Republic of the Philippines Evolutionary taxonomy and phylogenetic systematics are based in

Department of Science and Technology part on the production of optimal classifications. Techniques are applied
PHILIPPINE SCIENCE HIGH SCHOOL
Zamboanga Peninsula Region Campus
in areas of systematics and ecology to produce biological classifications.
Dipolog Sports Complex, Brgy. Olingan, Dipolog City
Most biologists agree that the classifications should be “natural,” to
EVOLUTIONARY RELATIONSHIP OF ORGANISMS AND the extent that it would reflect possible evolutionary relationships. Putting
CAMINALCULES CLASSIFIED BY SOLVING MANUALLY AND THE slime molds and whales in the same family is what should not be done.
USE OF SOFTWARE Systemics would then help with its two-part of endeavour. First, one must
devise a classification scheme that faithfully reflects the hypothesized
Janry Kyle N. Salcedo study.Usage of a series of imaginary animals to introduce to two rather
([email protected]) different methods that attempt to do this.

Ali Khan Miguel R. Lagapa The objective of this study is to examine the numerical data of the
([email protected]) Caminalcules to determine the evolutionary pattern of divergence and
disserfication in morphology.

ABSTRACT Relationships can also be inferred by the degree of general

similarity which can determine a numerical algorithm. Phenetic taxonomy
Organisms that have come forth on Earth are born with a sort of is a system of classification based on the overall similarity of the
relationship and a common origin. With the diverseness of life, single organisms. Phenetic arrangement of the taxa is developed with numerical
originating population have multiplied into several lineages. With a set of procedures applied to the character states of the organisms classified or
organisms namely the flowers, birds, and butterflies being studied in this to distance the matrixes applied to molecular data. In phenetics, molecular
paper, we can draw out a phylogenetic tree and phenograms with the use data are analyzed and characters are equal. The researchers sought to
of manually solving for phenetics and numerical data to distinguish create a hypothesis generated from similarities among taxa estimated
dissimilarities of organisms. The operations involve in sample organisms from the algorithm.
and characters to be recorded then resemblances are to be recorded in
which taxa are based on these resemblances and ta draw out In this paper, the researchers attempt to classify the relationship
generalizations are made about the taxa. Hypotheses of relationship are of the different special organisms: flowers, birds, butterflies, and
generated by a preponderance of similarity among taxa as estimated from caminalcule. Each special organisms are given with species to distinguish
the characters via the specific algorithm. We can also classify the each of their traits which determines the rate of relatedness through their
similarities of organisms and caminalcules by the use of cladograms and common ancestors. Not only on the manual processes, but also on the
their character matrices. But due to technological advancements, we can use of software to determine the evolutionary pattern of organisms from
use softwares such as the WinClada software where we can easily point their common ancestors.
out and identify which among the organisms and caminalcules are closely
evolutionary related to each other and with the bases of their common
ancestors. As based on the results of the process, it is observable that MATERIALS AND METHODS
manual computation can do the work, yet much easier with the use of
software in categorizing organisms and caminalcules. Organisms Studied:
There were a total of 16 organisms studied. In which 3
categories of organisms are classified to identify who are the closer related
Keywords: WinClada Software, Cladogram, Phylogenetic Tree, and the farther unrelated by means of such similarities and differences.
Evolutionary Relatedness, Phenetics, Phenogram, Taxonomic Systems, The 3 categories of organisms are: the flowers, the birds, and the butterfly.
OTUs
Materials/Equipment:
A lot of papers were used and spent as well as the pencils.
INTRODUCTION Several worksheets were also manually solved to have a draft and a
background of the ones closer related to each other before inputting the
A life can only arise once on Earth which indicates that each data on the software. After solving, the softwares called “WinClada” and
organism is inborn with a relationship and a common origin. The “NoNa” are then used to expound and elaborate the evolutionary
diverseness of life resulted from series of interaction and coexistence. relatedness of an organism to another organism in terms of the identified
Multiple new lineages arise from a single originating population. As time features of these organisms.
goes over by, change in characteristics are recognizable due to different
lineages.
Procedures: Solving manually
Compartmentalizing relatedness of each species is adjudicated
by modern taxonomy. Previous taxonomic systems use morphological and
anatomical methods which does not directly point the evolutionary
relationship of organisms. The researchers wanted to identify individuals
based on molecular pattern of evolution and to group them accordingly
with evolutionary classification together with the use of a WinClada
software as basis of the study. Figure 1.

