MOLECULAR PHYLOGENETIC

Molecular Phylogenetic
• Molecular phylogenetic is the branch of phylogeny that
analyzes genetic, hereditary molecular differences,
predominantly in DNA sequences, to gain information on
an organism’s evolutionary relationships.
• These are based on DNA and protein sequence data
• Chimpanzee is more closely related to human then gorilla .
• In this way we can recover correct order of Evolutionary
events
• To evaluate divergence time .
Breif History of Molecular Phylogenetic
• Darwin was the first to formulate the very idea of a phylogenetic
tree in the sense of newly established theory of evolution in 1837
• Charles Darwin published the idea of a tree of life in 1859.
• In 1866, Haeckel published his two-volume and with it he created
the first Darwinian phylogenetic trees (i.e., tree of life and tree of
plants) to illustrate the theory of evolution.
• The first practical approach of Molecular Phylogeny took place in
the 18th century by Lennaeus.
• The theoretical frameworks for molecular systematics were laid
in the 1960s in the works of Emile Zuckerkandl, Linus Pauling.
1900s
Immunochemical studies: cross-reactions stronger for closely
A Brief History
related of Molecular
organisms
Phylogenetics
• Nuttall (1902) – apes are closest relatives to humans
• Work with protein electrophoresis began around 1956.

1960s-1970s
Protein sequencing methods, electrophoresis, DNA
hybridization and PCR contributed to a boom in molecular
phylogeny

Late 1970s to present

Discoveries using molecular phylogeny:
- Endosymbiosis – Margulis, 1978
- Divergence of phyla and kingdom – Woese, 1987
 Goals of molecular phylogenetic
• Phylogenetic trees represent hypotheses about the
evolutionary relationships among a group of organisms.

• A phylogenetic tree may be built using morphological

(body shape), biochemical, behavioral, or molecular
features of species or other groups.

• Phylogenetic analysis provides an in-depth understanding

of how species evolve through genetic changes.
 Phylogenetic tree
• phylogenetic tree is a branching diagram or a tree showing the
evolutionary relationships among various biological species or
other entities based upon similarities and differences in their
physical or genetic characteristics.

• All life on Earth is part of a single phylogenetic tree, indicating

common ancestry
 Properties
• Branches

• Roots

• Tips

• Domain
 Types of phylogenetic tree
• ROOTED PHYLOGENETIC TREE • A rooted phylogenetic tree serves
as a useful diagram which shows the evolutionary history. It has a
basal node which is called the root, representing the common
ancestor of all the groups of the tree.. Hence, a rooted tree shows
the direction of evolutionary time. A rooted tree can be used to
study the entire groups of organisms.

• UN ROOTED PHYLOGENETIC TREE • An un rooted phylogenetic

tree is a phylogenetic diagram which lacks a common ancestor or a
basal node. This type of a tree does not indicate the origin of
evolution of the groups of interest. It depicts only the relationship
between organisms irrespective of the direction of the evolutionary
time line
• THE BIFURCATING TREE • A tree that
bifurcates has a maximum of 2 descendants
arising from each of the interior node

• THE MULTI-FURCATING TREE • A tree that

multi-furcates has multiple descendants
arising from each of the interior nodes.
 Applications of Phylogenetic Tree
• It is the fundamental tool to derive their most-useful evidence from
the fields of anatomy, embryology, palaeontology and molecular
genetics. Other significances of the phylogenetic tree are:
1. Used in the search for a new species.
2. Used to study evolutionary histories.
3. To study how the species were spread geographically.
4. To study the common ancestors of extant and extinct species.
5. It is used to identify the most recent common ancestors and to
recognize how closely related species are.
6. To relate the milestones of the evolution of major life forms to the
tree of life.
7. To represent evolutionary relationships between organisms that are
 Stages of phylogenetic analysis
There are five general stages/steps in carrying out a phylogenetic analysis:

(1) sequence data preparation,

(2) sequence alignment,
(3) choosing a phylogenetic reconstruction method,
(4) identification of the best tree,
(5) evaluating the tree.
Brief Description of stages of phylogenetic analysis

The flow chart displayed on the right visually demonstrates the

order of the five stages of Pevsner's molecular phylogenetic
analysis technique that have been described.
 1: sequence Data preparation
• The first stage comprises sequence acquisition.

• Data preparation is the process of gathering, combining,

structuring and organizing data so it can be used in business
intelligence (BI), analytics and data visualization applications.
 2- sequence alignment
• The following step consists of performing a multiple sequence
alignment, which is the fundamental basis of constructing a
phylogenetic tree.

• Sequence alignments can provide clues to evolutionary change

by examining the effect of mutations occurring over time in
species with a common ancestor.
 3- choosing a phylogenetic reconstruction method
• The third stage includes different models of DNA and amino
acid substitution.

• Several models of substitution exist. A few examples include

Hamming distance, the Jukes and Cantor one-parameter
model, and the Kimura two-parameter model (see Models of
DNA evolution)
4-Tree building or Identification of the best tree
• The fourth stage consists of various methods of tree building,
including distance-based and character-based methods.

• The normalized Hamming distance and the Jukes-Cantor

correction formulas provide the degree of divergence and the
probability that a nucleotide changes to another, respectively.
Common tree-building methods
 5- evaluation of the tree
• The last step comprises evaluating the trees. This assessment
of accuracy is composed of consistency, efficiency, and
robustness.
 Importance of Phylogenetics
• Phylogenetics is important because it enriches our understanding of
how genes, genomes, species (and molecular sequences more
generally) evolve.

• Through phylogenetics, we learn not only how the sequences came to

be the way they are today, but also general principles that enable us to
predict how they will change in the future.

• This is not only of fundamental importance but also extremely useful

for numerous applications