Republic of the Philippines

Department of Education
Regional Office IX, Zamboanga Peninsula

SHS

GENERAL BIOLOGY 2
2 nd Semester – Module 6
SYSTEMATICS:
Phylogeny and Cladistics

Name of Learner: ___________________________

Grade & Section: ___________________________
Name of School: ___________________________
General Biology 2 – Grade 11/12
Support Material for Independent Learning Engagement (SMILE)
Module 6 Systematics: Phylogeny and Cladistics
First Edition, 2021

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Development Team of the Module

Writer: Kent Alexis R. Vallecer
Editor: Shenah Mae J. Cuevas
Reviewers: Shenah Mae J. Cuevas, Zyhrine P. Mayormita
Layout Artist: Chris Raymund M. Bermudo
Management Team: Virgilio P. Batan Jr. - Schools Division Superintendent
Lourma I. Poculan - Asst. Schools Division Superintendent
Amelinda D. Montero - Chief Education Supervisor, CID
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Ronillo S. Yarag - Education Program Supervisor, LRMS
Zyhrine P. Mayormita - Education Program Supervisor, Science
Leo Martinno O. Alejo - Project Development Officer II, LRMS
Janette A. Zamoras - Public Schools District Supervisor
Joselito S. Tizon - Principal, Zambonga del Norte NHS

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 What I Need to Know
This module was designed and written with you in mind. The lessons are
arranged following the content standards of Senior High School STEM currcilum
and aligned with the corresponding learning competencies.

Before tackling this module, the students must already be familiar with
basic evolutionary concepts and have had already been introduced to the basics
of taxonomy. Within this module is a thorough discussion on cladistics, an
approach on systematics that aims to determine not only species diversity but the
evolutionary relationships of organisms with each other.

At the end of this module, the students are expected to:

1. Identify the unique/distinctive characteristics of a specific taxon

relative to other taxa (STEM_BIO11/12IIIhj-15)
2. Describe species diversity and cladistics, including the types of
evidence and procedures that can be used to establish evolutionary
relationships (STEM_BIO11/12IIIhj-16)

Specifically speaking, students should be able to:

1. Make cladograms;
2. Identify characteristics that is unique among taxa using
cladograms; and
3. Interpret cladograms.

What's In
LESSON 1: PHYLOGENY AND CLADISTICS

In the previous module, you have learned that Systematics is the study of
the diversity of organisms (Solomon et al., 2018). In order to classify organisms,
scientists have long used the Linnaean Classification System.

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Activity 1. What's the Sequence?
Direction: Recall the hierarchy established by the Linnaean Classification System
and fill in the blanks in the hierarchical diagram below to complete the Linnaean
Classification System.

Domain
1.
2.

3.
Order
4.
5.

Species

It is settled that systematics does not only aim to classify and describe
organisms. It also aims to establish evolutionary relationships among organisms.

So far, you have learned that taxonomy is the science of naming, describing,
and classifying organisms. However, it is established that systematics does not
only aim to classify and describe organisms. The goal of systematics is also to
establish evolutionary relationships among organisms.

Activity 2. Fill Me
Direction: List down two advantages and two disadvantages of the traditional
Linnaean system.

The Linnaean System

Advantage Disadvantage
1. 1.
2. 2.

What's New
Indeed, while the traditional Linnaean system conveniently places organisms
in various hierarchical classifications, it is quite apparent that the only basis for
such classification is an organism's observable features. What's more, in
determining the basis for classifications, characteristics are often ignored in favor
of other preferred characteristics. Such a system can be highly biased and
subjective.

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 However, scientists have adopted a modern system of classification which
not only categorizes organisms but also tells you the evolutionary history or
phylogeny of that organism. This is called the phylogenetic system.

In this module, you will learn about a certain type of phylogenetic system
called cladistics.

Activity 3. Understanding the Cladogram

Direction: Examine the illustration below and answer the questions thereafter.

Fig. 1. A cladogram of some familiar animals.

