1. Goals of Phylogenetic Analysis
Given a multiple sequence alignment, determine the ancestral relationships among the species.
We assume that residues in a column are homologous, and that all columns have the same history.
Time
Hu Ch Go Gi

2. Types of Phylogenetic Methods
Character-based
Parsimony
Likelihood
Distance-based
Neighbor joining (NJ)
UPGMA
Involve optimizing a criterion based on fit of the residues to the tree.
Involve optimizing a criterion based on fit of a matrix of pairwise distances to the tree

3. Parsimony
Select the tree that explains the data with the smallest number of substitutions.
Likelihood
Select the tree that has the highest probability of producing the observed data
Distance
Select the tree that best recreates the observed pairwise distances.

4. We usually estimate unrooted treesB C D A C B D A D C B
For 4 sequences, there are only 3 unique unrooted trees.

5. Parsimony Methods A ACGA B ATGC C GTGC D GCAA A B C D Tree 1 A C B D
Tot
Tree
Tree
Tree A D B C
Tree 3

6. is the collection of all data (sequences A, B, and G).
Likelihood Methods A B G x
is the collection of all parameters affecting the evolution of
sequences A, B, and G.
is the collection of all data (sequences A, B, and G).

7. Modeling sequence change
Typically, the evolution of DNA sequences is modeled at the level of single sites.
JC: Jukes-Cantor (1969)
K2P: Kimura (1980)
F81: Felsenstein (1981)
HKY: Hasegawa et al. (1985)
REV: Tavaré (1986)

8. General Time Reversible ModelC G T A C G T

9. (Nucleotide in Species A, site k)
Under this assumption, the likelihood simplifies to a product of
individual site likelihoods:
and
(Nucleotide in Species A, site k) A B G x

10. Distance Methods A B C D A 0 A ACGA B ATGC B .5 0 C GTGC C .75 .25 0
D GCAA

11. A B C D a c e b d
Many distance methods seek to find the tree that minimizes a score such as: