INTRODUCTION:-

Humans as a group are big on organizing things. Not necessarily

things like closets or rooms. Instead, people often like to group and
order the things they see in the world around them. Starting with the
Greek philosopher Aristotle, this desire to classify has extended to the
many and diverse living things of Earth.

Most modern systems of classification are based on evolutionary

relationships among organisms – that is, on the organisms’ phylogeny.
Classification systems based on phylogeny organize species or other
groups in ways that reflect our understanding of how they evolved
from their common ancestors.

In this article, we'll take a look at phylogenetic trees, diagrams that

represent evolutionary relationships among organisms. We'll see
exactly what we can (and can't!) infer from a phylogenetic tree, as well
as what it means for organisms to be more or less related in the
context of these trees.

We're all related—and I don't just mean us humans, though that's

most definitely true! Instead, all living things on Earth can trace their
descent back to a common ancestor. Any smaller group of species can
also trace its ancestry back to common ancestor, often a much more
recent one.
Given that we can't go back in time and see how species evolved, how
can we figure out how they are related to one another? In this article,
we'll look at the basic methods and logic used to build phylogenetic
trees, or trees that represent the evolutionary history and relationships
of a group of organisms.

Biological diversity is the topic of this module. All organisms that ever
existed on this planet are related to other organisms in a branching
evolutionary pattern called the tree of life.

To decipher this relatedness between the diversity of organisms, both

living and extinct, “tree thinking” is invaluable. Tree thinking, or
phylogenetic thinking, helps us unravel the branching evolutionary
relationships between extant species, while thinking about the
passage of time and the ancestors of each of those living species.
PHYLOGENETIC TREE:-

DEFINITION:-
1. A phylogenetic tree is a visual representation of the relationship
between different organisms, showing the path through
evolutionary time from a common ancestor to different
descendants. Trees can represent relationships ranging from the
entire history of life on earth, down to individuals in a population.
Trees that show species help us understand how new species
form from common ancestral species. The process of new species
formation, called speciation, is the starting point for a discussion
of biological diversity. The natural endpoint will be extinction.
2. A phylogenetic tree or evolutionary tree is a branching diagram
or "tree" showing the evolutionary relationships among various
biological species or other entities—their phylogeny 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.

3. A phylogenetic tree is a diagram that represents evolutionary

relationships among organisms. Phylogenetic trees are
hypotheses, not definitive facts. The pattern of branching in a
phylogenetic tree reflects how species or other groups evolved
from a series of common ancestors.
 4. Phylogenetic tree, also called Dendrogram, a diagram
showing the evolutionary interrelations of a group of
organisms derived from a common ancestral form. The
ancestor is in the tree “trunk”; organisms that have arisen
from it are placed at the ends of tree “branches.” The
distance of one group from the other groups indicates the
degree of relationship; i.e., closely related groups are
located on branches close to one another. Phylogenetic
trees, although speculative, provide a convenient method
for studying phylogenetic relationships.

The pattern of branching in a phylogenetic tree reflects how species or

other groups evolved from a series of common ancestors.
In trees, two species are more related if they have a more recent
common ancestor and less related if they have a less recent common
ancestor.

Phylogenetic trees can be drawn in various equivalent styles. Rotating

a tree about its branch points doesn't change the information it
carries.
REVIEW OF LITERATURE:-

To generate a phylogenetic tree, scientists often compare and analyze

many characteristics of the species or other groups involved. These
characteristics can include external morphology (shape/appearance),
internal anatomy, behaviors, biochemical pathways, DNA and protein
sequences, and even the characteristics of fossils.
To build accurate, meaningful trees, biologists will often use many
different characteristics (reducing the chances of any one imperfect
piece of data leading to a wrong tree). Still, phylogenetic trees are
hypotheses, not definitive answers, and they can only be as good as
the data available when they're made. Trees are revised and updated
over time as new data becomes available and can be added to the
analysis. This is particularly true today, as DNA sequencing increases
our ability to compare genes between species.

