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BIOE 109Summer 2009
Lecture 4- Part IIPhylogenetic Inference
What is phylogeny?
What is phylogeny?A
B
(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:
Phylogenetic Inference
Two points to keep in mind:
1. Phylogenetic trees are hypotheses-how reliable?
Phylogenetic Inference
Two points to keep in mind:
1. Phylogenetic trees are hypotheses 2. Gene trees are not the same as species trees
Phylogenetic Inference
Two points to keep in mind:
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.
Phylogenetic Inference
Two points to keep in mind:
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
Conflict between gene trees and species trees
Phylogenetic Inference
• phylogenetic trees are built from “characters”.
Phylogenetic Inference
• phylogenetic trees are built from “characters”. • characters can be morphological, behavioral, physiological, or molecular.
Phylogenetic Inference
• 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 Inference
• 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 Inference
• 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?
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:
Types of homoplasy:
1. Convergent evolution
Example: evolution of eyes, flight.
Examples of convergent evolution
Types of homoplasy:
1. Convergent evolution
Example: evolution of eyes, flight.
2. Parallel evolution
Example: drug resistance in HIV.
What is the difference between convergent and parallel evolution?
What is the difference between convergent and parallel evolution?
Convergent Parallel
What is the difference between convergent and parallel evolution?
Convergent Parallel
Species compared: distantly closely related related
What is the difference between convergent and parallel evolution?
Convergent Parallel
Species compared: distantly closely related related
Trait produced by: different genes/ same genes/ developmental developmental pathways pathways
Types of homoplasy:
1. Convergent evolution
Example: evolution of eyes, flight.
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
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)
Contending schools of systematics
1. Phenetics (Distance methods)
Objectives:
1. Tree should reflect overall degree of similarity.
Contending schools of systematics
1. Phenetics (Distance methods)
Objectives:
1. Tree should reflect overall degree of similarity.
2. Tree should be based on as many characters as possible.
Contending schools of systematics
1. Phenetics (Distance methods)
Objectives:
1. Tree should reflect overall degree of similarity.
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
Contending schools of systematics
2. Cladistics
Contending schools of systematics
2. Cladistics
Objectives:
1. Tree should reflect the true phylogeny.
Contending schools of systematics
2. Cladistics
Objectives:
1. Tree should reflect the true phylogeny.
2. Tree should use characters that are shared (among two or more taxa) and derived (from some inferred or known ancestral state).
Contending schools of systematics
2. Cladistics
Objectives:
1. Tree should reflect the true phylogeny.
2. Tree should use characters that are shared (among two or more taxa) and derived (from some inferred or known ancestral state).
• shared and derived characters are called synapomorphies.
Contending schools of systematics
2. Cladistics
Objectives:
1. Tree should reflect the true phylogeny.
2. Tree should use characters that are shared (among two or more taxa) and derived (from some inferred or known ancestral state).
• shared and derived characters are called synapomorphies.
3. Ancestral state of characters inferred from an outgroup that roots the tree.
Contending schools of systematics
2. Cladistics
Objectives:
1. Tree should reflect the true phylogeny.
2. Tree should use characters that are shared (among two or more taxa) and derived (from some inferred or known ancestral state).
• shared and derived characters are called synapomorphies.
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?
How do distance trees differ from cladograms?
Distance trees Cladograms
How do distance trees differ from cladograms?
Distance trees Cladograms
Characters used as many as synapomorphies possible only
How do distance trees differ from cladograms?
Distance trees Cladograms
Characters used as many as synapomorphies possible only
Monophyly not required absolute
requirement
How do distance trees differ from cladograms?
Distance trees Cladograms
Characters used as many as synapomorphies possible only
Monophyly not required absolute
requirement Emphasis branch lengths branch-splitting
How do distance trees differ from cladograms?
Distance trees Cladograms
Characters used as many as synapomorphies possible only
Monophyly not required absolute
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
How do we select the “best” tree?
No. of Taxa No. of possible trees
4 3 5 15
How do we select the “best” tree?
No. of Taxa No. of possible trees
4 3 5 15 6 105
How do we select the “best” tree?
No. of Taxa No. of possible trees
4 3 5 15 6 105 7 945
How do we select the “best” tree?
No. of Taxa No. of possible trees
4 3 5 15 6 105 7 94510 2 x 106
How do we select the “best” tree?
No. of Taxa No. of possible trees
4 3 5 15 6 105 7 94510 2 x 106
11 34 x 106
How do we select the “best” tree?
No. of Taxa No. of possible trees
4 3 5 15 6 105 7 94510 2 x 106
11 34 x 106
50 3 x 1074
How do we select the “best” tree?
How do we select the “best” tree?
A. Maximum parsimony: the “best” tree is that which minimizes the number of evolutionary steps (changes among characters).
How do we select the “best” tree?
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
How do we select the “best” tree?
B. Maximum likelihood: the “best” tree is that which maximizes the likelihood of producing the observed data.
How do we select the “best” tree?
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.
How do we select the “best” 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
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
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
Step 1. Randomly select a base to represent position 1
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
Step 1. Randomly select a base to represent position 1
Species 1 T Species 2 TSpecies 3 C Species 4 C
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
Step 2. Randomly select a base to represent position 2
Species 1 T GSpecies 2 T GSpecies 3 C GSpecies 4 C G
Evaluating tree support by bootstrapping
Step 3. Generate complete data set (sampling with replacement).
Evaluating tree support by bootstrapping
Step 3. Generate complete data set (sampling with replacement).
Step 4. Build tree and record if groupings match original tree.
Evaluating tree support by bootstrapping
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
Evaluating tree support by bootstrapping
98
92
