2. WHAT IS A PHYLOGENETIC TREE USED
FOR?
• A phylogenetic tree or evolutionary tree is a branching diagram or
tree showing the inferred evolutionary relationships among
various biological species or other entities their phylogeny based
upon similarities and differences in their physical or genetic
characteristics. The taxa joined together in the tree are implied to
have descended from a common ancestor. Phylogenetic trees are
central to the field of phylogenetic.
• A phylogenetic tree is used to help represent evolutionary
relationships between organisms that are believed to have some
common ancestry.
• The name “ dendogram ” is the broad term for trees.
3. WHERE DID THE IDEA FOR A TREE COME
FROM?
• Charles Darwin (1859) is credited with the earliest representation of
a phylogenetic tree published in his book The Origin of Species. Over a
century later, evolutionary biologists still use tree diagrams to
depict evolution.
4. PURPOSES OF PHYLOGENETIC
TREE
• Understanding human origin
• Understanding biogeography
• Understanding the origin of particular traits
• Understanding the process of molecular evaluation
• Origin of disease
• The aim of phylogenetic tree construction, is to find the tree which
best describes the relationships between objects in a set. Usually the
objects are species.
5. WHAT DOES THIS TREE LOOK LIKE?
• There are many different ways to represent the information found in a
phylogenetic tree.
• The basic format of a tree is generally in one of the two forms shown,
although there are other ways to represent the data.
6. WHAT DO THE LINES REPRESENT?
• Each line on the tree represents one particular organism of interest.
• The distance of the lines is used to determine how closely two
organisms are related to one another or how long ago the may have
had a common ancestor.
• The line that connect all the other lines is the representation of the
common ancestor that is being looked at to compare other
organisms to.
7. 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. The root of a tree is considered as
the oldest point in the tree which represents the last
common ancestor of all groups included in the tree. Hence,
a rooted tree shows the direction of evolutionary time.
Since the rooted tree depicts the direction of evolutionary
time, it is easy to find the older or newer groups it has. A
rooted tree can be used to study the entire groups of
organisms.
8. 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
9. THE “ROOTED” VS. “UNROOTED”
TREE
• A rooted tree is used to make inferences about the most
common ancestor of the leaves or branches of the tree.
• An un rooted tree is used to make an illustration about
the leaves or branches, but not make assumption
regarding a common ancestor.
10. THE BIFURCATING TREE
• A tree that bifurcates has a maximum of 2 descendants arising
from each of the interior nodes.
11. THE MULTI-FURCATING TREE
• A tree that multi-furcates has multiple descendants arising
from each of the interior nodes.
12. WHAT CRITERIA IS IMPORTANT
WHEN BUILDING A TREE?
• There are many different things that you should consider
as you get set to build your tree.
• Some examples are;
• Efficiency
• Power
• Consistency/Reliability
• Robustness
• Are underlying assumptions ever violated
13. WHERE DO I GO TO MAKE A
TREE?
• Many computational biology programs have dendogram
programs.
• An example of a free program that is available via the
EMBL-EBI (European Bioinformatics Institute) called
ClutsalW or ClustalX.
14. APPLICATIONS OF
PHYLOGENETIC TREE
• The inference of phylogenies with computational methods
has many important applications in medical and biological
research, such as drug discovery and conservation
biology.
• Phylogenetic trees have already witnessed applications in
numerous practical domains, such as in conservation
biology (illegal whale hunting), epidemiology (predictive
evolution), forensics (dental practice HIV transmission),
gene function prediction and drug development.
15. APPLICATIONS OF
PHYLOGENETIC TREE
• Other applications of phylogenies include multiple
sequence alignment, protein structure prediction, gene
and protein function prediction and drug design.
• The computation of the tree-of life containing
representatives of all living beings on earth is considered
to be one of the grand challenges in Bioinformatics.
16. LIMITATIONS TO THE USE OF
TREES
• It is important to remember that trees do have
limitations. For example, trees are meant to provide
insight into a research question and not intended to
represent an entire species history.
• Several factors, like gene transfers, may affect the output
placed into a tree.
• All knowledge of limitations related to DNA degradation
over time must be considered, especially in the case of
evolutionary trees aimed at ancient or extinct organisms.