Retrieved from https://ib.bioninja.com.au/standard-level/topic-5-evolution-and-biodi/54-cladistics/cladograms.html

Activity Questions:

1. What characteristics do primates and rodents have in common?

2. Which group of animals are birds more closely related to? Reptiles or
Rodents?
3. What do amphibians, reptiles, birds, rodents, and primates have in common?
4. What characteristic is unique only to birds and reptiles?
5. Fish and primates have a common ancestor. What characteristic does this
ancestor have?

What Is It
Species Diversity and Systematics

It is estimated that there are about 8.7 to 10 million species of eukaryotes

living today, but only 1.5 million species have been described (Solomon et al.,
2018). What's more jarring is that of all the species that have ever existed on Earth,
99.9 percent of them are now extinct. Even so, scientists discover tons of new
species every year. Species diversity is a rather vague term that could mean species
richness, taxonomic/phylogenetic diversity, or species evenness (Xu et al., 2020).

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 Simpson (2006), defines systematics as "the scientific study of the diversity of
organisms and their evolutionary relationships". The Linnaean System of
Classification, as discussed in the previous modules, groups organisms into
hierarchical categories for classification (See Fig. 2).

Fig. 2. Classifications of organisms according to the Linnaean system.

Retrieved from https://www.britannica.com/science/taxonomy/The-Linnaean-system

Fig. 3. Phylogenetic tree showing the three domains of life.

Retrieved from https://organismalbio.biosci.gatech.edu/biodiversity/phylogenetic-trees/

Cladistics

There are many different types of phylogenetic trees. In this module, we will
primarily focus on cladograms. Cladograms (See Fig. 4) are a kind of phylogenetic
tree that visually represents the criterion in which organisms are organized in a
system called cladistics (Campbell & Reece, 2008).

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 Cladistics is a method of classification of organisms according to the measure
of homologous characteristics shared by these organisms and their common
ancestor (Campbell & Reece, 2008). In cladistics, the higher the proportion of
characteristics that two organisms share, the more recently they diverged from a
common ancestor. Traditional systematics, like the Linnaean system, place
together organisms with similar or homologous characteristics. On the other hand,
cladistics places together organisms belonging to the same clade (Kardong, 2012).

A taxon (pl. taxa) is a named group of organisms. In Fig. 4, an example of a

taxon would be "Human," "Chimpanzee," "Bear," etc. Each branch in a cladogram
represents a clade, a group of organisms with a common ancestor. Thus, in Fig. 4,
"Chimpanzee" and "Human" together would belong in a single clade with a common
ancestor at "Node G." Furthermore, if we were to group "Chimpanzee" and "Human"
in a single taxon called "Ape," such a taxon would be a valid clade. Indeed, a taxon
can also be a clade. Each branching point referred to as a node (depicted by a
circle), represents the divergence, or splitting, of two or more new groups from a
common ancestor. Thus, the node represents the most recent common ancestor of
each clade depicted by the branches. A sister group is a taxon most closely related
to the taxon we are studying. Thus, in Fig. 4, if we were examining the taxon
"Human," its sister group would be the taxon "Chimpanzee." In this way, a
cladogram uses the positions of branch points to illustrate the hypothesized
evolutionary relationships among taxa. Each of the branches is formed based on
evidence in terms of observable traits that are shared by the organisms at the end
of the branch but are not found in organisms on other branches. Shared
characteristics can be indicated by labels or by bars across the branches (Campbell
& Reece, 2008).

Fig. 4. A cladogram depicting some common vertebrates.

Retrieved from Campbel & Reece (2008)

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 In constructing a cladogram, relationships between groups are recognized on
the basis of derived characteristics. The more derived characteristics there are
between two groups, the more likely it is they are closely related. The assortment of
taxa we are interested in examining is our ingroup; the outgroup is close to but not
part of this assortment and is used as a reference. In particular, the outgroup
helps us make decisions about which character state represents the derived
condition (Kardong, 2012). Hence, in Fig. 4, if we are interested in the evolutionary
relationships of "Lamprey", "Sunfish", "Frog", "Lizard", "Bear", "Chimpanzee", and
"Human" only. Those taxa would be the ingroup while the taxon "Lancelet" would
be the outgroup.

