1. Tree Reconstruction

2. Phylogenetic tree
Nodes – DNA (RNA, mtDNA) sequences, proteins, species = taxonomic units (TUs)
Branches – ancestral relations between Tus
Terminal (extant) nodes, leaves – OTUs (O for operational)

3. Tree reconstruction Neighbor joining (Distance) methods
Maximum parsimony methods (W. Fitch)
Maximum likelihood methods (J. Felsenstein)
W. H. Li, “Molecular Evolution”, 1997

4. Rooted, unrooted trees C D B E A
unrooted D E A B C
rooted

5. How many geneological trees can we propose for a given number of terminal nodes
n – number of OTUs

6. n NR NU 2 1 3 4 15 5
105 6
954 7
10 395 8 9 10

7. Neighbor joining
UPGMA – unweighted pair group method with arithmetic mean
Start from distance matrix
(*) Find the minimum distance OTUs
And merge them
Update distance matrix, go to (*)

8. Maximum parsimony
Principle of max parsimony searches for a tree that requires the smallest number of evolutionary changes to explain differences among OTUs
Informative sites

9. Assume topology of the tree – for each site compute minimal number of mutations to explain the configuration
Rule: The set at an interior node is the intersection of its two immediate descendants if the intersection is not empty, otherwise it is the union of the descendant sets

10. The index of the tree is the sum of indices for all informative sites
Go through all possible trees to search for optimal one

11. Maximum likelihood
Need a probabilistic model for nucleotide substitution
A,C,T,G – 1,2,3,4
time=0
We analyze evoution of
one site S. Given S=i, time=0
what is the probability
of S=j, time=t
time=t

12. Compute the likelihood function for a given tree
Go through all possible trees to search for optimal one

13. Software PHYLIP (Phylogeny Inference Package) Version 3.57c
by Joseph Felsenstein
July, 1995