HIGH

SCHOO
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Grade
12

BIOLOGY II
QUARTER 3 – MODULE 6

Systematics Based on
Evolutionary Relationships:
Cladistics and Phylogeny
General Biology 2– Grade 12
Alternative Delivery Mode
Quarter 3 –Module 6: Systematics Based on Evolutionary Relationships:
Cladistics and Phylogeny

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Development Team of the Module

Authors: Ilonah Jean M. Macato
Reviewer: Rodrigo T. Domingo
Julie G. De Guzman, EdD
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Layout Artist: Ilonah Jean M. Macato
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Division EPS-Science: Julie G. De Guzman, EdD

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Introductory Message
For the facilitator:

Welcome to the General Biology 2 Alternative Delivery Mode (ADM) Module on

Systematics Based on Evolutionary Relationships: Cladistics and
Phylogeny!
This module was collaboratively designed, developed, and reviewed by educators
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helping the learners meet the standards set by the K to 12 Curriculum while
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Welcome to the General Biology 2 Alternative Delivery Mode (ADM) Module on

Systematics Based on Evolutionary Relationships: Cladistics and
Phylogeny!
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 What I Need to Know

This module was designed and written with you in mind. It is here to help
learners to know the basic principles of taxonomy in the classification and naming
of organisms. This chapter focuses on a system classification based on the genetic
material of organisms and establishment of their revolutionary relatedness.

After going through this module, you are expected to describe species diversity and
cladistics, including types of evidence and procedures that can be used to establish
evolutionary relationships (STEM_BIO_IIIh-j-16).
The following are the specific objectives:
a. Demonstrate how shared derived characters can be used to reveal degrees of
relationship; and
b. Build cladograms to infer evolutionary relatedness.

What I Know

Choose the letter of the best answer. Write the chosen letter on a separate sheet of
paper.
1. Which of the following best define taxonomy?
a. Branch of science that deals with the study of living thing.
b. Branch of biology that deals with the studying of animals.
c. Branch of science that deals with the study of origin of diseases.
d. Branch of biology that deals with the classification and naming of
organism.
2. Who is the father of taxonomy?
a. Carl Linnaeus c. Robert Hooke
b. Gregor Mendel d. Gregor Mendel
3. It can be defined as the study of the pathways of evolution.
a. Cladistics c. Phenetics
b. Monophyletic d. Phylogenetics
4. The common ancestor of all taxa?
a. Root Branch c. Branch
b. Clade d. Node Root
5. It pertains to a taxon whose members were derived from two or more
ancestors not common to all members.
a. Monophyletic c. Polyphyletic
b. Paraphyletic d. Tetraphyletic
6. A group of two or more taxa or DNA sequences that includes both their
common ancestor and all their descendent.
a. Branch c. Node

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 b. Clade d. Root
7. A tool in molecular biology that uses computer technology to manage
biological information.
a. Bioinformatics c. Molecular clock
b. DNA barcoding d. Sequence alignment
8. It It shows the divergence of two species.
a. Branch c. Phylogenetic tree
b. Branch points d. Root
9. This constitutes the genetic information of all living entities that passes on
from generation to generation.
a. DNA c. RNA
b. Chromosomes d. All of the above
10.This uses a computer software to align and detect similarities of sequences
to construct a phylogenetic tree.
a. Bioinformatics c. Molecular clock
b. DNA barcoding d. Sequence alignment

Lesson
Cladistics and Phylogeny
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Biologists realized that the arrangement of organisms into taxa reflects the
pattern of evolutionary relationships among organisms in which the degree of
relatedness is proportional to the shared categories of two organisms.

What’s In:

Activity 1: Definition of Terms

Directions: Define the following terms of your own word.
1. Analogous character 4. Homologous character
2. Clade 5. Phylogeny
3. Cladogram

What’s New

Activity 2. Evolutionary Relationship

I. Objective:
The learners will be able to identify and explain the morphological structure,
developmental characteristics and DNA relatedness are used in the
classification of living things.

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II. Procedure:
Analyze the given questions. Explain and elaborate your answers.
1. Explain how morphological structure, developmental characteristics and DNA
relatedness are used in the classification of living things.
2. Explain how species diversity is shown by a cladogram. Consider the
following cladogram. How many clades does it show?

What is It

Systematic Biology
Along with the increase in understanding of scientist about the nature of the
living world, they began not only to name and classify organisms but also to
establish evolutionary relatedness and history. Scientists call this study of
diversification of organisms, both modern life forms and extinct, and their
evolutionary relationships as systematics is that the former only focuses on
naming, describing, classifying, and preserving collections of species whereas the
latter also examines their evolutionary histories and environmental adaptations
that entail their survival. Nowadays, the study organisms normally used molecular
biology and computer programs for bioinformatics.

