait 1
19
UPGMA
D
B
A
Example 1 morphology
Trait 2
C
Distance matrix
A B C D
A 1.0 3.0 4.9
B 3.3 3.0
C 3.0
D
Trait 1
A
B
20
UPGMA
D
B
A
Example 1 morphology
Trait 2
C
Distance matrix
A B C D
A 1.0 3.0 4.9
B 3.3 3.0
C 3.0
D
Trait 1
A
B
C
D
21
Distance methods with sequence data
A ATTGCAATCGG B ATTACGATCGG C GTTACAACCGG D
CTCGTAGTCGA
Distance matrix
A B C D
A 1 3 5
B 3 7
C 7
D
A
B
22
Distance methods with sequence data
A B C D
A 1 3 5
B 3 7
C 7
D
AB C D
AB 3 6
C 7
D
New Distance matrix take averages
A
B
23
Distance methods with sequence data
A B C D
A 1 3 5
B 3 7
C 7
D
A
B
C
AB C D
AB 3 6
C 7
D
A
B
C
D
24
Distance methods with sequence data
A B C D
A 1 3 5
B 3 7
C 7
D
A
B
C
AB C D
AB 3 6
C 7
D
A
B
C
D
25
Assumptions of distance methods
26
Strengths and weaknesses of distance methods
27
II. Parsimony Methods (Cladistics)

• Hennig (German entomologist) wrote in 1966
• Translated into English in 1976 very influential

28
Applying parsimony

• Consider four taxa (1-4) and four characters
  (A-D)
• Ancestral state abcd

Trait
A B C D
1 a b c d
2 a b c d
3 a b c d
4 a b c d
Taxon
29
Applying parsimony

• Consider four taxa (1-4) and four characters
  (A-D)
• Ancestral state abcd

Unique changes
Convergences or reversals
1 2 3 4 abcd abcd abcd abcd
Trait
A B C D
1 a b c d
2 a b c d
3 a b c d
4 a b c d
b
d
c
Taxon
b
a
5 steps
abcd
30
Applying parsimony

• Consider four taxa (1-4) and four characters
  (A-D)
• Ancestral state abcd

Unique changes
Convergences or reversals
1 4 3 2 abcd abcd abcd abcd
Trait
A B C D
1 a b c d
2 a b c d
3 a b c d
4 a b c d
d
c
Taxon
b
a
4 steps
abcd
31
Strengths and weaknesses of parsimony

• Strengths
• Weaknesses
• .

32
Parsimony practice

• Position
• Taxon 1234567
• K AGTACCG
• L AAGACTA
• M AACCTTA
• N AAAGTTA

Which unrooted tree is most parsimonious?
N
L
L
L
K
M
2
2
K
M
2
K
N
N
M
Plot each change on each tree. Positions 1 and 2
are done. Which positions help to determine
relationships?
33
Inferring the direction of evolution
ACGCTAGCTAGG
Mouse
Where did the mutation occur, and what was the
change?
Orangutan
ACGCTAGCTAGG
ACGCTAGCTAGG
Gorilla
ACGCTAGCTAGG
Human
ACGCTAGCTACG
Bonobo
ACGCTAGCTACG
Chimp
34
III. Maximum likelihood (and Bayesian)
35
Maximum likelihood a starting sketch

• Probabilities
• transition 0.2 transversion 0.1 no change 0.7

A
T
A
G
G
A
G
G
G
G
A
C
G
G
G
C
A
G
G
A
Find the tree with the highest probability
36
Maximum likelihood a starting sketch

• Probabilities
• transition 0.2 transversion 0.1 no change 0.7

A
T
A
G
G
P (.7)(.1)(.2)(.7)(.7)
A
T
G
G
G
A
T
A
G
G
A
G
G
G
G
A
C
G
G
G
C
A
G
G
A
Find the tree with the highest probability
37
Maximum likelihood a starting sketch

• Probabilities
• transition 0.2 transversion 0.1 no change 0.7

A
T
A
G
G
P (.7)(.1)(.2)(.7)(.7)
A
T
A
G
G
A
G
G
G
G
A
C
G
G
G
P (.7)(.1)(.7)(.7)(.7)
C
A
G
G
A
A
A
G
G
G
A
A
G
G
A
C
A
G
G
A
P (.1)(.2)(.7)(.7)(.2)
Find the tree with the highest probability
38
Assessment of Maximum Likelihood (also Bayesian)

• Strengths
• Weaknesses

39
Characters to use in phylogeny

• Morphology
• DNA sequence

40
Challenges of using DNA data

• Alignment can be very challenging!
• Taxon 1 AATGCGC
• Taxon 2 AATCGCT
• Taxon 1 AATGCGC
• Taxon 2

41
Informative sequences evolve at moderate rates

• Too slow?
• not enough variation
• Taxon 1 AATGCGC
• Taxon 2 AATGCGC
• Taxon 3 AATGCGC

Polytomy
42
Example of insufficient evidence metazoan
phylogeny
Metazoans
Fungi
43
Challenges sunflower phylogeny

• Recent radiation (200,000 years)
• Many species, much hybridization
• Need more rapidly evolving markers!!

