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 .
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.
phylogenetic tree branches:

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
• 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 characteristics . Historically,
comparison of morphological similarities and differences
have been used to construct evolutionary trees. In this
approach, species that share certain characteristics (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 establish.
Evolutionary relationship:

When comparing homologous genes in different species, the DNA sequences from closely
related species are more similar to each other than are the sequences from distantly related
species

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.
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
Maximum Parsimony
• Maximum Parsimony is a character-based
approach that infers a phylogenetic tree by
minimizing the total number of evolutionary
steps required to explain a given set of data
assigned on the leaves.
• It 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.
Example:
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 .Maximum parsimony example
First we need sequence data than Start from the first
nuclotide Construct a tree that represents minimum
evolutionary change
• 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 .
• Algorithms used in distance method having:
• UPGMA (Unweighted Pair Group method Using Arithmetic
Average.
• Neighbor joining.
UPGMA:
• It is unweighted pair group method using
arithmetic mean.
Neighbour joining
• The NJ (neighbor joining) algorithm is a widely used
method for constructing phylogenetic trees, based on
the distance between species. NJ is a greedy
algorithm, which endeavors to minimize the sum of all
the branch lengths of the resulting treeIn
bioinformatics.
Principle:
• The neighbor‐joining (NJ) technique is minimum
evolution, which selects the tree with minimum
branch‐length. It is based on a very fast, greedy
heuristic algorithm that generates sub‐trees, and
the closest sub‐trees are joined to each other to
yield the final tree, in a step‐wise manner. The total
branch length is the shortest for the true tree.
The NJ method can be applied for large datasets relating to
the taxa with varying degrees of divergence (hence, the tree
will show different lengths for different branches).
• Multiple substitutions can be corrected.
• Some of the sequence information is lost in the NJ method
due to the nature of the algorithm.
Assumption:
Minimum mutational events explain the evolution of the molecular
sequences.
The branch length of the tree with known topology represents the
different rate of evolutionary changes.
Advantages
• is fast and thus suited for large datasets and for bootstrap
analysis
• permist lineages with largely different branch lengths
• permits correction for multiple substitutions
Disadvantages
• sequence information is reduced
• gives only one possible tree
• strongly dependent on the model of evolution used.