S YST EMA TICS

BASED ON EVOLUTIONARY RELATIONSHIP

BY: ALFORQUE, CHIONG, AND JAMERO

ALFORQUE, CHIONG, & JAMERO GENBIO 2

What is this Module all about?

Systematics is the branch of biology that helps organize and classify the incredible
diversity of life on Earth based on evolutionary relationships. It allows scientists to
understand how different organisms are connected through a shared ancestry, just like
organizing books in a library so we can easily find and learn from them.

Today, we focused on how evolutionary traits and genetic evidence help scientists
determine the relatedness of organisms. Using tools like cladograms and phylogenetic
trees, we saw how shared characteristics can show common ancestry and help us group
organisms more accurately. This method of classification isn't just about physical traits, it
includes molecular data like DNA and RNA as strong evidence of evolutionary history.

What are you expected to do?

At the end of the module, the students must have:

identify the unique/distinctive characteristics of a specific taxon relative to other
taxas;
describe species diversity and cladistics, including the types of evidence and
procedures that can be used to establish evolutionary relationships; and
demonstrate the correct arrangement of taxonomic ranks by matching and
pasting the classification labels of a given organism.

Time Frame

April 7 - 15, 2025

ALFORQUE, CHIONG, & JAMERO GENBIO 2

SYTEMATICS
BASED ON EVOLUTIONARY RELATIONSHIP
Diversity is so immense that if one
wishes to put things together, huge
amount of work must be done. Imagine
walking into a library with tons of
different kinds of books and there is an
inevitable need to organize these
books so that information and
knowledge from them will be put into
better use. Systematics is analogous to
that scenario.

he system unto which the

living things were put into
T order by the scientists and
researchers underwent re -
visions and numbers of
collaboration before it had been
the way it is today. You will once again be immersed by the
beauty in the order that came from the
chaos of diversified life forms found on
Earth. It is also noteworthy that
systematics is also connected with
evolution. You will soon know how
science has tried to establish a way on
how to organize the data obtained from
various studies of living organisms and
their evolution.
 ALFORQUE, CHIONG, & JAMERO GENBIO 2

SYTEMATICS
BASED ON EVOLUTIONARY RELATIONSHIP
Classification - is the process of arranging objects, ideas or information
into groups based on shared characteristics or criteria. It is used to facilitate
finding, identifying, and studying of objects, ideas, or information.

TAXONOMY VS SYSTEMATICS
Taxonomy is primarily concerned with naming and classifying organisms
based on their similarities and differences. It involves creating hierarchical
groups (taxa) such as species, genus, family, order, class, phylum, and
kingdom. Taxonomists use morphological, anatomical, physiological, and
molecular characteristics to classify organisms into these groups. On the
other hand, systematics is a broader field that encompasses taxonomy but
goes beyond it. Systematics not only involves naming and classifying
organisms but also explores their evolutionary relationships.

ARISTOTLE'S SYSTEM OF CLASSIFICATION

In the fourth century, Aristotle (384-322 BC), the father of biology and
zoology, introduced a system for categorizing living organisms. He divided
organisms into two main groups: plants and animals. Animals were
categorized based on their mode of movement. He also distinguished
between animals with blood and those without blood. Additionally, he
classified animals according to their habitats and physical forms. In
contrast, plants were sorted based on their size of their stems.
 ALFORQUE, CHIONG, & JAMERO GENBIO 2

LINNEAN SYSTEM OF CLASSIFICATION

In 18th century, the father of Taxonomy, Carolus Linnaeus (1707–1778),
introduce the binomial nomenclature system, where each organism is given
a two part latin name consisting of its genus and species. He also created
the first formal, scientific classification system in the eighteenth century. It
was a taxonomy classification scheme. He categorized species according
to their observed morphology and behavior, just like Aristotle did. His work,
"Systema Naturæ" laid out a systematic approach to organizing and
naming living organisms, revolutionizing the way scientists classify and
communicate about the natural world.

The Linnaean system of classification consists of a hierarchy of groupings,

called taxa(singular, taxon). Taxa range from the kingdom to the species.
The kingdom is the largest and most inclusive grouping.

