Name: Jhon Patrick P.

Delmonte Course and Year: BS-Biology-1 MN

Date Performed: September 20, 2019 Score:

EXERCISE 8:
CREATING A PHYLOGENETIC TREE

INTRODUCTION
A phylogenetic tree or evolutionary tree is a diagrammatic representation of the
evolutionary relationship among various taxa. It illustrates the evolutionary relationships among
species. Usually such trees are constructed based on sequence similarity between the highly
conserved 16S rRNA genes or a set of housekeeping genes of several organisms. This limitation
to a small set of input sequences can be problematic as the phylogeny of single genes does not
necessarily reflect the phylogeny of the complete organisms. It is therefore highly desirable to
use all genes of the core genome as input for the tree calculation, which dramatically increases
its reliability (Gontcharov et al., 2004).

A phylogenetic tree is composed of nodes and branches. The branching pattern of a tree
is called the topology of the tree. The nodes represent taxonomic units, such as species (or higher
taxa), populations, genes, or proteins. A branch is called an edge, and represents the time
estimate of the evolutionary relationships among the taxonomic units. Usually, it is depicted in
different types showing the equivalent relationships depending on the organism’s being
observed.

It can be
either scaled or
unscaled. In a
scaled tree, the
Figure 1. Different types of phylogenetic trees showing equivalent relationships
branch length is proportional to the amount of evolutionary divergence (e.g. the number of
nucleotide substitutions) that has occurred along that branch. In an unscaled tree, the branch
Name: Jhon Patrick P. Delmonte Course and Year: BS-Biology-1 MN

length is not proportional to the amount of evolutionary divergence, but usually the actual
number is indicated somewhere on the branch.

Phylogenetic tree may be shown as phenogram or cladogram. In the Phenogram, the

branches are arranged Parallel to each other. In cladogram, branches are radiating outward from
central point. Both Phenogram and Cladogram explain the evolutionary origin of various species.

In general, 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.

OBJECTIVES

In this exercise, students were able to construct phylogenetic tree using morphological
characteristics of organisms- that is, by observing the physical attributes of the chosen organisms
and naming these organisms using the unique traits that were observed. Moreover, they were also
able to understand the basic concepts of systematics that classify organisms according to their
evolutionary relatedness.

PROCEDURE

In this particular exercise, students were first grouped composing of three members each.
Each group then chose a certain organism from the three different organisms found at the latter
part of the activity handout. Upon choosing, the students then think of seven features or
characteristics specifically physical ones that will help them identify and differentiate a group of
the same organism based on these attributes.

Specifically, our group has decided to choose the group of birds as the organism that
we’re going to observe. Right after, we had identified seven (7) features that makes one bird
different from the others. It was followed then by listing these features on the first row of the
Name: Jhon Patrick P. Delmonte Course and Year: BS-Biology-1 MN

given table alongside with the recorded data from the six (6) same organism but with different
characteristics.

Then, using another table, unique birds were then compared to each other with the
data recorded in table 1, focusing mainly on their differences. This is the data matrix that
will be used to build the phylogenetic tree in the next step. But prior to making the actual
phylogenetic tree, our group had first undergone series of calculations to make sure that the
phylogenetic tree to be created was correct. Upon verification, we were then able to create
the phylogenetic tree of the different birds. Lastly, distinct names were also created by the
group to each bird to differentiate one from the others.

RESULTS AND DISCUSSION

Seen below was the chosen organism of our group. Six (6) birds with unique
characteristics.

Figure 2. Birds of unique physical characteristics

Name: Jhon Patrick P. Delmonte Course and Year: BS-Biology-1 MN

Birds A and B were named the blue-winged and black-winged bird respectively. Bird C
on the other hand was named the long, black-beaked bird opposite to that of Bird F which was
named the short, black-beaked bird. Birds D and E were named the long, red-beaked bird and
short, red-beaked bird respectively. These names were coined by the members of the group for
the purpose of identifying each of these birds.

Meanwhile, the table below shows the recorded data generated through the help of the
seven features listed by the group.

