Phylogenetic Trees Methods

Dr. Shohag Barman

Assistant Professor
Department of Computer Science & Engineering
University of Liberal Arts Bangladesh
Email: sohag.barman@ulab.edu.bd
 Lecture Outlines
• Methods for constructing a phylogenetic tree
 Types of Phylogenetic Methods
■ Distance based
- Neighbor Joining(NJ)
- UPGMA(Unweighted Pair Group Method with
Arithmetic Mean)
■ Character based
- Maximum Parsimony
- Maximum Likelihood
 Maximum Parsimony
■ Maximum Parsimony is a character-based approach
that infers a phylogenetic tree by minimizing the
total number of evolutionary steps required to
explain a given set of data assigned on the leaves
■ The preferred phylogenetic tree is the one that
requires the fewest evolutionary steps
 Maximum Parsimony
■ Maximum Parsimony is a character-based approach
that infers a phylogenetic tree by minimizing the
total number of evolutionary steps required to
explain a given set of data assigned on the leaves
■ The preferred phylogenetic tree is the one that
requires the fewest evolutionary steps
 Maximum Parsimony
A A G G

G->A

G
𝑇1 𝑇2 𝑇3

1 2 3 4 5 6 7 8 9
Site 3 Site 6 Site 7 Total
Human T T A G C T A C T
Changes

Chimpanzee C T A G C T C C C 1

Gorilla C T G G C C A C T

Orangutan C T G G A C C C T
 Maximum Parsimony
T T C C

C->T

C
𝑇1 𝑇2 𝑇3

1 2 3 4 5 6 7 8 9
Site 3 Site 6 Site 7 Total
Human T T A G C T A C T
Changes

Chimpanzee C T A G C T C C C 1 1

Gorilla C T G G C C A C T

Orangutan C T G G A C C C T
 Maximum Parsimony
A C A C
>C
A-

C->A
C
𝑇1 𝑇2 𝑇3

1 2 3 4 5 6 7 8 9
Site 3 Site 6 Site 7 Total
Human T T A G C T A C T
Changes

Chimpanzee C T A G C T C C C 1 1 2 4

Gorilla C T G G C C A C T

Orangutan C T G G A C C C T
 Maximum Parsimony
A G A G

>G
A-
G->A
G
𝑇1 𝑇2 𝑇3

1 2 3 4 5 6 7 8 9
Site 3 Site 6 Site 7 Total
Human T T A G C T A C T
Changes

Chimpanzee C T A G C T C C C 1 1 2 4

2
Gorilla C T G G C C A C T

Orangutan C T G G A C C C T
 Maximum Parsimony
T C T C

C>
T-
C->T
C
𝑇1 𝑇2 𝑇3

1 2 3 4 5 6 7 8 9
Site 3 Site 6 Site 7 Total
Human T T A G C T A C T
Changes

Chimpanzee C T A G C T C C C 1 1 2 4

2 2
Gorilla C T G G C C A C T

Orangutan C T G G A C C C T
 Maximum Parsimony
A A C C

C->A C

C
𝑇1 𝑇2 𝑇3

1 2 3 4 5 6 7 8 9
Site 3 Site 6 Site 7 Total
Human T T A G C T A C T
Changes

Chimpanzee C T A G C T C C C 1 1 2 4

2 2 1 5
Gorilla C T G G C C A C T

Orangutan C T G G A C C C T
 Maximum Parsimony
A A G G

G->A

G->A

G
𝑇1 𝑇2 𝑇3

1 2 3 4 5 6 7 8 9
Site 3 Site 6 Site 7 Total
Human T T A G C T A C T
Changes

Chimpanzee C T A G C T C C C 1 1 2 4

2 2 1 5
Gorilla C T G G C C A C T
2
Orangutan C T G G A C C C T
 Maximum Parsimony
T T C C

C->T

C->T

C
𝑇1 𝑇2 𝑇3

1 2 3 4 5 6 7 8 9
Site 3 Site 6 Site 7 Total
Human T T A G C T A C T
Changes

Chimpanzee C T A G C T C C C 1 1 2 4

2 2 1 5
Gorilla C T G G C C A C T
2 2
Orangutan C T G G A C C C T
 Maximum Parsimony
A C A C

A->C

C->A
C
𝑇1 𝑇2 𝑇3

1 2 3 4 5 6 7 8 9
Site 3 Site 6 Site 7 Total
Human T T A G C T A C T
Changes

Chimpanzee C T A G C T C C C 1 1 2 4

2 2 1 5
Gorilla C T G G C C A C T
2 2 2 6
Orangutan C T G G A C C C T
 Maximum Parsimony for Unrooted Tree

■ The maximum parsimony analysis is illustrated in

the following example of four sequences shown in
later slides

■ This method finds the tree that changes any

sequence into all of the others by the least number
of steps.
 Maximum Parsimony for Unrooted Tree

■ The rules for analysis by maximum parsimony in this

example are:
- There are four taxa giving three possible unrooted
trees.
- Some sites are informative, i.e., they favor one
tree over another (site 5 is informative, but sites 1, 6,
and 8 are not)
- To be informative, a site must have the same
sequence character in at least two taxa (sites 1, 2, 3, 4,
6, and 8 are not informative; sites 5, 7, and 9 are
informative)
- Only the informative sites need to be analyzed.
Maximum Parsimony for Unrooted Tree
Maximum Parsimony for Unrooted Tree