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### 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

Introduction

Understanding Trees

Birds

Amphibians

Crocodiles

Birds

Mammals

Lizards

Snakes

Turtles

Crocodiles

Snakes

Lizards

Turtles

Mammals

Amphibians

Do these phylogenies agree?

Figure 14.17

A

B

C

D

E

A

B

C

D

E

A

B

C

D

E

Understanding TreesTrees can be used to describe taxonomic groups

Monophyletic

- Paraphyletic

Polyphyletic

Amniotes

Amphibians

Crocodiles

Mammals

Snakes

Lizards

Turtles

Birds

Amnion

What is the relationship between taxonomic names and phylogenetic groups?Reptiles

Crocodiles

Snakes

Lizards

Turtles

Birds

Cold Blooded

What is the relationship between taxonomic names and phylogenetic groups?Amphibians

Crocodiles

Rodents

Lizards

Snakes

Turtles

Birds

Bats

Wings

What is the relationship between taxonomic names and phylogenetic groups?Polyphyletic example: Amentiferae

Oaks

Walnuts

Willows

Evolution of catkins

Ancestor with separate flowers

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 rely on clustering algorithms (e.g. UPGMA)

D

B

A

Example 1: morphology

Trait 2

C

Distance matrix

Trait 1

Distance methods with sequence data

A: ATTGCAATCGG

B: ATTACGATCGG

C: GTTACAACCGG

D: CTCGTAGTCGA

Distance matrix

A

B

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

Unique changes

Convergences or reversals

- 1 2 3 4
- a’bcd a’b’c’d’ a’b’c’d a’b’cd

Trait

b

d’

c’

Taxon

b’

a’

5 steps

abcd

Applying parsimony

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

Unique changes

Convergences or reversals

- 1 4 3 2
- a’bcd a’b’cd a’b’c’d a’b’c’d’

Trait

d’

c’

Taxon

b’

a’

4 steps

abcd

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

2

M

K

N

N

M

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

Which positions help to determine relationships?

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

Transitions

Transversions

A

G

T

C

Maximum likelihood: a starting sketch- Probabilities
- transition: 0.2 transversion: 0.1 no change 0.7

Find the tree with the highest probability

Transitions

Transversions

A

G

T

C

Maximum likelihood: a starting sketch- Probabilities
- transition: 0.2 transversion: 0.1 no change 0.7

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

Find the tree with the highest probability

Transitions

Transversions

A

G

T

C

Maximum likelihood: a starting sketch- Probabilities
- transition: 0.2 transversion: 0.1 no change 0.7

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 AATGCGC

Taxon 2 AATCGCT

Taxon 1 AATGCGC

Taxon 2

Informative sequences evolve at moderate rates

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

Polytomy

Challenges: sunflower phylogeny

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

= 15 spp!

= 12 spp!

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.

ACTTGCT

ACCTGAA

AGCGGAA

ACCAGAA

ACGTGCT

ACGAGCT

GCGATCC

GAGCTCC

AGCCTCC

8 hours

12 hours

One hour

Four hours

Red indicates multiple mutations at a site

24 hours?

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: whales

Are whales ungulates (hoofed mammals)? Figure 14.4

How consistent are the data?

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

Whales: DNA sequence data

Hillis, D. A. 1999.

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?

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.

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.

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