Most modern systems of classification are based on Looking at the organisms shown in Figure 1 is the first method
evolutionary relationships among organisms. Classification systems that should be done. If there are 6 organisms (flowers), then there should
based on phylogeny organize species in terms that reflect the reader’s be 7 features to be able to identify relatedness promptly. Features are
understanding from such common ancestors that led to of how evolution listed in the first row, while the organisms are placed on the first column of
came to be. the table. Data is then recorded for each organisms.

Phylogenetic tree is a diagram that classifies evolutionary Table 1.

relationships among organisms based according to their affiliation, in
which the tree may be built with molecular data. 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.

BIO 1 Fundamentals of Biology 1

Third Quarter, SY 2018-2019
 Organisms and their features are used to differentiate by their Table 4.
traits and evolutionary relationship are shown in Table 1. After inputting
the data, each pair of organisms shall be compared as the second method.
The total number of differences between each pair shall be recorded such
as in A and B, their only difference is the Present and Absent which counts
as 1 difference. After computing for the total number of differences, data
shall be input on the data matrix that will be used to build the phylogenetic
tree in the next step. The data matrix is shown below:

Table 2.
After having the character matrix for data analysis, opening
WinClada software is now available. Once opened, directly look for
<Matrix> and then click on <New matrix (create)>. A window box will then
appear asking for the number of taxa and the number of characters. Enter
the correct value of what is to be used and then click on <Ok! Resize!>.
The desired output will then be shown on the WinClada Screen.

In changing the name of each taxon, look for <Terms> and then
The numbers in the data matrix can then be used to draw the click on <Terminal dialog>. A window box will again appear to change the
phylogenetic tree showing the relatedness of the six flowers organism. name of your taxon. After naming, look for <Edit> and then click on
Using the records from the first table, a data, matrix, recording the number <Unlock>. After unlocking, inputting the binary value for each organisms
of differences between pairs of organisms, has also been produced: is the next move in which there are only 0 and 1.
Currently living organisms will be placed at the top of the tree, After that, save the work in Winc format (.winc) and then look for
while going down the tree is moving into the past where in the last common <Analyze> and then click on <Spawn> next would be <Nona> and then
ancestors of the organisms will be shown on the very bottom of the tree. <enter path> then look for the file of WiNona. Then, wait until the code of
Nona shows and then wait for the codes to stop.
Table 3.
Enter <w;> and then the <tp;> and then <z;>. After the z, look
for <Analyze> and then click on <Heuristics> then wait for a window to pop
up and then look for <Submit ALL trees> then <Search>. After search,
Nona code will pop up again and then enter <w;>, <tp;>, <z;> again. After
this, the tree will then be displayed on the screen.

Look for the normal Cladogram and look for <View> and then
click on <Tree style> then <Align taxa (toggle)>. To save the file, first look
As for creating the tree, finding the closest relatives is where we for <Trees> and then click on <Keep current tree to ram file> then <Save
start off as the third method. The pair of organisms that have the fewest CURRENT tree to file>. Save the tree that was studied and then after it, a
difference. In the data matrix presented above, flower A and B, and flower window will pop and click <Name taxa (full names, NOT NONA
E and D are closest relatives since they have only one difference. The readable)>. After this part of hard work on trying to create a cladogram
closest related flowers are pinpointed as shown in Table 3. using a WinClada software, the file has been saved.
A B E D
F C

Figure 2.
Figure 4.
The fourth method shall be done by finding the organisms that
have more than one difference. Flower B and F are closer than Flower B As observed in Figure 4, Taxa C and E are closely related to
and E, on the other hand, Flower E and C are closer than Flower E and B. each other because they are near each other while Taxa A and E have
A B E D little or no relationship at all because they are far from each other in the
tree diagram.
F C
With this methods demonstrated, it is then applicable to other
set of different organisms that is to be followed. By applying the methods
common ancestor aforementioned, finding the phylogenetic tree is then found.
Figure 3. Table 5.
Lastly, the fifth method, organisms F and C differs the most then
they are the least related to each other, but not to the other flowers. F and
C will then be connected by linking them with a common ancestor as
shown in Figure 4.

This procedure abovementioned and discussed briefly applies

to the 2 more categories of organisms, birds and butterflies, which are
being studied in this paper.

Procedures: Using WinClada Software

Before starting off with WinClada application, characters need
to examine the organisms should be prepared first since it will mark the Figure 5.
points of degree in which the cladogram will result into a tree.

