Building Phylogenies

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Building Phylogenies
2
Phylogenetic (evolutionary) trees
Describe evolutionary relationships between
species
or
Cannot be known with certainty!
Nevertheless, phylogenies can be useful
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Applications of Phylogenetic Analysis

• Inferring function
• Closely related sequences occupy neighboring
  branches of tree
• Tracking changes in rapidly evolving populations
  (e.g., viruses)
• Which genes are under selection?

4
Phyloinformatics

• Comparative analysis through phylogenies helps to
  understand biological function
• Exploit phylogenies for data mining

5
Disease Transmission and Medical Forensics
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Discovering Snake Antivenin
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Methods

• Distance-based
• Parsimony
• Maximum likelihood

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Distance Matrices
a
b
c
d
9
Ultrametric Matrices
a
b
c
d
10
Least Squares
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Characters
A character can be a morphological trait or a
letter in a column of an alignment.
Characters are represented using matrices
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Parsimony
Goal Find the tree with least number of
evolutionary changes
a, b
f
c
d
e
d
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Markov models on trees

• Observed The species labeling the leaves
• Hidden The ancestral states
• Transition probabilities The mutation
  probabilities
• Assumptions
• Only mutations are allowed
• Sites are independent
• Evolution at each site occurs according to a
  Markov process

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Models of evolution at a site

• Transition probability matrix M mij, i, j
  ?A, C, T, G where mij Prob(i ? j mutation
  in 1 time unit)
• Different branches of tree may have different
  lengths

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The probability of an assignment
T
G
T
A
G
C
T
Probability mTG mGA mGG mTT mTC mTT
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Ancestral reconstruction most likely assignment
X
Y
Z
A
G
C
T
L maxX,Y,Z mXY mYA mYG mXZ mZC mZT