1. Domain: the broadest taxa or taxonomic category which contains closely

related kingdoms: Bacteria archaea and eukarya. They are placed based
on their cell composition and the differences in their nucleotide sequence
in the cell's ribosomal RNAs (rRNA).
2. Kingdom: the second highest rank which is composed of related phylum
or division. It's classification was based on the characteristics such as cell
structure, mode of nut, source of nutrition and body organization.
 ALFORQUE, CHIONG, & JAMERO GENBIO 2

LINNEAN SYSTEM OF CLASSIFICATION

After the discovery of the first unicellular organisms by Anton Van

Leeuwenhoek in 1674, scientists began to recognize unique characteristics
of microorganisms that cannot be placed in any of the two kingdoms of
living things. German naturalist, Ernst Haeckel (1834-1919), proposed a
third kingdom, which he called Protista. This kingdom included not just
bacteria but all unicellular organisms.

Later on, it was identified that prokaryotes are distinctly different from
single-celled eukaryotes. American biologist Herbert Copeland (1902-
1968) proposed a four-kingdom scheme. He classified prokaryotic
organisms (bacteria and blue-green algae) into a separate kingdom called
Monera. In 1969, Robert Whittaker, proposed a fifth kingdom called Fungi.
Kingdom Fungi included mushrooms, yeasts, and molds. Fungi were the
multicellular saprophytes or decomposers, and Protista represented
organisms that did not fit in any of the four kingdoms.

With advances in molecular biology in the 1970s, significant differences

were discovered inside prokaryotic cells, particularly with regard to their
cell membrane structure and cell wall composition. Carl Woese and his
colleagues at the University of Illinois proposed the division of Monera into
Eubacteria and Archaebacteria.
 WELL=KNOWN GENBIO 2

LINNEAN SYSTEM OF CLASSIFICATION

3. Phylum: consist of related classes. : It is a division of kingdom and forms
a grouping of similar characteristics organisms based on structural
features. Within the animal kingdom there are 35 total phyla, though 9 of
them are well-known.

4. Class: Each phylum is then divided into classes. Classes within the
chordata phylum include mammalia (mammals), reptilia (reptiles) and
osteichthyes (fish), among others.

5. Order: Order is a more specific rank than class. it consist of related

families.
 WELL=KNOWN GENBIO 2

LINNEAN SYSTEM OF CLASSIFICATION

6. Family: This category of taxonomic hierarchy consists of related genera.

7. Genus: is defined as a group of species that shares a common ancestor.

The first in the pair of names used worldwide to specify any particular
organism.

8. Species: the smallest and the most basic unit or category of

classification. A species is characterized as a collection of organisms with
comparable individuals with the ability to exchange DNA or breed with one
another.

TAXONOMY: BINOMIAL NOMENCLATURE

Carolus Linnaeus established the binomial nomenclature naming method in
his book Systema Naturae (1758). This approach assigns two names to
organisms. The genus group to which the creature belongs is indicated by
the first name in binomial nomenclature, and the secies group is indicated
by the second name. Because Latin is stable and has long been the
language of research and education, it is the language used in binomial
nomenclature.
 WELL=KNOWN GENBIO 2

Rules for writing the scientific names of organisms

include the following:

1. All the scientific names of organisms are usually Latin therefore they are
written in italics
2. The first word identifies the genus and the second word identifies the
species.
3. If printed in books or magazines, both names are italicized. If hand
written, both names should be underlined.

SPECIES CONCEPT
Measuring species diversity necessitates establishing a clear definition of
what constitutes a species. While we don't anticipate every individual
within a species to be the same, we need to evaluate the extent and nature
of variations among individuals that would prompt us to classify them as
separate species. Consequently, a species concept serves as a practical
definition of a species and/or a framework for assessing whether two
organisms belong to the same species.

Typological Species Concept - it is based on the idea that each

species is a distinct group of organisms that shares certain
characteristics, which distinguish them from other species. According
to Aristotle, species are unchanging, distinct, and a natural group of
organisms.
Biological Species Concept - according to Theodosius Dobzhansky and
Ernst Mayr, a species is a group of organisms that are able to
interbreed and produce fertile offspring.
Evolutionary Species Concept - a species is a single lineage of
ancestor-descendant sequence of populations with distinct identity
and evolutionary tendencies.
Phylogenetic species concept - species is a cluster of organisms that
are distinct from other cluster of organisms. Each cluster shows
evident patterns of ancestry and descent.
 ALFORQUE, CHIONG, & JAMERO GENBIO 2

THE DOMAIN CLASSIFICATION OF LIFE

FORMS
American Microbiologist Carl Woese together with Otto Kandler and Mark Wheelis
proposed in 1990 the creation of the new taxon called domain, a rank higher than
the kingdom. The most widely used and accepted biological classification system
has six kingdoms and three domains. The classification using the three-domain
system has been used for almost three decades. These three domains are Bacteria,
Archaea, and Eukarya.

