Phylogenetic Tree
A Phylogeny (Phylogenetic tree) or Evolutionary tree
represents the evolutionary relationships among
• a set of organisms or groups of organisms
• a family related nucleic acid or protein sequences
Every phylogenetic tree is an hypothesis about relationships
• some are well supported by data
• others are not
Dendrogram, Cladogram, Phylogram
• Dendron- Tree
• Dendrogram is any type of
diagrammatic representation of
phylogenetic trees.
• All four trees depicted here
are dendrograms.


Cladogram is a tree in which branch lengths DO NOT represent evolutionary
time;
clades just represent a hypothesis about actual evolutionary history
TREE1 and TREE2 are cladograms and TREE1 = TREE2
Phylogram is a tree in which branch lengths represent evolutionary time;
clades represent true evolutionary history (amount of character change)
TREE3 and TREE4 are phylograms and TREE3 ≠ TREE4
What data is used to build trees?
• Traditionally:
Physical characteristics (morphological
features)
• Currently:
Mostly Biomolecular sequences: DNA, RNA, amino acid etc.
and
Molecular markers (SNPs, RFLPs etc.)
Data for Phylogeny
– Numerical data
• Distance between objects
e.g., distance(man, mouse)=500,
distance(man, chimp)=100
Usually derived from sequence data
– Discrete characters
• Each character has finite number of states
e.g., number of lineages = 1, 2, 4
DNA = {A, C, T, G}
Types of trees: unrooted vs rooted


A rooted phylogenetic tree is a tree with a unique root
node corresponding to the most recent common
ancestor of all the entities at the leaves of the tree. A
rooted tree is a binary tree.
Unrooted trees illustrate the relatedness of the leaf
nodes without making assumptions about common
ancestry. An unrooted tree has a node with three edges;
the rest of the nodes have up to two edges.
Rooted, Binary Tree
Unrooted, Binary Tree
~
ORFP MG01127.1
NCU01640.1
ORFP YDL020C
Scastellii
Skluyeri
orf6.4920.prot
AN0709.2
H.
This Rooted, binary tree can be illustrated as
(((14, 15), (12, 13)), ((10, 11), (8, 9)))
Number of possible trees
# of rooted trees =
(2n-3)!
2n-2(n-2)!
# of unrooted trees =
(2n-5)!
2n-3(n-3)!
Number of possible trees
#no. of species /UTO (n)
#rooted trees
#unrooted trees
2
1
1
3
3
1
4
15
3
5
105
15
10
3.44x107
2.03x106
15
2.13x1014
7.91x1012
20
8.20x1021
2.21x1020
A details of all possible trees to find the best one is not
feasible!
Phylogenetic Tree Building
1.
Distance based methods
a. Calculate evolutionary distances between sequences (OTUs)
b. Build a tree based on those distances
2.
Maximum Parsimony (character based method)
a. Find the simplest tree that explains the data with the minimum number
of changes\substitutions
2.
Maximum Likelihood (probabilistic method based on explicit
model)
a. Find the tree that gives the highest likelihood of the observed data
4. New Baysian approaches (also probabilistic)
Distance based methods
Calculate evolutionary distances between sequences using a matrix of pairwise
distance
Build a tree based on the distances of the sequences
Find the tree with the shortest overall branch lengths
-- UPGMA method (‘unweighted pair group method using arithmetic
averages’)
1) Join the two sequences/species with the shortest distance
2) Add a sequence/species to that node if that average of all pairwise
distances is minimized
-- Neighbor Joining (NJ) method
keeps track of the nodes and the leaves (rather than just the leaves) during
tree building
Phylogeny Applications
• Tree of life:
Analyzing changes that have occurred in evolution of different
organisms
• Phylogenetic relationships
among genes can help predict which ones might have similar
functions (e.g., ortholog detection)
• Follow changes
occuring in rapidly changing species (e.g., HIV)