15 spp!
12 spp!
44
Informative sequences evolve at moderate rates

• Too fast?
• homoplasy likely
• saturation only 4 possible states for DNA
• Taxon 1 ATTCTGA
• Taxon 2 GTAGTGG
• Taxon 3 CGTGCTG

Polytomy
45
Saturation

• Imagine changing one nucleotide every hour to a
  random nucleotide
• Split the ancestral population in 2.

ACTTGCT
ACCTGAA
ACCAGAA
AGCGGAA
ACGTGCT
ACGAGCT
GCGATCC
AGCCTCC
GAGCTCC
12 hours
8 hours
One hour
Four hours
Red indicates multiple mutations at a site
24 hours?
46
Saturation mammalian mitochondrial DNA
47
Forces of evolution and phylogeny reconstruction

• How does each force affect the ability to
  reconstruct phylogeny?
• mutation?
• drift?
• selection?
• non-random mating?
• migration?

48
Phylogeny case study I whales
Are whales ungulates (hoofed mammals)? Figure
14.4
49
Whales DNA sequence data
Hillis, D. A. 1999.
How reliable is this tree? Bootstrapping.
50
How consistent are the data?

• Take the dataset (5 taxa, 10 characters)
• Create a new data set by sampling characters at
  random, with replacement

Taxon 1 2 3 4 5 6 7 8 9 10
Human A C G T T G T A C T
Chimp A G G T T C T A T T
Bonobo A G G T T C T A T G
Gorilla A C T T G C T G T C
Orang T C G T G T A C C C
Taxon 3 8 2 6 10 10 5 8 8 7 3
Human G A C G T T T A A T G
Chimp G A G C T T T A A T G
Bonobo G A G C G G T A A T G
Gorilla T G C C C C G G G T T
Orang G C C T C C G C C A G
51
Whales DNA sequence data
Hillis, D. A. 1999.
52
Molecular clocks
53
Basic idea of molecular clocks
chimps
6 substitutions
humans
whales
60 substitutions
hippos
56 mya
54
Challenges for phylogeny gene flow
55
Sunflower annuals
56
Different genes may have different histories!
57
Phylogeny summary
58
Phylogeny study questions

• Explain in words the difference between
  monophyletic, paraphyletic, and polyphyletic
  taxa. Draw a hypothetical phylogeny representing
  each type. Give an actual example of a commonly
  recognized paraphyletic taxon in both animals and
  in plants.
• 2) How can a reconstructed phylogeny be used to
  determine if a similar character in two taxa is
  due to homoplasy?
• 3) Whales are classified as cetaceans, not
  artiodactyl ungulates. This makes artiodactyls
  paraphyletic why? What is the evidence that
  whales belong in the artiodactyls?
• Phenetics (distance methods) and cladistics
  (parsimony) differ in the ways they recognize and
  use similarities among taxa to form phylogenetic
  groupings. What types of similarity does each
  school recognize, and how useful is each type of
  similarity considered to be for identifying
  groups?

59
Phylogeny study questions

• 5) What is bootstrapping in the context of
  phylogenetic analysis, and why is this procedure
  performed?
• 6) Why are maximum likelihood methods increasing
  in popularity for reconstructing phylogenies? In
  your answer, include a short description of how
  this method identifies the best phylogeny.
• 7) For what kinds of data can maximum likelihood
  methods of phylogeny construction be used? Why is
  this so? What types of data are typically not
  used, and why?
• 8) Would animal mitochondrial DNA provide a
  reasonable molecular tool for evaluating deep
  phylogenetic relationships between animal phyla?
  What about ribosomal DNA? Justify your answers.
• 9) Integrative question Draw a pair of axes with
  Time since divergence on the x axis and
  percent of sites that are the same on the y
  axis. Draw a graph that shows the basic pattern
  for third codon sites is your graph linear?
  Explain why or why not.

60
Phylogeny study questions

• 10) You are studying a group of species that
  lives in two very different environments. You
  build two phylogenies one is based on a locus
  that is probably under divergent selection in the
  two environments, while the other phylogeny is
  based on a neutral locus. Which phylogeny would
  be more likely to represent the species history?
  why?
• 11) For a number of years, Anolis lizards are
  found in similar micro-habitats on many separate
  islands in the Carribean are very similar to each
  other (for example, large lizards that feed on
  the ground, smaller lizards that feed on tree
  trunks, and very small lizards that feed at the
  tops of branches). Two different, historical
  explanations have been proposed to explain this
  pattern each morph has evolved repeatedly on
  each island, or each morph has evolved just once,
  then dipsersed. Sketch a phylogeny that would
  support each hypothesis.
• 12) Integrative question the Cameroon lake
  cichlid phylogeny, showing that the lake species
  were monophyletic, was based on mitochondrial
  DNA. Explain why this might not reflect the
  species history. How could you be more certain
  about the phylogeny?
• 13) Explain why allopolyploid taxa pose problems
  for phylogenies.