Phenetics versus Cladistics

Phenetics aim to classify organisms on the overall similarity of morphological
characteristics among them without considering the organismal evolutionary
relationships. Typically, in constructing the tree of life using phenetics, members of
the group may be of different evolutionary origin but have similarities in
morphological features due to convergent evolution. On the contrary, the
evolutionary history of classified organisms is in cladistics where each category or
group consists of the most common ancestor and all its descendants. This group is

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a clade wherein each member may be morphologically distinct from each other
because of divergent evolution.

DNA Analysis in Systematics

The discovery of DNA structure led to the advancement of the science of
classifying organisms. Every organism has a DNA, an RNA, and proteins. DNA
constitutes the genetic information of all living entities that passes on from
generation to generation without being largely altered. Some genes are also well
conserved-as similar or identical sequences of DNA, RNA, and even amino acids are
detected across multiple species. This means that closely related species will have a
greater chance of having high similarities on sequences of these molecules and that
the more distantly related a species is from other species, the lower the degree of
similarity between their sequences. Since even conserved genes undergo mutations
that are spontaneous at a constant rate, the mutations accumulate over time. This
accumulation of mutations provides the basis for generating a molecular clock for
dating divergence. Sequencing of these conserved genes is becoming more and
more conventional because of continuous development such as the Sanger
sequencing developed in 1977 and now the even more automated next generation
sequencing.
One approach to systematics and molecular phylogeny is sequence
alignment that uses a computer software to align and detect similarities of
sequences to construct a phylogenetic tree (i.e., Clustal Omega). These computer-
generated alignment techniques are conventional methods in bioinformatics --- a
tool in molecular biology that uses computer technology to manage biological
information. Another approach used in systematics is the DNA barcoding that
utilizes short genetic markers in the DNA to identify an unknown organism or
make sure that an organism belongs to pre-existing classification. The most used
barcode region for animals is a 600 base-pair long mitochondrial gene cytochrome
oxidase I.

Constructing the three of Life

Phylogenetics is a field of systematics that studies phylogeny-the
evolutionary relationships among individuals or groups of species and their
evolutionary history based on the comparison of their genetic characteristics.
Systematics describe evolutionary history and relationships by creating a
phylogenic tree. This tree is a branching diagram depicting inferred evolutionary

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origin among classified organisms. Each branch represents the hierarchical
classification of groups while the branch points show the divergence of two species.
The length of branches is equivalent to the amount of character change in the
species.

Figure 1. Cladogram showing members of the clade Sauria

(1) tuatara (2) lizards (3) snakes (4) crocodiles (5) birds.

Groups in Phylogenetic Trees

A monophyletic group is a group that consists of a single most recent common
ancestor and all species that descends from (Fig.1). On the other hand, the
paraphyletic group is a taxon or group composed of the common ancestor and
some descendants in the monophyletic. Finally, polyphyletic consists of unrelated
lineages and the common ancestor of all members is not included. In this case, the
lizards in Fig. 1 are paraphyletic.

Fig 2. The concept of monopoly,

paraphyly and polyphyly.

Phylogram versus Cladogram

A phylogram is a tree showing an estimate of a phylogeny(relationships) and the
degree of evolutionary changes depicted in each span of the tree’s branch. In
contrast, a cladogram is a tree that also shows an estimate of a phylogeny but does
not determine several evolutionary changes since the branches are equal length.
(Fig. 3).

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 Fig. 3. The difference between a cladogram and a phylogram.

Domain: The three Great Clades

As the understanding of the molecular bases of life progresses, the molecular T
y
criteria replace the classical phenotypic criteria in modern systematics in which
molecular sequences expose underlying evolutionary relationships. Because of this,
Carl Woese and his colleague published a paper in 1990 suggesting that there
must be a higher taxon or clade than the existing kingdoms, which he called
domains. These are the domain archae, bacteria, and the eucarya. He separated
the kingdom Monera into two domains, the archea and the bacteria because they
differ at the molecular level although they are both prokaryotes at the cellular level.
Then he placed all the remaining eukaryotes into the domain eucarya. Fig. 4
shows the three domains as proposed by Woose et al. (1990), organized into the
universal phylogenetic tree. This reconstruction of the systematic classification is
partly due to the rRNA genes, which are suitable for establishing phylogeny
because these genes are highly conserved across all members in a clade.