The idea of a "tree of life" arose from ancient notions of a ladder-like

progression from lower into 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.

The term phylogenetic, or phylogeny, derives from the two ancient

greek words (phûlon), meaning "race, lineage", and (génesis),
meaning "origin, source".
In a phylogenetic tree, the species of interest are shown at the tips of
the tree's branches. The branches themselves connect up in a way that
represents the evolutionary history of the species—that is, how we
think they evolved from a common ancestor through a series of
divergence (splitting-in-two) events. At each branch point lies the most
recent common ancestor shared by all of the species descended from
that branch point. The lines of the tree represent long series of
ancestors that extend from one species to the next.
METHODOLOGY

1. Construction method
2. Studying method

1.CONSTRUCTION METHOD

The idea behind tree construction:-

How do we build a phylogenetic tree? The underlying principle is
Darwin’s idea of “descent with modification.” Basically, by looking at
the pattern of modifications (novel traits) in present-day organisms,
we can figure out—or at least, make hypotheses about—their path of
descent from a common ancestor.
As an example, let's consider the phylogenetic tree below (which
shows the evolutionary history of a made-up group of mouse-like
species). We see three new traits arising at different points during the
evolutionary history of the group: a fuzzy tail, big ears, and whiskers.
Each new trait is shared by all of the species descended from the
ancestor in which the trait arose (shown by the tick marks), but absent
from the species that split off before the trait appeared.
When we are building phylogenetic trees, traits that arise during the
evolution of a group and differ from the traits of the ancestor of the
group are called derived traits. In our example, a fuzzy tail, big ears,
and whiskers are derived traits, while a skinny tail, small ears, and lack
of whiskers are ancestral traits. An important point is that a derived
trait may appear through either loss or gain of a feature. For instance,
if there were another change on the E lineage that resulted in loss of a
tail, taillessness would be considered a derived trait.
Derived traits shared among the species or other groups in a dataset
are key to helping us build trees. As shown above, shared derived traits
tend to form nested patterns that provide information about when
branching events occurred in the evolution of the species.
When we are building a phylogenetic tree from a dataset, our goal is
to use shared derived traits in present-day species to infer the
branching pattern of their evolutionary history. The trick, however, is
that we can’t watch our species of interest evolving and see when new
traits arose in each lineage.
Instead, we have to work backwards. That is, we have to look at our
species of interest – such as A, B, C, D, and E – and figure out which
traits are ancestral and which are derived. Then, we can use the shared
derived traits to organize the species into nested groups like the ones
shown above. A tree made in this way is a hypothesis about the
evolutionary history of the species – typically, one with the simplest
possible branching pattern that can explain their traits.

Terminology of phylogenetic trees

Notice that the tree above tree branches from a single trunk into two
branches, the vertical lines, and then the left side branches again. The
vertical branches represent a lineage, which is a taxon, shown at the
tip, and all its ancestors. The nodes are where lineages diverge,
representing a speciation event from a common ancestor. The trunk at
the base of the tree is actually called the root, and the root node
represents the most recent common ancestor of all of the taxa
represented on the tree. Time is represented vertically, proceeding
from the oldest at the bottom to the most recent at the top.

What this particular tree tells us is that taxon A and taxon B are more
closely related to each other than either taxon is to taxon C. The reason
is that taxon A and taxon B share a more recent common ancestor than
A and B do with taxon C. The least related taxon in a tree is called the
outgroup of that phylogeny, and it often included because it has
contrasting characteristics relative to the other included taxa. A group
of taxa that includes a common ancestor and all of its descendants is
called a monophyletic group, or a clade. Groups that exclude one or
more descendants or that exclude the common ancestor are not
monophyletic groups, or clades.
CONSTRUCTION OF PHYLOGENETIC TREE:-
When we are building phylogenetic trees, traits that arise during
the evolution of a group and differ from the traits of the ancestor of
the group are called derived traits. In our example, a fuzzy tail, big
ears, and whiskers are derived traits, while a skinny tail, small ears,
and lack of whiskers are ancestral traits. An important point is
that a derived trait may appear through either loss or gain of a
feature. For instance, if there were another change on the E lineage
that resulted in loss of a tail, taillessness would be considered a
derived trait.

