The document discusses phylogenetic trees, which represent the evolutionary relationships among organisms based on shared characteristics and common ancestry. It outlines the methods for constructing these trees, including the maximum parsimony and maximum likelihood approaches, as well as steps involved in analysis like sequence alignment and tree evaluation. The importance of homology in phylogeny and how molecular data has changed the study of evolutionary relationships is emphasized.

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