Cladograms show that previous classifications reflect three different types of

taxonomic relationships (see Fig. 5): monophyletic groups, paraphyletic groups,
and polyphyletic groups (Solomon et al., 2018). Monophyletic groups are groups of
taxa that consists of an ancestral species and all its descendants; paraphyletic
groups consist of a species and some but not all of its descendants; and
polyphyletic groups are taxa with different characteristics (Campbell & Reece,
2008). A taxon is only a clade if it is monophyletic.

Fig. 5. Monophyletic, paraphyletic, and polyphyletic groups. Grouping 1, consisting of the

seven species B-H, is a monophyletic group, or clade. Grouping 2 consists of an ancestor (A in
this case) and some, but not all, of that ancestor's descendants and is thus a paraphyletic
group. Grouping 3 is polyphyletic, which means that it lacks the common ancestor (A) of the
species in the group. Retrieved from Campbell & Reece (2005)

Evidence Establishing Evolutionary Relationships

The main goal of systematics is to reconstruct the evolutionary history of

organisms from a common ancestor. To achieve this, systematists employ a wide
range of evidence, from shared traits and characteristics to geographic
distributions and strata positions of fossils, and even molecular traits like an
organism's DNA (Solomon et al., 2018).

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Homologous Characteristics

Homologous characteristics are those which are shared by organisms that

come from a common ancestor (Campbell & Reece, 2008). For example, most
vertebrates have a similar number and sequence of bones in the forelimbs since a
common ancestor of all these animals had the same bone sequence (see Fig. 6).
Verily, these similarities indicate a common ancestry among these animals.

Fig. 6. Bone structure in the forelimbs of some animals.

Retrieved from https://www.biologyonline.com/dictionary/homologous

However, not all similar characteristics are homologous. These similarities

might arise due to convergent evolution. These are called analogous characteristics
(Campbell & Reece, 2008). A classic example of this is the wings of bats and the
wings of birds. The wings of a bat evolved independently from those of birds. Birds
and bats do not share a common ancestor that had wings. A grouping containing
birds and bats together would produce a polyphyletic group which is not a valid
clade. Systematists must not confuse homologous characteristics from analogous
characteristics

Molecular Homologies

Homologies are not always exhibited phenotypically. Some evolutionary

changes may happen at the molecular level. Two different species may appear
exactly the same, but their DNA, proteins, and amino acids may be very different
(Simpson, 2006). That is why, aside from the visible homologous characteristics,
scientists also examine the molecules of organisms.

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 Thus, systematists often use DNA sequences of organisms to construct
cladograms.

Constructing a Cladogram

Constructing a cladogram usually involves outgroup analysis. Outgroup

analysis is a "research method for estimating which attributes are shared derived
characters in a given group of organisms" (Solomon et al., 2018). An ideal outgroup
is the closest relative of the group being studied and has not been highly modified
since its origin. An outgroup is likely to retain the ancestral state for characters
being used in the analysis, allowing the researchers to identify the evolutionary
changes leading to derived characters (Solomon et al., 2018).
Solomon (2018) has outlined the steps in constructing a cladogram. To
illustrate these steps, we will refer to illustrations in his book – Diversity in Biology:
Definitions, Quantifications, and Models.
The first step is to select the taxa, which may be individuals, species, genera,
or any other taxonomic level. In his example, Solomon (2018) used lancelets,
lamprey, sunfish, frog, lizard, bear, chimpanzee, and human. The next step is to
select the homologous characteristics to be analyzed. Then, the different conditions
of the characteristics were determined. For simplicity's sake, the conditions were
only either present or absent. It might be best to organize these characteristics in a
table. Table 1 shows the homologous characteristics for the taxa that we are using
as an example. The next and final step is to construct the cladogram itself by
organizing the characteristics into their correct evolutionary steps (Solomon et al.,
2018). This often takes trial and error. Fig. 8 shows a step-by-step process of
creating a cladogram from the information found in Table 1 as illustrated by
Solomon (2018).

Table 1. Homologous characteristics and their states for the chosen taxa (A =
absent, P = present). Retrieved from Solomon (2018).