Derived traits shared among the species or other groups in a dataset

are key to helping us build trees. As shown above, shared derived
traits tend to form nested patterns that provide information about
when branching events occurred in the evolution of the species.

When we are building a phylogenetic tree from a dataset, our goal is

to use shared derived traits in present-day species to infer the
branching pattern of their evolutionary history. The trick, however,
 is that we can’t watch our species of interest evolving and see when
new traits arose in each lineage.

Instead, we have to work backwards. That is, we have to look at our

species of interest – such as A, B, C, D, and E – and figure out which
traits are ancestral and which are derived. Then, we can use the
shared derived traits to organize the species into nested groups like
the ones shown above. A tree made in this way is a hypothesis about
the evolutionary history of the species – typically, one with the
simplest possible branching pattern that can explain their traits.

Example: Building a phylogenetic tree

Bald Sea If we
Feature Lamprey Antelope eagle Alligator bass were

Lungs 0 + + + 0

Jaws 0 + + + +

Feathers 0 0 + 0 0

Gizzard 0 0 + + 0

Fur 0 + 0 0 0

biologists building a phylogenetic tree as part of our research, we

would have to pick which set of organisms to arrange into a tree.
We'd also have to choose which characteristics of those organisms to
base our tree on (out of their many different physical, behavioral, and
biochemical features).

If we're instead building a phylogenetic trees for a class (which is

probably more likely for readers of this article), odds are that we'll
be given a set of characteristics, often in the form of a table, that we
need to convert into a tree. For example, this table shows presence
(+) or absence (0) of various features:

Next, we need to know which form of each characteristic is ancestral

and which is derived. For example, is the presence of lungs an ancestral
trait, or is it a derived trait? As a reminder, an ancestral trait is what
we think was present in the common ancestor of the species of
interest. A derived trait is a form that we think arose somewhere on a
lineage descended from that ancestor.
Without the ability to look into the past (which would be handy but,
alas, impossible), how do we know which traits are ancestral and
which derived?
In the context of homework or a test, the question you are solving may
tell you which traits are derived vs. ancestral.
If you are doing your own research, you may have knowledge that
allows you identify ancestral and derived traits (e.g., based on fossils).
You may be given information about an outgroup, a species that's
more distantly related to the species of interest than they are to one
another.
If we are given an outgroup, the outgroup can serve as a proxy for the
ancestral species. That is, we may be able to assume that its traits
represent the ancestral form of each characteristic.
For instance, in our example (data repeated below for convenience),
the lamprey, a jawless fish that lacks a true skeleton, is our outgroup.
As shown in the table, the lamprey lacks all of the listed features: it
has no lungs, jaws, feathers, gizzard, or fur. Based on this
information, we will assume that absence of these features is
ancestral, and that presence of each feature is a derived trait.

Bald Sea
Feature Lamprey Antelope eagle Alligator bass

Lungs 0 + + + 0

Jaws 0 + + + +

Feathers 0 0 + 0 0

Gizzard 0 0 + + 0

Fur 0 + 0 0 0

Table

Now, we can start building our tree by grouping organisms

according to their shared derived features. A good place to start is by
looking for the derived trait that is shared between the largest
number of organisms. In this case, that's the presence of jaws: all the
organisms except the outgroup species (lamprey) have jaws. So, we
can start our tree by drawing the lamprey lineage branching off from
the rest of the species, and we can place the appearance of jaws on
the branch carrying the non-lamprey species.

