Phylogenetic trees depict the evolutionary relationships among various biological species or entities based on similarities and differences in their physical or genetic characteristics. They imply that taxa joined together in the tree have descended from a common ancestor. Phylogenetic trees are useful in fields like bioinformatics, systematics, and phylogenetic comparative methods. However, phylogenetic trees have limitations as they do not necessarily accurately represent evolutionary history and can be confounded by factors like genetic recombination and horizontal gene transfer.

1. Introduction-
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.
In a rooted phylogenetic tree, each node with descendants represents the inferred most
recent common ancestor of the descendants, and the edge lengths in some trees may
be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes
are generally called hypothetical taxonomic units, as they cannot be directly observed.
Trees are useful in fields of biology such as bioinformatics, systematics,
and phylogenetic comparative methods.
The idea of a "tree of life" arose from ancient notions of a ladder-like progression from
lower to higher forms of life (such as in the Great Chain of Being). Early representations
of "branching" phylogenetic trees include a "paleontological chart" showing the
geological relationships among plants and animals in the book Elementary Geology, by
Edward Hitchcock (first edition: 1840).
Charles Darwin (1859) also produced one of the first illustrations and crucially
popularized the notion of an evolutionary "tree" in his seminal book The Origin of
Species. Over a century later, evolutionary biologists still use tree diagrams to
depict evolution because such diagrams effectively convey the concept
that speciation occurs through the adaptive and semirandom splitting of lineages. Over
time, species classification has become less static and more dynamic.
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.
By using computational phylogenetic methods, we can construct phylogenetic tree.
There are two main types of method we used to construct phylogenetic tree.

2. Character based methods-
A character or trait is a discrete property of a species (leaf). It can be assigned to each
species. E.g.
• “mammal” (all species are either mammals or not)
• “multicellular” (all species are either unicellular or multicellular)
• eye-color (grey, blue, green, brown, none)
• in general: any property with a finite number of states where changing from one state
to any other state is roughly equally likely
Under this classification internal nodes are assigned characters to minimize the total
number of character changes. The method that minimizes the number of character
changes is called parsimony. The tree selected is the topology which has maximum
parsimony.
Another character based method is maximum likelihood methods), in this type the
species are described by characteristics which evolve under some probabilistic model.
This is normally applied to genomic sequences (either DNA or amino acid sequences).
The tree (topology and branch lengths), which maximizes the likelihood of evolving from
a common root to all leaves is selected.
Distance based methods:
These methods require the definition of a distance function between the considered
species (i.e. the leaves of the tree). A tree is constructed (topology and branch length)
so that the distances between any pair of leaves can be mapped over the tree as
accurately as possible. Mapping the distance between a pair of leaves over the tree
means taking the sum of all branch lengths between these two leaves.
UPGMA:
UPGMA and neighbor joining are two widely used distance based method.
 Abbreviation of “Unweighted Pair Group Method with Arithmetic Mean”
 Originally developed for numeric taxonomy in 1958 by Sokal and Michener
 Simplest algorithm for tree construction, so it's fast!

3. New average
Distance between C and AB is: C to AB = (60 + 50) / 2 = 55
Distance between D and AB is: D to AB = (100 + 90) / 2 = 95
Distance between E and AB is: E to AB = (90 + 80) / 2 = 85
AB C D E
AB 0
C 55 0
D 95 40 0
E 85 50 30 0
New average
Distance between AB and DE is: AB to DE = (95 + 85) / 2 = 90
Distance between C and DE is: C to DE = (40 + 50) / 2 = 45
AB C DE
AB 0
C 55 0
DE 90 45 0
New Average
Distance between CDE and AB is: CDE to AB = (90 + 55) / 2 = 72.5
AB CDE

4. AB 0
CDE 72.5 0
There are only two clusters. so this completes the calculation!
Tree constructing methods should have several criteria:
 Efficiency (how long does it take to compute the answer, how much memory does it
need?)
 Power (does it make good use of the data, or is information being wasted?)
 Consistency (will it converge on the same answer repeatedly, if each time given
different data for the same model problem?)
 Robustness (does it cope well with violations of the assumptions of the underlying
model?)
 Falsifiability (does it alert us when it is not good to use, i.e. when assumptions are
violated?)
What does this tree look like?
 There are many different ways to represent the information found in a
phylogenetic tree.

5.  The basic format of a tree is generally in one of the two forms shown, although
there are other ways to represent the data.
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.
Types of Phylogenetic Tree-
Rooted Tree: A rooted tree is used to make inferences about the most common
ancestor of the leaves or branches of the tree. Most commonly the root is
referred to as an “outgroup”.
Unrooted Tree: An unrooted tree is used to make an illustration about the leaves
or branches, but not make assumption regarding a common ancestor.

