PRIVATE EDUCATION ASSISTANCE COMMITTEE

ADAPTIVE TEACHING GUIDE

MET #4: The Process of Evolution

Lesson # 2. Cladistics and Phylogeny

BASIS: Cladistics and phylogeny are often misunderstood by students

and not thoroughly taught by teachers due to their complex nature and
the abstract concepts involved. Teachers may prioritize other topics
perceived as more foundational or accessible, leading to limited coverage
of these subjects. Additionally, the intricate terminology and methods
used in cladistics and phylogeny can be challenging for both teachers
and students to grasp fully without dedicated time and resources. As a
result, these topics may be glossed over or not emphasized enough in
educational curricula, leaving students with gaps in understanding this
topic.

Prerequisite Content-knowledge:
● Understanding that organisms share a common ancestor.
● It is necessary for the students to possess the knowledge on the structural and
developmental characteristics and relatedness of DNA sequences of different
organisms.

Prerequisite Skill:
● Establishing relationships
● For the students to construct cladograms, they should make connections on
how the different characteristics of organisms can be used to establish
relationships.

Prerequisites Assessment: (This can be administered in three modalities: In-Person,

Online & Offline)

Multiple Choice: Write the CAPITAL letters that correspond to the correct answer.

1. Some molecular data place the giant panda in the bear family (Ursidae) but place
The lesser panda in the raccoon family (Procyonidae). However, scientists observed
morphological similarities of these two species. Which of the following can explain this
observation?
A. inheritance of acquired characteristics
B. inheritance of shared derived characters.*
C. possession of structures.
D. possession of shared primitive characters.
2.Vertebrate forelimbs are most likely to be studied in what discipline?
A. Ecology
B. Embryology
C. Biogeography
D. Comparative anatomy*
PRIVATE EDUCATION ASSISTANCE COMMITTEE

MET #4: The Process of Evolution

Lesson # 2. Cladistics and Phylogeny

3.Which is accurate about the description of homologous structures?

A. Structure that functions and later on disappears.
B. Structure has no relevance in origin and function.
C. Structures are similar in origin and structure. They evolve to fit the animal’s way
of life.*
D. Structure in different organisms that serve the same function. They show no
evolutionary relationships.
4. What is generally true about two very closely related species?
A. Genes are unable to be passed on from each other.
B. There is a reproductive isolation between the two species.
C. They shared a common ancestor recently in evolutionary time.*
D. They are unable to produce hybrid offspring upon interbreeding.
5. What do sponges lack that separates it from other groups of animals?
A. Body cavity
B. True tissues*
C. Sexual reproduction
D. Complete digestive tract
6. The leg structures of many different vertebrates are quite similar in number and
location of bones. Most scientists would probably explain this on the basis of what
significant concept?
A. Common society
B. Chance occurrence
C. Needs of an organisms
D. Inheritance of acquired traits*
7. Which of the following is a shared characteristic of all chordates?
A. Movable Jaws
B. Bony vertebrae
C. Dorsal nerve cord*
D. Four-chambered heart
8. The wing of the bat and the forelimb of the dog are said to be homologous structures.
This indicates what essential concept?
A. They have the same function.
B. Bats evolved from a lineage of dogs.*
C. The limb bones are anatomically identical.
D. Their structures are similar due to common ancestry.
9. What explains the observation about the similarities in DNA sequences of humans and
chimpanzees?
A. Chimpanzees evolved with humans.
B. Humans evolved from chimpanzees.
C. Humans and chimpanzees are not closely related.
PRIVATE EDUCATION ASSISTANCE COMMITTEE

MET #4: The Process of Evolution

Lesson # 2. Cladistics and Phylogeny

D. Humans and chimpanzees share a common ancestor.*

10. Which of the following pieces of evidence most strongly supports the common origin
of all life on Earth?
A. All organisms require energy.
B. All organisms reproduce sexually.
C. All organisms have undergone evolution.
D. All organisms share the same genetic code.*

Evaluate the student in the Prerequisite Assessment. Based on their levels, the
following pre-lesson remediation activity will be given to them appropriately.
● A score of 0-3 correct words out of 16 belongs to the “Insufficient Level”.
● A score of 4-7 correct words out of 16 belongs to the “Fairly Sufficient Level”.
● A score of 8-10 correct words out of 16 belongs to the “Sufficient Level”.

