Phylogeny reconstruction How do we reconstruct the tree of life?

Outline:

Terminology

Methods

distance

parsimony

maximum likelihood

bootstrapping

Problems

homoplasy

hybridisation

Dr. Sean Graham, UBC.

Phylogenetic reconstruction

•Rooted trees

Phylogenetic reconstruction

•Rooted trees

Outgroup:

Phylogenetic reconstruction

Phylogenetic reconstructionIntroduction

Bir

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Cro

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Tu

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Am

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ibia

ns

Ma

mm

als

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Sn

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Tu

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Am

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ibia

ns

Ma

mm

als

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Sn

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Cro

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Bir

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Understanding Trees

Do these phylogenies agree?

Figure 14.17

Branch lengths

A

B

C

D

A

B

C

D

1 nt change

Understanding Trees

A B C D EMonophyletic

A B C D E

Paraphyletic

A B C D E

Polyphyletic

Trees can be used to describe taxonomic groups

What is the relationship between taxonomic names and phylogenetic

groups?

Bir

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Cro

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Am

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Ma

mm

als

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Sn

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sAmnion

Amniotes

What is the relationship between taxonomic names and phylogenetic

groups?

Bir

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Cro

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dile

s

Tu

rtle

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Liz

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Sn

ake

s

Cold Blooded

Reptiles

What is the relationship between taxonomic names and phylogenetic

groups?

Bir

ds

Cro

co

dile

s

Tu

rtle

s

Am

ph

ibia

ns

Ro

de

nts

Liz

ard

s

Sn

ake

s

Wings

Ba

ts

Polyphyletic example: Amentiferae

Polyphyletic example: Amentiferae

Ancestor with separate flowers

Willows WalnutsOaks

Evolution of catkins

Vertebrate Phylogeny

Are these groups monophyletic, paraphyletic or polyphyletic?

fish?

tetrapods? (= four limbed)

amphibians?

mammals?

ectotherms (= warm blooded)?

Constructing Trees

Methods:

distance (UPGMA, Neighbor joining)

parsimony

maximum likelihood (Bayesian)

Distance Methods (phenetics)

Distance methods rely on clustering algorithms (e.g. UPGMA)

Trait 1T

rait

2

AB

C

D

Distance matrix

A B C D

A 1.0 3.0 4.9

B 3.3 3.0

C 3.0

D

Example 1: morphology

UPGMA

Trait 1T

rait

2

AB

C

D

Distance matrix

A B C D

A 1.0 3.0 4.9

B 3.3 3.0

C 3.0

D

A

B

Example 1: morphology

UPGMA

Trait 1T

rait

2

AB

C

D

Distance matrix

A B C D

A 1.0 3.0 4.9

B 3.3 3.0

C 3.0

D

A

B

C

D

Example 1: morphology

Distance matrix

A B C D

A 1 3 5

B 3 7

C 7

D

Distance methods with sequence data

A: ATTGCAATCGG

B: ATTACGATCGG

C: GTTACAACCGG

D: CTCGTAGTCGA

A

B

New Distance matrix: take averages

AB C D

AB 3 6

C 7

D

Distance methods with sequence data

A

B

A B C D

A 1 3 5

B 3 7

C 7

D

AB C D

AB 3 6

C 7

D

Distance methods with sequence data

A

B

A B C D

A 1 3 5

B 3 7

C 7

D

C

A

BC

D

AB C D

AB 3 6

C 7

D

Distance methods with sequence data

A

B

A B C D

A 1 3 5

B 3 7

C 7

D

C

A

BC

D

Assumptions of distance methods

Strengths and weaknesses of distance methods

II. Parsimony Methods (Cladistics)

Hennig (German entomologist) wrote in 1966

Translated into English in 1976: very influential

Applying parsimony

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

• Ancestral state: abcd

A B C D

1 a’ b c d

2 a’ b’ c d’

3 a’ b’ c’ d

4 a’ b’ c d

Trait

Ta

xon

Applying parsimony

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

A B C D

1 a’ b c d

2 a’ b’ c’ d’

3 a’ b’ c’ d

4 a’ b’ c d

Trait

Ta

xon

1 2 3 4

a’bcd a’b’c’d’ a’b’c’d a’b’cd

a’

d’

c’

b

Unique changes

Convergences or reversals

b’

5 steps

abcd

Applying parsimony

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

A B C D

1 a’ b c d

2 a’ b’ c’ d’

3 a’ b’ c’ d

4 a’ b’ c d

Trait

Ta

xon

1 4 3 2

a’bcd a’b’cd a’b’c’da’b’c’d’

a’

d’

c’

Unique changes

Convergences or reversals

b’

4 steps

abcd

Strengths and weaknesses of parsimony

Strengths

Weaknesses

.