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 Fig. 8. Step by step (a-b) process of organizing the data in Table 1 into a cladogram.
Retrieved from Solomon (2018)

What's More
Activity 4. The Cladogram
Direction: With the cladogram below as a basis, answer the following questions in
the space provided.

Skin Two
shields Horn

Horn

Fig. 9. A hypothetical cladogram with taxa

designated as the letters O, A, B, C, and D.
Retrieved from Kardong (2012)

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 1. Which is the outgroup here? O, A, B, C, or D?
2. Which is the sister of the group of D?
3. Grouping A, B, and D together (excluding C) creates which kind of
grouping?
4. Which taxa share the characteristic of "skin shields"?
5. What characteristic is homologous among A, B, C, and D?
6. Write down the taxa that would make a paraphyletic grouping.
7. Write down the taxa that would make a monophyletic grouping.
8. Which characteristic is absent in O but is a homologous characteristic
among A, B, C, and D?
9. Which is a unique characteristic present in A, B, and C which is absent
in D?
10. Will grouping O, A, B, C, and D create a valid clade?

What I Have Learned

Activity 5. Complete Me
Direction: Fill in the blanks with the words from the word bank below.

cladistics phylogeny systematics

cladogram species diversity taxonomy

1. _________________ refers to the diversity of organisms which may be in

terms of species richness, taxonomic and phylogenetic diversity, and
species evenness.

2. A _________________ is a visual representation of a system of constructing

phylogeny called cladistics.

3. Cladistics differ with traditional taxonomy in that it shows the

_________________ or evolutionary history of taxa.

4. _________________ is the study of the diversity of organisms and their

evolutionary relationships.

5. _________________ assumes the higher the proportion of characteristics

that two organisms share, the more recently they diverged from a
common ancestor.

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Activity 6. Matchy-match
Direction: Match Column A with Column B. Write the letter of the correct
answer in the space provided.

COLUMN A COLUMN B
______ 1. Taxa/taxon a. The group of taxa being examined in
a cladogram

______ 2. Outgroup b. A taxon used as a reference in

examining taxa in a cladogram
______ 3. Ingroup c. The taxon that is most closely
related to a certain taxon in a
cladogram.
______ 4. Sister group d. A named group of organisms.
e. The branching point in a cladogram
______ 5. Node

What I Can Do
Activity 7. Build Me Up
Direction: Construct a cladogram in the template provided using the data
provided in the table below.

TAXA CHARACTERISTIC
Mammary
Backbone Lungs Amniotic Egg
Glands
Goldfish Present Absent Absent Absent

Frog Present Present Absent Absent

Owl Present Present Present Absent

Rhino Present Present Present Present

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 Assessment
Direction: Read the questions carefully. Choose the best answer from the choices
provided.

1. Species diversity refers to the number of different species in a given

community. Which of the following is a component of species diversity?
i. Species richness
ii. Species evenness
iii. Population
iv. Taxonomic diversity
a. i and ii only c. ii, iii, and iv only
b. i,ii, and iii only d. i, ii, and iv only
2. Which of the following is NOT a piece of evidence used to establish an
evolutionary relationship?
a. Physical appearance and morphology
b. Fossil records and strata
c. Preferences based on subjectivity
d. Genetics and heredity
3. What type of characteristic is derived by evolution from a common ancestor?
a. Homologous characteristics
b. Analogous characteristics
c. Heterologous characteristics
d. Homeopathic characteristics
4. It refers to the grouping in a cladogram which consists of the ancestor
and some but not all of its descendants.
a. Paraphyletic c. Polyphyletic
b. Monophyletic d. Pareplegic
5. Cladistics is used to establish the evolutionary relationship among organisms.
What does it indicate when the proportion of characteristics that two
organisms share is high?
a. The two organisms recently diverge from a common ancestor.
b. The two organisms recently converge from a common ancestor.
c. The two organisms are distantly related to each other.
d. The two organisms are closely related to each other.
6. In constructing a cladogram, the relationship between the ingroup and
outgroup are recognized. What is the difference between the two groups?
a. The ingroup is a set of taxa that is investigated for evolutionary
relationships, while outgroup is a reference group that is distantly
related to the group being analyzed.
b. The ingroup is not under investigation, while outgroup is under
consideration.
c. The taxa of the ingroup are hypothesized to be more closely related to
each other while taxon in outgroup is hypothesized to be less closely
related to each other of the taxa under consideration.
d. The taxa of the ingroup are sister groups of the outgroup.