6. Bifurcating Tree:
A tree that bifurcates has a maximum of 2 descendants arising from each of the
interior nodes.
Multi-furcating Tree:
A tree that multi-furcates has multiple descendants arising from each of the interior
nodes.

7. Another representation two type’s are-
o Labeled
o Unlabeled
A labeled tree has specific values assigned to its leaves, while an unlabeled tree,
sometimes called a tree shape, defines a topology only.
The number of possible trees for a given number of leaf nodes depends on the specific
type of tree, but there are always more multi-furcating than bifurcating trees, more
labeled than unlabeled trees, and more rooted than unrooted trees.
Application of Phylogenetic tree-
The most direct use is to find out the evolutionary history of your taxa and how they're
related to each other.
It can lead to other uses, both practical and pure. For example, in conservation biology
we can measure phylogenetic diversity using phylogenetic trees. The branches on the
evolutionary tree aren't drawn at random lengths, they're calculated to that length.
Phylogenetic diversity takes those lengths to give you an idea of how evolutionarily

8. diverse the fauna in our ecosystem is and to give conservation people priorities. For
example, long branches mean that we have basal taxa which are more important to
conserve because they originated earlier and thus have more information about
evolution to give. On the other hand, very short branches tell us that these species are
very new, possibly the result of an adaptive radiation and are also in need of
protection.
Another use is in the search for natural products. Say we have a sponge species that
produces a chemical that works very well to reduce inflammation. But drugs produced
from it tend to have nasty side-effects. We do a systematic survey of the sponge genus
and find out the species related most to it, and we test their versions of the chemical in
order of relatedness.
In medicine, we can use phylogenetic trees of infectious bacteria and viruses to trace
their evolutionary histories and find out what trends they've undergone in their history.
This will give us new ideas of what to focus on with the drugs.
On the pure side, we can use phylogenetic trees to guide our search for new species. If
we plot it on a map, we will find out how our species spread geographically in their
evolution. We can then go to these places and search for any populations that were
isolated and formed new species.
We can use phylogenetic trees to tell us when taxa originated and where. We find the
nearest fossiliferous rocks of that age, and hopefully we have a chance at getting the
elusive stem-group fossil that explains how the group originated.
Source:
- https://www.quora.com/What-are-phylogenetic-trees-used-for
Limitations of phylogenetic tree-
Most importantly, they do not necessarily accurately represent the evolutionary history
of the included taxa. In fact, they are literally scientific hypotheses.
The data on which they are based is noisy; the analysis can be confounded by genetic
recombination horizontal gene transfer, hybridization between species that were not

9. nearest neighbors on the tree before hybridization takes place, convergent evolution,
and conserved sequences.
Also, there are problems in basing the analysis on a single type of character, such as a
single gene or protein or only on morphological analysis, because such trees
constructed from another unrelated data source often differ from the first, and therefore
great care is needed in inferring phylogenetic relationships among species.
When extinct species are included in a tree, they are terminal nodes, as it is unlikely
that they are direct ancestors of any extant species. Skepticism might be applied when
extinct species are included in trees that are wholly or partly based on DNA sequence
data, because little useful "ancient DNA" is preserved for longer than 100,000 years,
and except in the most unusual circumstances no DNA sequences long enough for use
in phylogenetic analyses have yet been recovered from material over 1 million years
old.
Another aspect of phylogenetic trees is that, unless otherwise indicated, the branches
do not account for length of time, only the evolutionary order.
In other words, the length of a branch does not typically mean more time passed; nor
does a short branch mean less time passed, unless specified on the diagram. A tree
may not indicate how much time passed between the evolution of amniotic eggs and
hair.
What the tree does show is the order in which things took place. For example, the tree
in the diagram shows that the oldest trait is the vertebral column, followed by hinged
jaws, and so forth.
Remember, any phylogenetic tree is a part of the greater whole and, as with a real tree,
it does not grow in only one direction after a new branch develops. So, simply because
a vertebral column evolved does not mean that invertebrate evolution ceased. It only
means that a new branch formed. Also, groups that are not closely related, but evolve
under similar conditions, may appear more phenotypically similar to each other than to a
close relative.
Source:
1. https://en.wikipedia.org/wiki/Phylogenetic_tree
2. https://www.boundless.com/biology/textbooks/boundless-biology-textbook/phylogenies-and-the-
history-of-life-20/organizing-life-on-earth-133/limitations-of-phylogenetic-trees-540-11749/
The End