Next, we can look for the derived trait shared by the next-largest group
of organisms. This would be lungs, shared by the antelope, bald eagle,
and alligator, but not by the sea bass. Based on this pattern, we can
draw the lineage of the sea bass branching off, and we can place the
appearance of lungs on the lineage leading to the antelope, bald eagle,
and alligator.
Following the same pattern, we can now look for the derived trait
shared by the next-largest number of organisms. That would be the
gizzard, which is shared by the alligator and the bald eagle (and absent
from the antelope). Based on this data, we can draw the antelope
lineage branching off from the alligator and bald eagle lineage, and
place the appearance of the gizzard on the latter.
What about our remaining traits of fur and feathers? These traits are
derived, but they are not shared, since each is found only in a single
species. Derived traits that aren't shared don't help us build a tree, but
we can still place them on the tree in their most likely location. For
feathers, this is on the lineage leading to the bald eagle (after
divergence from the alligator). For fur, this is on the antelope lineage,
after its divergence from the alligator and bald eagle.

Parsimony and pitfalls in tree construction

When we were building the tree above, we used an approach called
parsimony. Parsimony essentially means that we are choosing the
simplest explanation that can account for our observations. In the
context of making a tree, it means that we choose the tree that
requires the fewest independent genetic events (appearances or
disappearances of traits) to take place.
For example, we could have also explained the pattern of traits we saw
using the following tree:
This series of events also provides an evolutionary explanation
for the traits we see in the five species. However, it is less
parsimonious because it requires more independent changes in
traits to take place. Because where we've put the sea bass, we
have to hypothesize that jaws independently arose two separate
times (once in the sea bass lineage, and once in the lineage
leading to antelopes, bald eagles, and alligators). This gives the
tree a total of 6 tick marks, or trait change events, versus 5 in the
more parsimonious tree above.
In this example, it may seem fairly obvious that there is one best tree,
and counting up the tick marks may not seem very necessary.
However, when researchers make phylogenies as part of their work,
they often use a large number of characteristics, and the patterns of
these characteristics rarely agree 100\%100%100, percent with one
another. Instead, there are some conflicts, where one tree would fit
better with the pattern of one trait, while another tree would fit better
with the pattern of another trait. In these cases, the researcher can use
parsimony to choose the one tree (hypothesis) that fits the data best.
This may be wondering: Why don't the trees all agree with one
another, regardless of what characteristics they're built on? After all,
the evolution of a group of species did happen in one particular way in
the past. The issue is that, when we build a tree, we are reconstructing
that evolutionary history from incomplete and sometimes imperfect
data. For instance:
• We may not always be able to distinguish features that reflect
shared ancestry (homologous features) from features that are
similar but arose independently.

• Traits can be gained and lost multiple times over the evolutionary
history of a species. A species may have a derived trait, but then
 lose that trait (revert back to the ancestral form) over the course
of evolution

Biologists often use many different characteristics to build

phylogenetic trees because of sources of error like these. Even when
all of the characteristics are carefully chosen and analyzed, there is still
the potential for some of them to lead to wrong conclusions (because
we don't have complete information about events that happened in
the past).

2.STUDYING METHOD

Unless indicated otherwise, a phylogenetic tree only depicts the

branching history of common ancestry. The pattern of branching (i.e.,
the topology) is what matters here. Branch lengths are irrelevant--they
are

Figure x
simply drawn in whatever way makes the tree look most tidy. Thus, the
three trees shown in Figure x all contain the same information.
The three trees in Figure y , for example, have the

