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1. NAME : SNEH LATA
ROLL NO. CUHP18ZOO26
SUBMITTED TO . MS. EKTA
GULERIA

2. PHYLOGENETIC TREE
 Phylogeny is the evolutionary history of a
kind of organism .
 In phylogenetic studies , the most convenient
way to study the evolutionary relationship
among a group of organism is through the
illustration of phylogenetic tree.
 DEFINITION –Phylogenetic tree is a two
dimensional graph showing evolutionary
relationship between organism , or genes
from various organism .

3. Characteristics :
Nodes can be internal or external .
Each internal node represent the last common
ancestor of the two lineage .
External node (also termed as terminal node ,
leaves ) represent the tip of the tree .
Node correspond to species , organism or
sequences .
Similarly, branches can be internal or external .
Internal branches or internodes connect two
nodes , whereas external branches connect a tip
and a node .

7. A phylogenetic tree branches either be :
- Scaled
- Unscaled
In scaled branches , their length are
proportional to the evolutionary change .
Example - phylogram .
In unscaled branches , the branch length is
not proportional to the number of changes .
Example -cladogram

9.  When constructing phylogenetic trees ,researcher identify
homologous features that are share shared by some species
but not by others.
 This allows them to group species based On their shared
characterstics .
 Historically, comparison of morphological similarities and
differences have been used to construct evolutionary trees.
 In this approach, species that share certain charactersticts
(i.e.,homologous trait) tend to be placed closer together on
the tree .
 In 1963,Linsus pauling and Emile Zuckerkandl were the first
to suggest the use of molecular data to estabolish

10. Evolutionary relationship
 When comparing homologous genes in different species,
the DNA sequences from closely related species are more
similer to each other than are the sequences from
distantly related species .

11. Phylogenetic tree based on homology
 Phylogenetic tress are now based on homology which
refers to similarities among various species that occur
because the species are derived from a common
ancestor.
 Attributes that are the result of homology are said to
be homologous. For eg.

13. Phylogenetic tree reconstruction
Phylogenetic trees are constructed :
- To reconstruct the evolutionary past.
- To develop an understanding of when and
which speciation event may have occurred to
give rise to the organism exhibited today .
A phylogenetic analysis consist of four steps and
these are :
 SEQUENCE ALIGNMENT :- Sequence
alignment is the essential preliminary to the
tree reconstruction . The data used in
reconstruction of a DNA –based phylogenetic
tree are obtained by comparing nucleotide
sequences.

14. These comparison are made by aligning the
sequences so that nucleotide differences can
be scored .
 DETERMINING THE SUBSITUTION
MODEL
 TREE BUILDING
 TREE EVALUATION

15. Cladistic approach for the construction of tree

16. Cladogram

18. Steps involved in the construction of
cladogram :
 Choose the species in whose evolutionary
relationship you are interested .
 Choose characters for comparing
different species .
 Determine the polarity of character states
i.e. character state is ancestral or derived .
 Group species ( or higher taxa ) based on
shared derived characters .

19.  Build a cladogram based on following
principles :
1. All species are placed on the tip in the
phylogenetic tree , not at branch points . A
cladogram does not include ancestral species
at branch points .
2. Each cladogram branch point should have a
list of one or more shared derived characters
that are common to all species .
3. All shared derived character appear together
only once in a cladogram unless they
independently arose during evolution .

20. Choose the best cladogram among possible
option .
When grouping species (or higher taxa)
more than one cladogram may be
possible . Therefore , analyzing the
data and producing the best possible
cladogram is a key aspect of this
process .

21. Construction of phylogenetic tree
2 types of method
Character based Distance based
method method
A. Maximum parsimony
B. Maximum likelihood

24. Character based method :
This method is also called as discrete
method and are based directly on the
sequence characters rather than on pairwise
distances .
The two most popular character based
methods are :
1. MAXIMUM PARSIMONY
2. MAXIMUM LIKELIHOOD

25. Maximum parsimony
Parsimony method is one of the pioneer
method of phylogeny construction .
Parsimony groups taxa together in way that
minimize the number of changes .
It assume that the best hypothesis is one
that requires the fewest number of
evolutionary changes hence it is also called
as minimum evolution method .
It also states that the preferred hypothesis is
the one that is simplest .

26. EXAMPLE : If two species possess a tail then
there are two hypothesis :
First assuming that a tail arose once during
evolution and that both species have descended
from a common ancestor with a tail .
Second hypothesis assuming that tails arose
twice during evolution and that the tails in the
two species are not due to descent from a
common ancestor .
So the first assumption is simplest one and is
accepted .

27. Maximum parsimony example
First we need sequence data
than Start from the first
nuclotide
Construct a tree that
represents minimum
evolutionary change

28. Repeat this for the second nucleotide site .
Calculate the number of substitution steps on
each branch .
The maximum parsimony tree is one with
minimum total number of substitution .
The maximum parsimony depends on the
sequences of ancestral nodes so we need
different algorithms to reconstruct the ancestral
node . Algorithms used are :
FITCH ALGORITHM
Constructing maximum parsimony trees from
protein /DNA sequence data using MEGA (
molecular evolutionary genetics analysis )
software .

30. Maximum likelihood approach
The maximum likelihood method presents
an additional opportunity to evaluate trees
with variations in mutation rates in
different lineage .
The method can be used to explore
relationship among more diverse sequences
and condition that are not well handled by
maximum parsimony methods .

31. Distance based method :
Distance method are based on the amount of
dissimilarity ( distance ) between two aligned
sequences .
Such method remain important when using
fossil data to build phylogenies for extinct
species and for living species it is more common
to use DNA sequences from the two species .
This method assume that all sequence involved
are homologous and that tree branches are
additive , meaning the distance between the
two taxa equals the sum of all branch branch
lengths connecting them .

34. Algorithms used in distance method
UPGMA (Unweighted Pair Group
method Using Arithmetic Average )
Neighbor joining

48. Pliohippus