Pre-lesson Remediation Activity:

1. For Students with Insufficient Level of Prerequisite Content-knowledge and/or
Skill(s):
Reading activity: Students will be given readings about the topic and answer the
following questions.

Reading Material:
During Darwin's trip to the Galapagos Islands located off the coast of South America,
Darwin observed that the individual islands differed from each other in climate and soil.
He also observed that the plants and animals on the islands differed. The tortoises on
different islands had different shells, and it was possible to tell which island the tortoise
came from by looking at the shell. Darwin's observations helped him formulate his
theory of evolution on how organisms change, or evolve, over time and how evolution
occurs by natural selection.
Natural selection explains the great diversity of life. Over time, the traits that are best
suited to the environment will prevail and over time, the species will evolve. Organisms
with physical traits that are best fitted to the environment will survive. Fitness refers to
how well an organism is able to get food and produce fertile offspring. If there were two
organisms with two different traits, the "more fit* organism would be better adapted to
the environment than the other organism. Unlike the idea of inheritance of acquired
characteristics, the phenotypes (and the underlying genotypes) of the organisms are
the only important things to consider when understanding natural se-lection. An
individual does not evolve; a population does. The survival and reproduction of the
animals with the best traits to the environment causes a change in the genetic diversity
of the population.
Humans can affect the evolution of a population or species by artificial selection.
Artificial selection works much like natural selection does, but with humans, instead of
nature, favoring specific traits. Evidence of Evolution focuses on fossil records,
comparative anatomy, comparative embryology, and direct observation that
demonstrates how life diversifies and adapts over time.

Process Question 1: What is evolution?

PRIVATE EDUCATION ASSISTANCE COMMITTEE

MET #4: The Process of Evolution

Lesson # 2. Cladistics and Phylogeny

Process Question 2: How do organisms evolve?

2. For Students with Fairly Sufficient Level of Prerequisite Content-knowledge and/or

Skill(s):

The students will be given an image to analyze. Set of questions must be answered on
the comparative anatomy of the animal structure.

Question 1: What function do these structures share?

Question 2: How are these structures different?
Question 3: Do birds and insects share any structural similarities that would suggest that
they are closely related taxonomically?

Introduction:
The students will be oriented on the following:
1.

● Time Frame: 3 Hours

● Means of Communication: E – mail, LMS chatbox, Facebook messenger, call

and text.

2. Present to the students the Knowledge (RUA) they are expected to gain from
learning the topic/lesson
Remember: List down all possible relationships that can be derived from the
phylogenetic trees.
Understand: Classify organisms based on the provided characteristics.
Apply: Construct a simple cladogram/phylogenetic tree for a chosen group of
organisms.
3. Context where the student is going to apply his/her learning (In what PAA/EFAA
and personal use?)

● Students hone their classification skills using the context of cladograms.

PRIVATE EDUCATION ASSISTANCE COMMITTEE

MET #4: The Process of Evolution

Lesson # 2. Cladistics and Phylogeny

● Students will produce a cladogram/phylogenetic tree of closely related

organisms.

● Application of learning / outcome: Students will develop an in-depth

comprehension of the evolutionary relationship of organisms as the foundation
for promoting an effective plan for the protection and conservation of species.
(Drawing attention to meaning)

Motivational Activity: Who is my Relative? Drawing Attention to Meaning

Students will be presented a picture of an animal (e.g., cat) and will give other
animals that they believe to be the closest relative of that animal.
The teacher may ask the following questions:
▪ What makes the two organisms closely related to each other?
▪ What makes the two organisms different from each other?