Figure y
same topology and thus the same evolutionary implications. In each
case, the first divergence event separated the lineage that gave rise to
tip A from the lineage that gave rise to tips B, C, and D. The latter
lineage then split into two lineages, one of which developed into tip B,
and the other which gave rise to tips C and D. What this means is that
C and D share a more recent common ancestor with each other than
either shares with A or B. Tips C and D are therefore more closely
related to each other than either is to tip A or tip B. The diagram also
shows that tips B, C, and D all share a more recent common ancestor
with each other than they do with tip A. Because tip B is an equal
distance (in terms of branch arrangement) from both C and D, we
could say that B is equally related to C and D. Likewise, B, C, and D are
all equally related to A.
It might seem confusing that such different-looking trees can contain
the same information. Here, it might be helpful to remember that the
lines of a tree represent evolutionary lineages — and evolutionary
lineages do not have any true position or shape. It is therefore equally
valid to draw the branch leading to tip A as being on either the right or
the left side of the split, as shown in Figure z . Similarly, it doesn't
matter whether branches are drawn as straight diagonal lines, are
kinked to make a rectangular tree, or are curved to make a circular
tree. Think of lineages as flexible pipe cleaners rather than rigid rods;
similarly, picture nodes as universal joints that can swivel rather than
fixed welds. Using this sort of imagery, it becomes easier to see that
the three trees in Figure 7, for example, are equivalent. The basic rule
is that if you can change one tree into another tree simply by twisting,
rotating, or bending branches, without having to cut and reattach
branches, then the two trees have the same topology and therefore
depict the same evolutionary history.
 Figure z
Finally, it's important to note that in some instances, rectangular
phylogenetic trees are drawn so that branch lengths are meaningful.
These trees are often called phylograms, and they generally depict
either the amount of evolution occurring in a particular gene sequence
or the estimated duration of branches. Usually, the context of such
trees makes it clear that the branch lengths have meaning. However,
when this is not the case, it is important to avoid reading in any
temporal information that is not shown. For example, Figure 8 may
appear to suggest that the node marking the last split leading to tips
A and B (marked x) occurred after the node separating tip C from tips
D and E (marked y). However, this should not be read into the tree; in
reality, node x could have occurred either before or after node y.
ANALYSIS:-

A phylogenetic tree is a visual representation of the relationship

between different organisms, showing the path through evolutionary
time from a common ancestor to different descendants. Trees can
represent relationships ranging from the entire history of life on earth,
down to individuals in a population. Trees that show species help us
understand how new species form from common ancestral species.
The process of new species formation, called speciation, is the starting
point for a discussion of biological diversity. The natural endpoint will
be extinction.

Anatomy of a phylogenetic tree

When we draw a phylogenetic tree, we are representing our best

hypothesis about how a set of species (or other groups) evolved from
a common ancestor^11start superscript, 1, end superscript. As we'll
explore further in the article on building trees, this hypothesis is
based on information we’ve collected about our set of species – things
like their physical features and the DNA sequences of their genes.

Are phylogenetic trees only for species?

In a phylogenetic tree, the species or groups of interest are found at

the tips of lines referred to as the tree's branches. For example, the
phylogenetic tree below represents relationships between five
species, A, B, C, D, and E, which are positioned at the ends of the
branches:

Taxonomy phylogeny: Figure

The pattern in which the branches connect represents our

understanding of how the species in the tree evolved from a series of
common ancestors. Each branch point (also called an internal
node) represents a divergence event, or splitting apart of a single
group into two descendant groups.

At each branch point lies the most recent common ancestor of all
the groups descended from that branch point. For instance, at the
branch point giving rise to species A and B, we would find the most
recent common ancestor of those two species. At the branch point
right above the root of the tree, we would find the most recent
common ancestor of all the species in the tree (A, B, C, D, E).
Why is this the most recent common ancestor of all
the species?

Taxonomy and phylogeny: Figure

Each horizontal line in our tree represents a series of ancestors,

leading up to the species at its end. For instance, the line leading up
to species E represents the species' ancestors since it diverged from
the other species in the tree. Similarly, the root represents a series of
ancestors leading up to the most recent common ancestor of all the
species in the tree.
Key Points
• Phylogenetic trees are constructed using various data derived
from studies on homologous traits, analagous traits, and
molecular evidence that can be used to establish relationships
using polymeric molecules ( DNA, RNA, and proteins ).
 • Evolutionary relationships between animal phyla, or Metazoa,
are based on the the presence or absence of differentiated
tissues, referred to as Eumetazoa or Parazoa, respectively.
• Eumetazoa can be further classified into categories that are
based on whether they have radial or bilateral symmetry,
referred to as Radiata or Bilateria, respectively.
Key Terms
• orthologous: having been separated by a speciation event
• homoplasy: a correspondence between the parts or organs of
different species acquired as the result of parallel evolution or
convergence