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For items 7-8, refer to Fig. 10 below

Fig. 10. A simple cladogram for various familiar animals.

Retrieved from https://www.slideshare.net/stubeck/cladograms-73805705

7. Which of the following is NOT TRUE about the "Chimp"?

a. It has a homologous characteristic with "Mouse".
b. It has a common ancestor with the "Perch" which has jaws.
c. "Chimp", "Pigeon", "Mouse" can be grouped in a clade together with
their ancestor.
d. Only "Chimp" has furs and mammary glands out of all the taxa.
8. Which of the following would make a monophyletic group?
a. Chimp, Mouse, Pigeon, Lizard and their common ancestor.
b. Chimp, Mouse, Lizard and their common ancestor.
c. All the taxa and their common ancestor except Perch.
d. Perch and Salamander and their common ancestor which has jaws.
9. Which of the taxa does Chimp has most in common with?
a. Mouse
b. Pigeon
c. Hagfish
d. Perch
10.Which of the following statements is correct?
a. Salamander, Lizard, Pigeon, Mouse, and Chimp have a homologous
characteristic that they derived from a common ancestor.
b. Perch and chimp have no homologous characteristics.
c. Fur and Mammary glands are analogous characteristics for Mouse and
Chimp.
d. The ancestor of the chimp is an organism that has feathers.

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 Additional Activities
Activity 8. Cladogram
Direction: Construct your own cladogram and follow the instructions below.

1. Examine the characteristics of the animals listed on the table below and
establish characteristics that they share and ones that are unique to each
group.
2. Using the table, indicate whether the characteristic is present or not. The
first one is done for you.

With cells
Octopus Present
Catfish Present
Crocodile Present
Dogs Present
Human Present

3. Using the data you have in your table, construct a cladogram in the space
provided below.

Answer Key General Biology 2 Module 6

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References

Printed

Campbell, N. A., & Reece, J. B. (2005). Biology (7th ed). Pearson, Benjamin
Cummings. Campbell, N. A., & Reece, J. B. (2008). Biology (8th ed). Pearson
Benjamin Cummings. Kardong, K. V. (2012). Vertebrates: Comparative anatomy,
function, evolution (6th ed). McGraw-Hill.
Simpson, M. G. (2006). Plant systematics. Elsevier/Academic Press.
Solomon, E. P., Martin, C. E., Martin, D. W., & Berg, L. R. (2018). Biology (11th
edition). Cengage Learning.

Electronic Source

Xu, S., Böttcher, L., & Chou, T. (2020). Diversity in biology: Definitions,
quantification and models. Physical Biology, 17(3), 031001.
https://doi.org/10.1088/1478-3975/ab6754

Images

Cain, A. J. (n.d.). Taxonomy. Britannica.

https://www.britannica.com/science/taxonomy Campbell, N. A., & Reece,
J. B. (2008). Biology (8th ed). Pearson Benjamin Cummings.
Cladograms. (n.d.). Bioninja. https://ib.bioninja.com.au/standard-level/topic-5-
evolution-and-biodi/54-cladistics/cladograms.html
Edgecombe, G. D., & Giribet, G. (2006). A century later—A total evidence re-
evaluation of the phylogeny of scutigeromorph centipedes
(Myriapoda:Chilopoda).
Invertebrate Systematics, 20(5), 503. https://doi.org/10.1071/IS05044
Homologous. (n.d.). Biology Online.
https://www.biologyonline.com/dictionary/homologous Kardong, K. V.
(2012).
Phylogenetic trees and Geologic Time. (n.d.). Organismal Biology.
https://organismalbio.biosci.gatech.edu/biodiversity/phylogen
etic-trees/
Solomon, E. P., Martin, C. E., Martin, D. W., & Berg, L. R. (2018). Biology (11th
edition). Cengage Learning.
Vertebrates: Comparative anatomy, function, evolution (6th ed). McGraw-Hill