THE THREE DOMAIN SYSTEMS

The Three Domain System, proposed by Woese and others, is an evolutionary model of
phylogeny based on differences in the sequences of nucleotides in the cell's ribosomal
RNAs (rRNA), as well as the cell's membrane lipid structure and its sensitivity to antibiotics.
Comparing rRNA structure is especially useful. Because rRNA molecules throughout nature
carry out the same function, their structure changes very little over time. Therefore
similarities and dissimilarities in rRNA nucleotide sequences are a good indication of how
related or unrelated different cells and organisms are.

There are various hypotheses as to the origin of prokaryotic and eukaryotic cells.
Because all cells are similar in nature, it is generally thought that all cells came from
a common ancestor cell termed the last universal common ancestor (LUCA). These
LUCAs eventually evolved into three different cell types, each representing a
domain. The three domains are the Archaea, the Bacteria, and the Eukarya.
 ALFORQUE, CHIONG, & JAMERO GENBIO 2

THE THREE DOMAIN SYSTEMS

1. Domain Bacteria
Bacteria (also known as eubacteria or "true bacteria") are prokaryotic cells that are
common in human daily life, encounter many more times than the archaebacteria.
Eubacteria can be found almost everywhere and kill thousands upon thousands of people
each year, but also serve as antibiotics producers and food digesters in our stomachs.
Domain bacteria is the group that includes all prokaryotic, single-celled bacteria
whose cell walls are composed of a polysaccharide called peptidoglycan. Domain bacteria
are so diverse that they can survive different environmental conditions.

a. Aerobic Bacteria - Some members of this group need

oxygen to survive.
e.g. Pseudomonas aeruginosa, Mycobacterium
tuberculosis
They have the ability to
detoxify oxygen with the help
of enzymes. The final electron
acceptor is molecular oxygen.
Water is produced from the
final electron acceptor. When
in the liquid medium, they are
seen on the surface of the
medium.
b. Anaerobic Bacteria - Bacteria that die
because of the presence of oxygen. The
bacteria that grow in the absence of
oxygen are called anaerobic bacteria. It
does not have the ability to detoxify oxygen.
The final electron acceptor is carbon
dioxide, sulfur, fumarate or ferric. Acetate-
like substances, methane, nitrate and
sulfide are produced by these bacteria.
When in the liquid medium, they are seen at
the bottom of the medium.
e.g. Escherichia coli
in terms of their mode of nutrition, some are autotrophs that can produce their own food,
but most are heterotrophs that depend on others for food. The kingdom under this domain
is the Eubacteria, which is also known as the true bacteria.
The Bacteria possess the following characteristics:
1. Bacteria are prokaryotic cells.
2. Like the Eukarya, they have membranes composed of unbranched fatty acid chains
attached to glycerol by ester linkages (Figure 1.3.31.3.3).
3. The cell walls of Bacteria, unlike the Archaea and the Eukarya, contain peptidoglycan.
4. Bacteria are sensitive to traditional antibacterial antibiotics but are resistant to most
antibiotics that affect Eukarya.
5. Bacteria contain rRNA that is unique to the Bacteria as indicated by the presence
molecular regions distinctly different from the rRNA of Archaea and Eukarya.
Bacteria include mycoplasmas, cyanobacteria, Gram-positive bacteria, and Gram-negative
bacteria.
 ALFORQUE, CHIONG, & JAMERO GENBIO 2

2. Domain Archaea
Organisms that are classified under the domain Archaea are perceived to be more
primitive than bacteria. They are considered to be more closely related to eukaryotes.
Their cell walls do not contain peptidoglycan, but a complex form of glycoprotein called
pseudopeptidoglycan. They are diverse in shape and mode of nutrition. Archaea are said
to be extreme thermophiles because of their ability to survive in extreme environmental
conditions.
The Archaea possess the following characteristics:
1. Archaea are prokaryotic cells.
2. Unlike the Bacteria and the Eukarya, the Archaea have membranes composed of
branched hydrocarbon chains (many also containing rings within the hydrocarbon
chains) attached to glycerol by ether linkages.
3. The cell walls of Archaea contain no peptidoglycan.
4. Archaea are not sensitive to some antibiotics that affect the Bacteria, but are sensitive
to some antibiotics that affect the Eukarya.
5. Archaea contain rRNA that is unique to the Archaea as indicated by the presence
molecular regions distinctly different from the rRNA of Bacteria and Eukarya.