4. Overview of the lesson Drawing Attention to Meaning

The study of evolution has already established the idea that all organisms shared a
common ancestor. As new species emerged from these common ancestors, variations
were seen in each species that made them unique. However, similarities among
different groups are still visible to some extent. To visualize how each organism is
related to each other, scientists use cladograms to establish these relationships to
better understand life in its various groups.
Students will be given pictures of the following organisms: worm, spider, carpenter ant,
house fly, and dragonfly. They shall study the different parts they can see in each
organism by answering the following character matrix:

The teacher may ask the following questions:

a. What characteristic is similar to all organisms?
b. Which organisms have the most shared characteristics?
c. Why do you think these organisms have varied levels of similarities?

Student’s Experiential Learning: (Note: Use the Flexible Learning Activity Identified
for the topic/lesson relative to the General Enabling Teaching Strategy) Prompting
Connections to Prior Knowledge
Systematics is the study of the diversity of organisms in the evolutionary context. It
intends to use phylogeny in classifying organisms. Phylogeny is the study of the
evolutionary history and relationships among organisms. Evidence from a wide variety
of sources including paleontology, embryology, morphology, anatomy and molecular
PRIVATE EDUCATION ASSISTANCE COMMITTEE

MET #4: The Process of Evolution

Lesson # 2. Cladistics and Phylogeny

biology can be used to establish phylogeny.

Over the last few centuries systematists have developed different approaches to show
relationships among organisms. The most commonly used is cladistics.

NOTE. The intervention to address the problem will be done here. Teachers will
be coached in terms of what content should be focused on.

Chunk 1: Cladistics
Formative Question: How do cladistics help in the present system of
classification? Prompting for Effortful Thinking + Using Examples and
Non-examples

Cladistics studies relationships between taxa using shared derived characters. The
basic assumption behind cladistics is that members of a group share a common
recent ancestor and are thus more "closely related" to one another than they are to
other groups of organisms. Related groups of organisms are recognized because they
share a set of derived characters. These derived characters were inherited from a
recent ancestor.
Cladistics is a method of classifying organisms into groups of species called clades
(from Greek ‘klados' = branch)
Each clade consists of an ancestral organism and all of its evolutionary descendants.
Members of a clade will possess common characteristics as a result of their shared
evolutionary lineage
Clades can be organized according to branching diagrams (cladograms) in order to
show evolutionary relationships

Cladograms are tree diagrams where each branch point represents the splitting of two
new groups from a common ancestor
● Each branch point (node) represents a speciation event by which distinct
species are formed via divergent evolution
Cladograms show the probable sequence of divergence and hence demonstrate the
likely evolutionary history (phylogeny) of a clade
● The fewer the number of nodes between two groups the more closely related
they are expected to be
Cladograms can show evolutionary relationships and demonstrate how recently two
PRIVATE EDUCATION ASSISTANCE COMMITTEE

MET #4: The Process of Evolution

Lesson # 2. Cladistics and Phylogeny

groups shared a common ancestry

● As each node represents a point of divergence, closely related species will be
separated by fewer nodes

According to a cladogram outlining the evolutionary history of humans and other

primates:
● Humans, chimpanzees, gorillas, orangutans and gibbons all belong to a
common clade – the Hominoids
● The Hominoid clade forms part of a larger clade – the Anthropoids – which
includes Old World and New World monkeys

Constructed cladograms all typically share certain key features:

Root – The initial ancestor common to all organisms within the cladogram
(incoming line shows it originates from a larger clade)
Nodes – Each node corresponds to a hypothetical common ancestor that
speciated to give rise to two (or more) daughter taxa
Outgroup – The most distantly related species in the cladogram which functions
as a point of comparison and reference group
Clades – A common ancestor and all of its descendants (i.e. a node and all of
its connected branches)

Constructing Cladograms
Cladograms can be constructed based on either a comparison of morphological
(structural) features or molecular evidence. Historically, structural features were used
to construct cladograms, but molecular evidence is now more commonly used.
1. Using Structural Evidence
Step 1: Organize selected organisms according to defined characteristics
Use characteristics that are developmentally fixed (i.e. innate) and not influenced by
environmental pressures
PRIVATE EDUCATION ASSISTANCE COMMITTEE