Figure 4. The universal phylogenetic tree is showing the three domains

as proposed by Woese st.al., 1990

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 What’s More

Activity 3: Constructing a Cladogram

Homalozoa
Echinoid Asteroid Crinoid Holothuroid Opthiuriod
(outgroup)
Water
vascular YES YES YES YES YES YES
system
No. of
ambulacral 3 5 5 5 5 5
grooves
Madreporite Aboral Aboral Aboral None Internal Oral
Suckers Non on On
On podia Absent On podia On podia
podia podia
Closed
ambulacral No Yes Yes No Yes Yes
grooves
Aboral surface
No Yes No No Yes Yes
reduced
Ambulacral
grooves
No Yes No No Yes No
extended from
oral to aboral
Endoskeleton Highly Not Highly Highly Highly
Flexible
flexible flexible flexible flexible flexible

Directions: Constructing a Cladogram

1. Use the data above to arrange the group of organisms based on their shared
derived traits.
2. For each group, the traits or characters are already listed. For each character,
determine which state is ancestral or primitive and which is derived. This is
usually done by comparing with the outgroup. Traits found in the outgroup are
likely to be ancestral or primitive. Similarly, traits not found in the outgroup are
considered derived. In cladistics, it is the derived traits shared among taxa that
that should be placed in the cladogram.
3. Group taxa according to their shared derived character(s).
4. Once you evaluated the characters, you may start constructing your cladogram.
(note: Outgroup is always placed at the base of the cladogram)

T
y
p
e

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 What I Have Learned

Summary:
 Phenetics aim to classify organisms on the overall similarity of morphological
characteristics among them without considering the organismal evolutionary
relationships.
 The discovery of DNA structure led to the advancement of the science of
classifying organisms.
 Every organism has a DNA, an RNA, and proteins. DNA constitutes the genetic
information of all living entities that passes on from generation to generation
without being largely altered.
 Bioinformatics-- a tool in molecular biology that uses computer technology to
manage biological information.
 Phylogenetics-is a field of systematics that studies phylogeny-the evolutionary
relationships among individuals or groups of species and their evolutionary
history based on the comparison of their genetic characteristics.
 A monophyletic group is a group that consists of a single most recent common
ancestor and all species.

What I Can Do

Activity 4. Inquiry and Research Project

Case Presentation: Applying Phylogenies
Why do biologists care about phylogenies?
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Assessment

Directions: Choose the letter of the best answer. Write the chosen letter on a
separate sheet of paper.
1. The first scientist to classify organisms was____?
A. Aristotle C. Robert Hooke
B. Carolus Linnaeus D. Robert Kocks
2. Which term best describes a group of species without a known common
ancestor?
A. Binomial group C. Paraphyletic group
B. Monophyletic group D. Polyphyletic group
2. It is an attempt to classify organisms based on overall similarity, usually in
morphology or other observable traits, regardless of their phylogeny or
evolutionary relation.
A. Cladistics C. Phenetics
B. Cladogram D. Taxonomy
3. What is the difference between phenetics, and cladistics is the method used in
classifying organisms?
A. Phenetics classifies organisms based on their paraphyletic and structural
features while cladistics classifies organisms based on morphological group.
B. Phenetics classifies organisms based on morphological ancestry and
evolutionary relationship while cladistics classifies organism based on
structural features only.
C. Phenetics classifies organisms based on morphological and structural
features while cladistics classifies organisms based on their ancestry and
evolutionary relationships.
D. Phenetics classifies organisms based on ancestry and structural features
while cladistics classifies organisms based on their structural and
evolutionary relationships.
4. A yardstick for measuring the absolute time of evolutionary change on the
observation that some genes and other regions of genomes appear to evolve at
constant rates.
A. Bioinformatics C. Sanger sequencing
B. Molecular clock D. Sequence alignment clock
5. Phylogenetic trees:
A. Aim to show phenotype similarity.
B. Are static and never change.
C. Show the exact ages of species.
D. Aim to show evolutionary histories through common ancestors.
6. Shared derived characteristics of phylogenetic are?
A. Phenotypically the same
B. Used to characterize a clade.
C. Used only to characterize species.
D. Characters that originated in an ancestor of the taxon.
7. A tool in molecular biology that uses computer technology to manage biological
information.

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 A. Bioinformatics C. Sequence alignment
B. DNA Barcoding D. Sanger sequencing
8. What is the importance of DNA barcoding?
A. Power of genetic resources
B. Protection of endangered specie
C. Stock assessments and Water quality monitoring
D. All of the Above
9. A tree showing an estimate of a phylogeny and the degree of evolutionary
changes depictedd in eacg span of the tree’s branch.
A. Cladistics C. Phylogenetics
B. Cladogram D. Phylogram

Additional Activities

Activity 5. Explain the percentage of Earth's species that are now extinct.

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