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 Region IX: Zamboanga Peninsula Hymn – Our Eden Land
Here the trees and flowers bloom Gallant men And Ladies fair Cebuanos, Ilocanos, Subanons, Boholanos, Ilongos,
Here the breezes gently Blow, Linger with love and care All of them are proud and true
Here the birds sing Merrily, The Golden beams of sunrise and sunset Region IX our Eden Land
liberty forever Stays, Are visions you'll never forget
Oh! That's Region IX Region IX
Our..
Here the Badjaos roam the seas Hardworking people Abound, Eden...
Here the Samals live in peace Every valleys and Dale Land...
Here the Tausogs thrive so free Zamboangueños, Tagalogs, Bicolanos,
With the Yakans in unity

My Final Farewell
Farewell, dear Fatherland, clime of the sun caress'd Let the sun draw the vapors up to the sky,
Pearl of the Orient seas, our Eden lost!, And heavenward in purity bear my tardy protest
Gladly now I go to give thee this faded life's best, Let some kind soul o 'er my untimely fate sigh,
And were it brighter, fresher, or more blest And in the still evening a prayer be lifted on high
Still would I give it thee, nor count the cost. From thee, 0 my country, that in God I may rest.

On the field of battle, 'mid the frenzy of fight, Pray for all those that hapless have died,
Others have given their lives, without doubt or heed; For all who have suffered the unmeasur'd pain;
The place matters not-cypress or laurel or lily white, For our mothers that bitterly their woes have cried,
Scaffold or open plain, combat or martyrdom's plight, For widows and orphans, for captives by torture tried
T is ever the same, to serve our home and country's need. And then for thyself that redemption thou mayst gain

I die just when I see the dawn break, And when the dark night wraps the graveyard around With only
Through the gloom of night, to herald the day; the dead in their vigil to see
And if color is lacking my blood thou shalt take, Break not my repose or the mystery profound
Pour'd out at need for thy dear sake And perchance thou mayst hear a sad hymn resound 'T is I, O
To dye with its crimson the waking ray. my country, raising a song unto thee.

My dreams, when life first opened to me, And even my grave is remembered no more
My dreams, when the hopes of youth beat high, Unmark'd by never a cross nor a stone
Were to see thy lov'd face, O gem of the Orient sea Let the plow sweep through it, the spade turn it o'er
From gloom and grief, from care and sorrow free; That my ashes may carpet earthly floor,
No blush on thy brow, no tear in thine eye. Before into nothingness at last they are blown.

Dream of my life, my living and burning desire, Then will oblivion bring to me no care
All hail ! cries the soul that is now to take flight; As over thy vales and plains I sweep;
All hail ! And sweet it is for thee to expire ; Throbbing and cleansed in thy space and air
To die for thy sake, that thou mayst aspire; With color and light, with song and lament I fare, Ever
And sleep in thy bosom eternity's long night. repeating the faith that I keep.

If over my grave some day thou seest grow, My Fatherland ador'd, that sadness to my sorrow lends Beloved
In the grassy sod, a humble flower, Filipinas, hear now my last good-by!
Draw it to thy lips and kiss my soul so, I give thee all: parents and kindred and friends
While I may feel on my brow in the cold tomb below The For I go where no slave before the oppressor bends, Where faith
touch of thy tenderness, thy breath's warm power. can never kill, and God reigns e'er on high!

Let the moon beam over me soft and serene, Farewell to you all, from my soul torn away,
Let the dawn shed over me its radiant flashes, Friends of my childhood in the home dispossessed!
Let the wind with sad lament over me keen ; Give thanks that I rest from the wearisome day!
And if on my cross a bird should be seen, Farewell to thee, too, sweet friend that lightened my way; Beloved
Let it trill there its hymn of peace to my ashes. creatures all, farewell! In death there is rest!

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