Modern Advances in Phylogenetic Understanding

Come from Molecular Analyses
The phylogenetic groupings are continually being debated and
refined by evolutionary biologists. Each year, new evidence
emerges that further alters the relationships described by a
phylogenetic tree diagram. Previously, phylogenetic trees were
constructed based on homologous and analogous morphology;
however, with the advances in molecular biology, construction of
phylogenetic trees is increasingly performed using data derived
from molecular analyses.

Many evolutionary relationships in the modern tree have only

recently been determined due to molecular evidence. Nucleic
acid and protein analyses have informed the construction of the
modern phylogenetic animal tree. These data come from a
variety of molecular sources, such as mitochondrial DNA,
nuclear DNA, ribosomal RNA (rRNA), and certain cellular
proteins. Evolutionary trees can be made by the determination
of sequence information of similar genes in different organisms.
Sequences that are similar to each other frequently are
considered to have less time to diverge, while less similar
sequences have more evolutionary time to diverge. The
evolutionary tree is created by aligning sequences and having
each branch length proportional to the amino acid differences of
the sequences. Furthermore, by assigning a constant mutation
rate to a sequence and performing a sequence alignment, it is
possible to calculate the approximate time when the sequence
of interest diverged into monophyletic groups.

Phlyogenetic tree of life: Advances in molecular biology and

analysis of polymeric molecules such as DNA, RNA, and
proteins have contributed to the development of phylogenetic
trees.

Sequence alignments can be performed on a variety of

sequences. For constructing an evolutionary tree from proteins,
for example, the sequences are aligned and then compared.
rRNA (ribosomal RNA) is typically used to compare organisms
since rRNA has a slower mutation rate and is a better source for
evolutionary tree construction. This is best supported by
research of Dr. Carl Woese that was conducted in the late 1970s.
Since the ribosomes are critical to the function of living
organisms, they are not easily changed through the process of
evolution. Taking advantage of this fact, Dr. Woese compared
the minuscule differences in the sequences of ribosomes among
a great array of bacteria and showed that they were not all
related.
For example, a previously-classified group of animals called
lophophorates, which included brachiopods and bryozoans,
were long-thought to be primitive deuterostomes. Extensive
molecular analysis using rRNA data found these animals to be
protostomes, more closely related to annelids and mollusks. This
discovery allowed for the distinction of the protostome clade: the
lophotrochozoans. Molecular data have also shed light on some
differences within the lophotrochozoan group. Some scientists
believe that the phyla Platyhelminthes and Rotifera within this
group should actually belong to their own group of protostomes
termed Platyzoa.

Molecular research similar to the discoveries that brought about

the distinction of the lophotrochozoan clade has also revealed a
dramatic rearrangement of the relationships between mollusks,
annelids, arthropods, and nematodes; a new ecdysozoan clade
was formed. Due to morphological similarities in their segmented
body types, annelids and arthropods were once thought to be
closely related. However, molecular evidence has revealed that
arthropods are actually more closely related to nematodes, now
comprising the ecdysozoan clade, and annelids are more closely
related to mollusks, brachiopods, and other phyla in the
lophotrochozoan clade. These two clades now make up the
protostomes.

Another change to former phylogenetic groupings because of

molecular analyses includes the emergence of an entirely new
phylum of worm called Acoelomorpha. These acoel flatworms
were long thought to belong to the phylum Platyhelminthes
because of their similar “flatworm” morphology. However,
molecular analyses revealed this to be a false relationship and
originally suggested that acoels represented living species of
some of the earliest divergent bilaterians. More recent research
into the acoelomorphs has called this hypothesis into question
and suggested a closer relationship with deuterostomes. The
placement of this new phylum remains disputed, but scientists
agree that with sufficient molecular data, their true phylogeny will
be determined.
FINDINGS:-