MET #4: The Process of Evolution

Lesson # 2. Cladistics and Phylogeny

Step 2: Sequentially order organisms according to shared characteristics to construct

a cladogram
Grouping of organisms may be facilitated by constructing a Venn diagram prior to
developing a cladogram. Each characteristic will be represented by a node, with more
common characteristics representing earlier nodes. The species with the least number
of characteristics in common will represent the outgroup (establishes baseline
properties)

2. Using Molecular Evidence

Step 1: Select a gene or protein common to a range of selected organisms
● Examples of molecules which are ubiquitously found in many animals include
haemoglobin and cytochrome c
Step 2: Copy the molecular sequence (DNA or amino acid) for each of the selected
organisms
● Use online databases such as Genbank or Ensembl to identify relevant DNA or
amino acid sequences
● Sequences can be collated in a Word document and then saved as a document
in plain text format (.txt)
● Before each sequence, designate a species name preceded by a forward arrow
(e.g. '>Human’ or ‘>Chimpanzee’)
Step 3: Run a multiple alignment to compare molecular sequences (DNA or amino
acid)
● Multiple alignment software compares DNA or protein sequences for similarities
and differences
● Closely related species are expected to have a higher degree of similarity in
their molecular sequence
● Clustal Omega is a free online tool that will align multiple DNA or amino acid
sequences for comparison
Step 4: Generate a phylogeny tree (cladogram) from multiple alignment data
● Clustal Omega can generate branched phylograms after a sequence alignment
is completed (select ‘Phylogenetic Tree’)
● Below is a plain text file that can be uploaded to compare amino acid
sequences from different species:
PRIVATE EDUCATION ASSISTANCE COMMITTEE

MET #4: The Process of Evolution

Lesson # 2. Cladistics and Phylogeny

● HBA – Haemoglobin alpha chain (amino acid sequence) from various species

Chunk 2: Phylogeny
Formative Question: How does phylogeny help in the present system of
classification? Prompting for Effortful Thinking + Using Examples and Non-
examples
The foremost question that every systematist would ask himself is what makes one
unique and what makes one similar to one another. One of the major tasks of
systematics is to determine by means of comparison what the unique properties of
each species and higher taxon are. Another is to determine what properties certain
taxa have in common and the biological causes of the differences or shared
characters. In this way, one begins to understand the relatedness and relationships of
organisms in the tree of life. Systematics has been used to construct the evolutionary
relationship of life’s diverse forms. In recent years, we have gained insight into the very
deepest branches of the tree of life through molecular systematics.
Systematics is the study of the kinds and diversity of organisms and of any and all
relationships among them. Tracing phylogeny is one of the goals of systematics;
hence, it is considered as the study of biological diversity in an evolutionary context.
Systematists use data ranging from fossils to molecules and genes to infer
evolutionary relationships. This information enables biologists to construct a
comprehensive tree of life that will continue to be refined as additional data are
collected.
Biologists use phylogenetic trees for
many purposes, including:
- Testing hypotheses about
evolution
- Learning about the
characteristics of extinct species and
ancestral lineages
- Classifying organisms
The connection between classification and phylogeny is that hierarchical classification
is reflected in the progressively finer branching of phylogenetic trees. The branching
patterns in some cases match the hierarchical classification of groups nested within
more inclusive groups. In other situations, however, certain similarities among
organisms may lead taxonomists to place a species within a group of organisms (for
example genus or family) other than the group to which it is closely related. If
PRIVATE EDUCATION ASSISTANCE COMMITTEE

MET #4: The Process of Evolution

Lesson # 2. Cladistics and Phylogeny

systematists conclude that such a mistake has occurred, the organism may be
reclassified (that is placed in a different genus or family) to accurately reflect its
evolutionary history.
The Connection between Classification and Phylogeny.
Hierarchical classification can reflect the branching patterns of phylogenetic trees. The
figure below shows the tree that traces possible evolutionary relationships between
some of the taxa within order Carnivora, itself a branch of class Mammalia. The branch
point (1) represents the most recent common ancestor of all members of the weasel
(Mustelidae) and dog (Canidae) families. The branch point (2) represents the most
recent common ancestor of coyotes and gray wolves.
Activity 1: Constructing Phylogeny
Investigation: Is a dog more closely
related to a coyote or a wolf?