Feature Length of Color of Color of Color of Length of Color of Length of

beaks beaks spots wings legs legs tails
Organism

Long Red Maroon Blue Short Red Short

A
Long Yellow Yellow Black Short Red Long
B
Long Black Red Brown Long Black Long
C
Long Red Maroon Gray Short Yellow Short
D
Short Red Maroon Gray Short Yellow Short
E
Short Black Red Brown Long Black Long
F

Table 1. Recorded data of the six birds

Looking at the table above, it can be inferred that each of the birds differ in some
unique characteristics. In terms of beak length, A, B, C, D all share the same length that differ on
Birds E and F. For the color of the beaks, Birds A, D, and E shares the same color which is red.
However, Birds C and F have black as the beak color while Bird B is the only one that is yellow-
colored. Color of spots is distributed the same as the color of the beaks. For their wings color,
Birds C and F are brown-colored, D and E are gray-colored, B is black-colored and A is blue-
colored. In terms of their length of legs, only Birds C and F are long-legged while the remaining
others are short-legged. For the color of the legs, this time they come by pairs with A and B
Name: Jhon Patrick P. Delmonte Course and Year: BS-Biology-1 MN

having red as their color, C and F having black, and D and E sharing the same color yellow.
Lastly, for the length of tails, Birds A, D, and E were all short-tailed while Birds B, C, and F are
long-tailed birds.

Meanwhile, the next tables below, the first one shows the recorded data through
comparing each pair of the organism, jotting down the differences between them. The second
and third table however, were used to show the relatedness of each of the birds, with the
calculations of how far do they differ in terms of number.

B C D E F A B C F C/F B
A 4 6 2 3 7 D/E 2.5 5.5 6.5 6.5 From the
B 5 5 6 6 4 6 7
A D/E/A
C 6 7 1 4.5 4
B 5 6
D 1 7
C/F
E 6 C 1 5.5

Table 2.1 Data Table 2.2 Data Table 2.3 Data

matrix that shows matrix that shows matrix that shows
the relatedness of the relatedness of the relatedness of
all six organisms. D and E to other paired D/E/A and
organisms. C/F to others.

above data, we could say that Birds C and F and Birds D and E are closely related to each other
with having only 1 difference. This only means that these pairs share the common ancestor. In
table 2.2, D/E was compared to other birds specifically A, B, C, and F. It turned out that among
the mentioned birds, Bird A was closely related to Birds D and E with having only a 2.5
difference compared to that of others. In table 2.3, it shows already that Birds D, E and F are
related to each other similar to Birds C and F. Among the six birds, Bird B was the one that was
a bit far from others in terms of their relatedness.

Using all these data, our group has arrived with the Phylogenetic tree of our chosen
organism:
Name: Jhon Patrick P. Delmonte Course and Year: BS-Biology-1 MN

D Gray long-beaked bird

E Gray short-beaked bird

A Blue-winged bird

B Black-winged bird

C Brown long-beaked bird

F Brown short-beaked bird

Figure 3. Phylogenetic Tree of Birds

Aside from their names that makes different from the others, what can be seen also in this
Phylogenetic tree is the clearer view of the relationships between the six birds. This only shows
how helpful it is to construct a Phylogenetic tree in order to enrich our understanding on the how
different organisms evolved through time.

CONCLUSION

Knowing and understanding how different organisms had undergo evolution through time
is an important concept that we all have to instill in our thoughts. Sometimes in the journey of
unravelling and digging for the roots of certain organism, difficulties may be encountered. It isn’t
an easy thing especially when you are dealing with the convergent evolution between groups of
unrelated organisms because it’s usually hard to unearth.

But with phylogenetic analysis, however, we can easily distinguish between features that
are due to evolutionary relatedness. 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 like classification of various organisms, answering biological
questions, as well as in the field of bioinformatics.
Name: Jhon Patrick P. Delmonte Course and Year: BS-Biology-1 MN

REFERENCES

https://www.sciencedirect.com/topics/medicine-and-dentistry/phylogenetic-tree

https://www.ebi.ac.uk/training/online/course/introduction-phylogenetics/why-phylogenetics-
important

https://www.slideshare.net/bansaripatel89/basic-concepts-in-systamaticstaxonomy-and-

phylogenetic-tree-91572337

https://bioenv.gu.se/digitalAssets /1580/1580956_fyltreeeng.pdf