Figure 1. Membrane Lipids of Archaea, Bacteria, and Eukarya. The Bacteria and the Eukarya have membranes composed of
unbranched fatty acid chains attached to glycerol by ester linkages. The Archaea have membranes composed of branched
hydrocarbon chains attached to glycerol by ether linkages.

Some members of domain archaea have been found to live in boiling ocean floors and in
mud marshes in the absence of oxygen. The kingdom under this domain is the
Archaebacteria.
Archaea often live in extreme environments and include methanogens, extreme halophiles,
and hyperthermophiles. One reason for this is that the ether-containing linkages in the
Archaea membranes is more stable than the ester-containing linkages in the Bacteria and
Eukarya and are better able to withstand higher temperatures and stronger acid
concentrations.

3. Domain Eukarya
Other main characteristics of the members of this group is the presence of
membrane-bound nucleus and other membrane-bound organelles. All members of this
group are called eukaryotes.
The Eukarya (also spelled Eucarya) possess the following characteristics:
1. Eukarya have eukaryotic cells.
2. Like the Bacteria, they have membranes composed of unbranched fatty acid chains
attached to glycerol by ester linkages (Figure 1.3.31.3.3).
3. Not all Eukarya possess cells with a cell wall, but for those Eukarya having a cell wall,
that wall contains no peptidoglycan.
4. Eukarya are resistant to traditional antibacterial antibiotics but are sensitive to most
antibiotics that affect eukaryotic cells.
5. Eukarya contain rRNA that is unique to the Eukarya as indicated by the presence
molecular regions distinctly different from the rRNA of Archaea and Bacteria.
 ALFORQUE, CHIONG, & JAMERO GENBIO 2

This domain includes Kingdom Protista, Kingdom Fungi, Kingdom Plantae, and Kingdom
Animalia.
Microbes are known to live in remarkably diverse environments, many of which are
extremely harsh. This amazing and rapid adaptability is a result of their ability to quickly
modify their repertoire of protein functions by modifying, gaining, or losing their genes.
This gene expansion predominantly takes place by horizontal transfer.
 ALFORQUE, CHIONG, & JAMERO GENBIO 2

EVOLUTIONARY CLASSIFICATION
Classification is the process of creating a hierarchical system of categories
based on the characteristics and natural relationships among organisms. There are
different systems of classifications based on the structure, habitats, behaviour and
various other characteristics of organisms.

Artificial System of Classification

The system of classification which uses few observable characters such as
habitat, colour and morphology etc., is called an artificial system of classification. In
this classification many organism do not seem to fit clearly into certain categories.

Examples:
Classification of organisms by Aristotle: Aristotle classified organisms into
three types based on the habitat. He classified animals into air dwellers, land
dwellers and water dwellers based on their habitat.
Classification of plants by Aristotle: Aristotle classified plants, during the
second century, based on the simple morphological characteristics such as
height and girth. The classification includes herbs, shrubs and trees.
Linnaean System of Classification: Carl Linnaeus classified 7,300 flowering
plants into 24 classes based on superficial morphological characteristics such
as the structure of the reproductive organs (number and arrangement of male
and female organs).

Natural System of Classification

The system of classification which uses all important characteristics of the
organisms like cytological, biochemical, developmental, physiological,
anatomical, reproductive etc., is called the natural system of classification. The
characters which are considered here are relatively constant.

Example:
This system classified organisms into mammals, birds and fishes.
1. Mammal possess mammary glands and have hairs on their body. They are
viviparous (giving birth to young ones). They possess four chambered hearts.
2. Bird possess wings and their body is covered by feathers. They possess
pneumatic bones which help in flight. They are oviparous (laying eggs). They
also possess four chambered hearts.
3. Fish do not possess limbs, instead they have fins. Their bodies are covered by
scales. They possess gills for respiration. They are cold blooded and possess
two chambered hearts.
 ALFORQUE, CHIONG, & JAMERO GENBIO 2

BASIS OF CLASSIFICATION
Characters are inherited features that vary among species. Scientist are able
to infer phylogenies based on these heritable characters which includes
morphological and molecular data. Because these data could reflect evolutionary
relationship among different species of organisms, scientist were able to determine
common ancestry.

1. MORPHOLOGICAL CHARACTERS
Morphological Characters are the physical features and structures of an
organism that are used to identify and classify different species. This includes the
form and structure of an organism or a part of an organism.

Homologous Structures are body parts that are

similar in structure but may have different
function. This indicates inheritance of a trait from a
common ancestor. A body part inherited from a
common ancestor that is modified differently in
different lines of descent is a result of an
evolutionary pattern called Morphological
Divergence.