Part 1
1. Examine the images and descriptions
above.
Underline any similarities between the
dog and the wolf.
Place a star next to any coyote traits
that are similar to the dog.
2. Based on appearance alone, which
do you think is the most closely related
to a dog?

Part 2: Phylogenetic Trees

Once scientists learned how to sequence DNA, that became a great resource for
determining relationships. A phylogenetic tree shown below is based on DNA
evidence and similarities in appearance.
3. Branch points are called “nodes” and they indicate a more recent common
ancestor from which each branch species has descended from.
- Place a box to indicate the node or common ancestor of all the fox species.
- Place a triangle🔺 to indicate the node or common ancestor of all the canis
species.
4. Which two members of the canis group have the most recent common ancestor?
___________________
5. A species name has two words, a system called BINOMIAL NOMENCLATURE.
The first word of a species name refers to its GENUS. For example, wolves, coyotes
and dogs all belong to the genus “CANIS.”
What is the genus for the foxes? ________________________________
6. In some cases, a third name is given to the animal to indicate a SUBSPECIES.
What animal on the chart is a subspecies?
_______________________________________
What is this animal’s full scientific name?
_______________________________________
7. Final Synthesis: Is a dog more closely related to a coyote or a wolf?
PRIVATE EDUCATION ASSISTANCE COMMITTEE

MET #4: The Process of Evolution

Lesson # 2. Cladistics and Phylogeny

______________________
Provide EVIDENCE from the phylogenetic tree to support your position.

Synthesis Prompting for Effortful Thinking + Using Examples and Non-examples

How do cladistics and phylogeny help in the present system of classification?
● Students will understand that cladistics and phylogeny help describe and
present a better system of classification.
● Cladistics study relationships between taxa using shared derived
characters.both structures and molecular evidence.
● Phylogeny is the representation of the evolutionary history and relationships
between groups of organisms.

RUA of a Student’s Learning: Drawing Attention to Meaning + Prompting

Connections to Prior Knowledge

This is the part where the students express their learning in their own unique ways.
They will manifest learning of the knowledge, skills, and attitudes they achieve in this
lesson through their individual learning style (visual, auditory, reading and writing, and
kinesthetic).
Remember: List down all possible relationships that can be derived from the
phylogenetic trees.
Understand: Classify organisms based on the provided characteristics.
Apply: Construct a simple cladogram/phylogenetic tree for a chosen group of
organisms.

Post-lesson Remediation Activity:

For Students with Insufficient Level of Prerequisite Content-knowledge and/or

Skill(s) will do the following:

Matching Type. Examine the cladogram below. Each letter represents a derived
characteristic. Match the letter to its characteristic.
PRIVATE EDUCATION ASSISTANCE COMMITTEE

MET #4: The Process of Evolution

Lesson # 2. Cladistics and Phylogeny

1._________ Wings
2._________ 6 legs
3._________ Segmented Body
4._________ Double set of wings
5._________ Cerci (back appendages)
6._________ Crushing mouthparts
7._________ Legs
8._________ Curly Antennae

For Students with Fairly sufficient Level of Prerequisite Content-knowledge

and/or Skill(s):
Picture Analysis. Answer the question comprehensively. Refer to the image below.

The students will explain the concepts in 3 essential points. The teacher will provide
feedback.

● How can you compare gymnosperms to angiosperms in terms of the

evolution of seeds and vascular tissue?

References:
● Environmental Resistance. Retrieved from:
PRIVATE EDUCATION ASSISTANCE COMMITTEE

MET #4: The Process of Evolution

Lesson # 2. Cladistics and Phylogeny

https://www.biologyonline.com/dictionary/environmental-resistance
● What is Biotic Potential? Retrieved from:
https://populationeducation.org/what-biotic-potential/
● Carrying Capacity. Retrieved from:
https://www.nationalgeographic.org/topics/resource-library-carrying-
capacity/?q=&page=1&per_page=25