Parsimony practicePosition

Taxon 1234567K AGTACCGL AAGACTAM AACCTTAN AAAGTTA

Which unrooted tree is most parsimonious?

L

M

N

K

L

K N

M

N

L

M

K

Plot each change on each tree. Positions 1 and 2 are done.

Which positions help to determine relationships?

22

2

Inferring the direction of evolution

Chimp

Human

Gorilla

Bonobo

Orangutan

Mouse

ACGCTAGCTACG

ACGCTAGCTACG

ACGCTAGCTAGG

ACGCTAGCTAGG

ACGCTAGCTAGG

ACGCTAGCTAGGWhere did the mutation occur, and what was the change?

III. Maximum likelihood (and Bayesian)

Maximum likelihood: a starting sketch

• Probabilities – transition: 0.2 transversion: 0.1 no change 0.7

A

CT

GTransitions

Tra

nsv

ersi

on

s

A

T

A

G

G

C

A

G

G

A

A

C

G

G

G

A

G

G

G

G

Find the tree with the highest probability

Maximum likelihood: a starting sketch

• Probabilities – transition: 0.2 transversion: 0.1 no change 0.7

A

CT

GTransitions

Tra

nsv

ersi

on

s

A

T

A

G

G

C

A

G

G

A

A

C

G

G

G

A

G

G

G

G

A

T

G

G

G

A

T

A

G

G

Find the tree with the highest probability

P = (.7)(.1)(.2)(.7)(.7)

Maximum likelihood: a starting sketch

• Probabilities – transition: 0.2 transversion: 0.1 no change 0.7

A

CT

GTransitions

Tra

nsv

ersi

on

s

A

T

A

G

G

C

A

G

G

A

A

C

G

G

G

A

G

G

G

G

A

T

A

G

G

A

A

G

G

G

A

A

G

G

A

C

A

G

G

A

P = (.7)(.1)(.2)(.7)(.7)

P = (.7)(.1)(.7)(.7)(.7)

P = (.1)(.2)(.7)(.7)(.2)Find the tree with the highest probability

Assessment of Maximum Likelihood (also Bayesian)

• Strengths

• Weaknesses

Characters to use in phylogeny

• Morphology

• DNA sequence

Challenges of using DNA data

Alignment can be very challenging!

Taxon 1 AATGCGCTaxon 2 AATCGCT

Taxon 1 AATGCGCTaxon 2

Informative sequences evolve at moderate rates

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

Polytomy

Example of insufficient evidence: metazoan phylogeny

Fungi

Metazoans

Challenges: sunflower phylogeny

= 15 spp!= 12 spp!

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

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

Saturation• Imagine changing one nucleotide every hour to a random

nucleotide• Split the ancestral population in 2.

ACGTGCT

One hour

Four hours

12 hours

ACTTGCT

ACGAGCT

ACCTGAA

GCGATCC

ACCAGAA

AGCCTCC

8 hours

AGCGGAA

GAGCTCC

Red indicates multiple mutations at a site

24 hours?

Saturation: mammalian mitochondrial DNA

Forces of evolution and phylogeny reconstruction

How does each force affect the ability to reconstruct phylogeny?

mutation?

drift?

selection?

non-random mating?

migration?

Phylogeny case study I: whalesAre whales ungulates (hoofed mammals)? Figure 14.4

Whales: DNA sequence data

Hillis, D. A. 1999.

How reliable is this tree? Bootstrapping.

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

Whales: DNA sequence data

Hillis, D. A. 1999.

Molecular clocks

Basic idea of molecular clocks

chimps

humans

whales

hippos56 mya

60 substitutions

6 substitutions

Challenges for phylogeny: gene flow

Sunflower annuals

Different genes may have different histories!

Phylogeny summary

Phylogeny study questions1) 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?

4) 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?

Phylogeny study questions5) 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.

Phylogeny study questions10) 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.