The diagram shows the evolutionary diversification of

forelimbs from a common ancestor (stem reptile). The
forelimbs of various animals, including pterosaurs, chickens,
penguins, porpoises, bats, and humans, are shown,
highlighting how similar bone structures have adapted to
different functions.

Analogous Structures may have similar functions but are of different

morphological construction. These structures do not indicate a common
descent. This is a result of an evolutionary pattern called Morphological
Convergence, wherein structures eventually take similar form because of
similar environmental stresses.

The digram shows three animals—a dolphin (mammal),

an ichthyosaur (reptile), and a shark (fish)—that,
despite belonging to different taxonomic groups, have
evolved similar streamlined body shapes adapted for
aquatic life.
 ALFORQUE, CHIONG, & JAMERO GENBIO 2

2. BIOCHEMICAL CHARACTERS
The most convincing evidence for determining evolutionary relationships
among species is the biochemistry of cells. DNA and RNA analyses are powerful
tools in determining species similarities and reconstructing phylogenies. In general,
the greater the number of shared genes, the greater the evidence of common
descent.

The table shows that the amino acid

sequences of human and monkey
cytochrome-c are nearly identical.
This high degree of similarity
strongly suggests a close
evolutionary relationship between
humans and monkeys. The one
difference in amino acid sequence
reflect the time since their
divergence from a common
ancestor.

EVOLUTIONARY
RELATIONSHIP OF ORGANISM
The evolutionary relationship of organisms can be represented by a
phylogenetic tree or a cladogram.

PHYLOGENETIC TREE
Biologist traditionally represent
evolutionary relationships among
organisms in phylogenetic tree.
Phylogenetic tree illustrates how related
organisms evolved from a common
ancestor based on the best reliable
resources. This is based on the
comparison on ribosomal RNA base
sequences among living organisms.
Phylogenetic trees are hypotheses, not
definitive facts. Two species are more
related if they have a more recent
common ancestor and less related if they
have a less recent common ancestor.
ALFORQUE, CHIONG, & JAMERO GENBIO 2

ANATOMY OF A PHYLOGENETIC TREE

In a phylogenetic tree, the species or
groups of interest are found at the tips of lines
referred to as the tree's branches. Each
branch point (also called an internal node)
represents a divergence event, or splitting
apart of a single group into two descendant
groups.
At each branch point lies the most recent
common ancestor of all the groups
descended from that branch point. For
instance, at the branch point giving rise to
species A and B, we would find the most
recent common ancestor of those two
species. At the branch point right above the
root of the tree, we would find the most
recent common ancestor of all the species in
the tree (A, B, C, D, E). The root represents a
series of ancestors leading up to the most
recent common ancestor of all the species in
the tree.

The three trees represent identical

relationships among species A, B, C, D, and
E.The identical information in these different-
looking trees reminds us that it's the
branching pattern (and not the lengths of
branches) that's meaningful in a typical tree.

CLADOGRAM
Systematists use cladistics, an analytical method
of hypothesizing evolutionary relationships. This is
depicted through a branching diagram called a
cladogram.
Clade or Monophyletic group- A branch of
cladogram with a common ancestor and all
descendants.
Example: If we group organism to Archosaurs, it can
include all descendants from crocodile to bird
Paraphyletic group - are groups of organisms that
include a common ancestor but not all
descendants of that ancestor.
Example: Reptiles include lizard and crocodile, but it
excludes bird, so not all descendants were included
ALFORQUE, CHIONG, & JAMERO GENBIO 2

Polyphyletic group- a group that

includes organisms with separate
evolutionary origins
Example: Warm-blooded animals include
mammal and bird, but they don't have a
common ancestor

Since cladograms are constructed to show the sequence or order in which

derived charsacters evolved, the close proximity of clades in the cladogram
implies the number of shared characters. Groups that are closest share the
most derived characters, therefore they share a more recent common
ancestor. The nodes where the branches originate represent a common
ancestor. Meanwhile an outgroup is the most distantly related group of
animals that isn’t necessarily a clade.

HOW TO MAKE A CLADOGRAM?

ALFORQUE, CHIONG, & JAMERO GENBIO 2

WORKSHEET 4: MAKING A CLADOGRAM

Objective:
To let students familiarize making a cladogramof representative organisms.

Procedure:
Using the table of traits below, create a cladogram for the given organisms.
Make sure to properly label each branch. You can do this activity by pair. Write
this in a 1 whole sheet of paper.
ALFORQUE, CHIONG, & JAMERO GENBIO 2

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