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 As observed in Figure 5, Taxa D and E, and Taxa C and F are having similarities and to identify its evolutionary relatedness to other
closely related to each other because they are near each other while Taxa caminalcules.
A and F have little or no relationship at all because they are far from each
other in the tree diagram. Find the pair of OTUs that have the highest similarity ranking.
Then, combine the OTUs and treat them as a single composite unit from
Table 6. this point on. the similarity of OTU D with OTU 2 is 0.2, and the similarity
of OTU D with OTU A is 0.1, then the similarity of OTU D with OTU A/H
will be the average of those two similarities: [(0.1 + 0.1)/2], or 0.1.
Construct a new matrix and reduce the matrix with similarity values
recomputed for al OTUs with composite OTU.

Table 8.

Figure 6.
A/H is written in the 2nd row as shown in Table 8. that is because
As observed in Figure 6, Taxa B and C, and Taxa D and F are
from the data on Table #13 having the highest similarity between
closely related to each other because they are near each other while
caminalcules. To solve for the values in the column of A/H is to add the
Taxa A and C have little or no relationship at all because they are far
two values of A/H and other letters and divided by 2. Then, continue to
away from each other in the tree diagram.
construct reduced matrices, each time recalculating the similarity indices
between your new composite OTU with all remaining OTUs.
Organisms Studied:
There were 8 caminalcules. Caminalcules are artificial species
Table 9.
invented as a tool for better understanding on phylogenetics. These
organisms are uniquely named by the Operational Taxonomic Unit to
avoid assigning these organisms to any other taxonomic ranks. In the
given activity, the organisms used as a basis on creating the phyogentic
is shown below.
Then, add more reduced matrices, recalculating the similarity
indices between your new composite OTU with remaining OTUs.

Table. 10.

Figure 7. Table. 11.

Materials/Equipment:
Papers were used and consumed as well as with the aid of
pencils and ballpens in writing. Several worksheets were also manually
solved to have a draft and a background of the ones closer related to each .
other before inputting the data on the software. After solving, the softwares Table. 12.
called “WinClada” and “NoNa” are then used to expound and elaborate
the evolutionary relatedness of an organism to another organism in terms
of the identified features of these organisms

Procedures: Solving manually The solution in solving for Tables 9 to 12 are the same as in the
Operational Taxonomic Units (OTUs)--a name we use to avoid solution for Table 8.
assigning them to any particular taxonomic rank. It is a subjective
judgment about the overall similarity between all pair-wise combinations
of the eight OTUs, using a scale of 1.0 (maximum similarity) to 0 (complete RESULTS AND DISCUSSION
dissimilarity).

Table 7.

Figure 8.

First, identify 7 features in order to find the relatedness of each

organisms or birds to one another. List it on a table/cards and record the
data.

Numbers written above are the result from giving criteria on the
caminalcules if it fits a characteristics. This is to classify a caminalcule

BIO 1 Fundamentals of Biology 1

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Table 13. . Organisms and its features used to differentiate each of them by
characteristics and evolutionary relationship are listed in this table.Find
and draw the differences in a data matrix to be able to draw the
phylogenetic tree.

Table 17.

Organisms and its features used to differentiate each of them by

traits and evolutionary relationship are listed in this table. Account for the
differences of each organsims found in the data.
The numbers in the data matrix can then be used to identify the
Table 14. relatedness of the six bird organisms.

Table 18.

The numbers in the data matrix can then be used to draw the
phylogenetic tree and identify the relatedness of the six bird organisms.

Table 15. In this table, the closest related butterflies with one difference
are pointed out in red circles and identified by red arrows. Butterflies C
and B, Butterflies E and A, and Butterflies D and F are closely related to
each other.

In this table, the closest related birds with one difference are
pointed out in red circles and identified by red arrows. Birds E and D and
Birds F and C are closely related to each other. Figure 11.

Butterflies had been related to other butterflies with one

difference which made that there are no more than one difference. By
connecting each end of the relationships, they become related due to the
linking common ancestor.

CONCLUSION

Based on the results, WinClada is technological or electronic

Figure 9. way to construct a phylogenetic tree and a cladogram as the software
automatically builds the tree based on the data given. In the manual
Organisms that have more than one difference. Bird A is closer process, calculations are needed to be performed to identify the degree of
to Bird D and Bird B is closer to Bird A. Lastly, Birds F and C differs the relationship between the species analyzed. The advantage of manual
most with other birds since they are farther to each other, but they are process, however, it can identify the degree of relationship while the
connected by linking them with a common ancestor. WinClada software can not. Nonetheless, the characters used for the
manual process and WinClada software are not much alike, results still
show the efficiency of the software. Thus, implementing WinClada
software in phenetics on manual computations are efficient as a way to
construct phenograms since the software can automatically create a tree
based on the given data. In the manual process, calculations are still
required to be performed to identify the degree between the species that
were being examined.
Figure 10.

Identifying 7 features out of these six butterfly organisms to REFERENCES

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