BIOE 109 Summer 2009 Lecture 4- Part II Phylogenetic Inference

BIOE 109Summer 2009

Lecture 4- Part IIPhylogenetic Inference

What is phylogeny?

What is phylogeny?A

(a) None(b) Both are phylogenetic trees(c) Only A is phylogenetic tree(d) Only B is phylogenetic tree

Phylogeny: evolutionary history of a group of speciesor a gene.

What is phylogeny?

Phylogeny: evolutionary history of a group of speciesor a gene

Phylogenetic tree: graphical summary of theevolutionary history

What is phylogeny?

Phylogeny describes:-1. Pattern and/or timing of events that occurred as species

diversified.

2. Sequence in which lineages appeared

3. Which organisms are more closely or distantly related.

Phylogenetic Inference

Two points to keep in mind:

1. Phylogenetic trees are hypotheses-how reliable?

1. Phylogenetic trees are hypotheses 2. Gene trees are not the same as species trees

• a species tree depicts the evolutionary history of a group of species.

• a gene tree depicts the evolutionary history of a specific locus.

Conflict between gene trees and species trees

• phylogenetic trees are built from “characters”.

• phylogenetic trees are built from “characters”. • characters can be morphological, behavioral, physiological, or molecular.

• phylogenetic trees are built from “characters”. • characters can be morphological, behavioral, physiological, or molecular. • there are two important assumptions about the characters used to build trees:

• phylogenetic trees are built from “characters”. • characters can be morphological, behavioral, physiological, or molecular. • there are two important assumptions about the characters used to build trees: 1. they are independent.

• phylogenetic trees are built from “characters”. • characters can be morphological, behavioral, physiological, or molecular. • there are two important assumptions about characters used to build trees: 1. they are independent. 2. they are homologous.

What is a homologous character?

• a homologous character is shared by two species because it was inherited from a common ancestor.

What is a homologous character?

• a homologous character is shared by two species because it was inherited from a common ancestor.

• a character possessed by two species but was not present in their recent ancestors, it is said to exhibit “homoplasy”.

Types of homoplasy:

1. Convergent evolution

Example: evolution of eyes, flight.

Examples of convergent evolution

Types of homoplasy:

2. Parallel evolution

Example: drug resistance in HIV.

What is the difference between convergent and parallel evolution?

Convergent Parallel

Species compared: distantly closely related related

Convergent Parallel

Species compared: distantly closely related related

Trait produced by: different genes/ same genes/ developmental developmental pathways pathways

Types of homoplasy:

2. Parallel evolution

Example: lactose tolerance in human adults

3. Evolutionary reversals

Example: back mutations at the DNA sequence level (C A C).

Evolutionary reversals are common in DNA sequences

Our objective is to identify monophyletic groups

A monophyletic group is derived from a single ancestral species and includes all descendants (e.g., mammals).

Three monophyletic groups:

Two mistakes are possible:

1. A paraphyletic group is derived from a single ancestral species but does not include all descendants.

Reptiles are paraphyletic

Two mistakes are possible:

1. A paraphyletic group is derived from a single ancestral species but does not include all descendants (e.g., reptiles).

2. A polyphyletic group fails to include the most recent common ancestor.

“Warm blooded animals” is a polyphyletic group

Contending schools of systematics

1. Phenetics (Distance methods)

Objectives:

1. Tree should reflect overall degree of similarity.

Objectives:

2. Tree should be based on as many characters as possible.

Objectives:

2. Tree should be based on as many characters as possible.

3. Tree should minimize the distance among taxa.

Examples of distance trees-HIV strains

Discrete character data is converted into a distance value

Distance tree—HIV strains

- Captures overall degree of similarity- Branch lengths are important

-Drawbacks: (a) loss of information about which traits have

changed.(b) have to correct for multiple substitutions at

the same site.(c) the tree may not reflect “true” phylogenetic

relationship

2. Cladistics

Objectives:

1. Tree should reflect the true phylogeny.

2. Cladistics

Objectives:

2. Tree should use characters that are shared (among two or more taxa) and derived (from some inferred or known ancestral state).

2. Cladistics

Objectives:

• shared and derived characters are called synapomorphies.

2. Cladistics

Objectives:

3. Ancestral state of characters inferred from an outgroup that roots the tree.

2. Cladistics

Objectives:

3. Ancestral state of characters inferred from an outgroup that roots the tree.

• an outgroup is ideally picked from the fossil record.

Example of a cladogram

How do distance trees differ from cladograms?

Distance trees Cladograms

Characters used as many as synapomorphies possible only

Monophyly not required absolute

requirement

requirement Emphasis branch lengths branch-splitting

Outgroup not required absolute requirement

How do we select the “best” tree?

No. of Taxa No. of possible trees

4 3 5 15

4 3 5 15 6 105

4 3 5 15 6 105 7 945

4 3 5 15 6 105 7 94510 2 x 106

11 34 x 106

4 3 5 15 6 105 7 94510 2 x 106

11 34 x 106

50 3 x 1074

A. Maximum parsimony: the “best” tree is that which minimizes the number of evolutionary steps (changes among characters).

-the simplest explanation is preferred over more complicated ones.

Examples of convergent evolution

Independent gain of camera eye requires two changes

Evolution and loss of camera eye requires six changes

B. Maximum likelihood: the “best” tree is that which maximizes the likelihood of producing the observed data.

- likelihood scores are estimated from a specific model of base substitution and a specific tree.

C. Bootstrapping

Evaluating tree support by bootstrapping

Species 1 A A C G C C T… GSpecies 2 A T C G C C T… GSpecies 3 A T T G A C C… GSpecies 4 A T T G A C C… G

Species 1

Species 2

Species 3

Species 4

Step 1. Randomly select a base to represent position 1

Species 1 T Species 2 TSpecies 3 C Species 4 C

Species 1 T GSpecies 2 T GSpecies 3 C GSpecies 4 C G

Step 3. Generate complete data set (sampling with replacement).

Step 4. Build tree and record if groupings match original tree.

Step 5. Repeat 1,000 times.

Species 1

Species 2

Species 3

Species 4

BIOE 109 Summer 2009 Lecture 4- Part II Phylogenetic Inference

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