General Biology 2

Quarter 1: Week 5 and 6 -

Module 5
Taxonomy and Systematics
 Target

Truly overwhelming is the variety of living species on earth. Throughout

human history, people have come up with ways of organizing, or classifying biological
diversity. Organisms, including general similarities, colors, ecological functions, etc.,
can be categorized according to any number of parameters.
However, it is widely understood that the most effective way for scientists to
organize biological diversity is according to shared evolutionary background. In this
way, not only does the grouping result in an organized classification, it also
incorporates and transmits knowledge about our understanding of these groups'
evolutionary past.

Although in the last century, our understanding of evolutionary relationships

between species has greatly improved, it is by no means complete. As new
information becomes available, interactions between species and groups of organisms
continue to be updated.
. In your previous lessons, you learned how to infer evolutionary relationships
among organisms using the evidences of evolution.

This module will provide you with basic principles, concepts and activities that
will help you understand taxonomy and systematics based on evolutionary relationships
of organisms.

After going through this module, you are expected to:

1. Explain how the structural and developmental characteristics and relatedness

of DNA sequences are used in classifying living things (STEM_BIO11/12-IIIh-
j-14);
2. Identify the unique/ distinctive characteristics of a specific taxon relative
to other taxa (STEM_BIO11/12-lIIh-j-15); and
3. Describe species diversity and cladistics, including the types of evidence
and procedures that can be used to establish evolutionary relationships.
(STEM_BIO11/12-IIIh-j-16)
Pretest: Read each question carefully then select the best answer from the
given choices.

1. Which of the following refers to the science of naming and grouping

organisms.
A. genetics B. linnaeanology C. speciation D. taxonomy

2. Which of the following is used to group organisms based on modern

systematics?
A. ecological niche B. evolutionary relationships
C. physical appearance D. size

3. Which of the following is true about unrooted phylogenetic trees?

A. Has a single lineage at the base.
B. They show the ancestry relationship.
B. They show relationships among organisms.
D. They show relationship but not lineage between species.

4. According to the evolutionary tree in the which would make a monophyletic

group?
A. A and B C. A and C
B. B and C D. C and D

5. Which of the following pairs is least related?

A. insects and birds B. human and chimpanzee
C. dogs and cats D. monarch and butterfly
 Jumpstart

Similarities are always easy to see as one looks at two species that evolved
from a common ancestor, and until recently, the only way to assess how closely
related two organisms are was to look at physical characteristics and behavior.

Activity 1: Relationship Goals

Directions: List down 2 organisms that you think are closely related. Fill in the table
below to show structural/anatomical similarities and unique features.
Name of organism Unique feature/s Similarities

Discover

Through evolution, all species are related to one another, more or less
distantly. This is not an insignificant announcement. Although it appears that
most have nothing in common, they share the different characteristics of life
like the ability to reproduce or make something of themselves.

Latest estimates of the biological diversity of the planet indicate that

there are as low as half a million or as high as 100 million species, or possibly
more. To effectively research the myriad organisms that occupy the biosphere,
we attempt to classify species into groups that represent evolutionary
relationships.
Structural and developmental characteristics and relatedness of DNA
sequences

Anatomy and embryology

Anatomical features shared between organisms (including ones that are
visible only during embryonic development) can indicate a shared evolutionary
ancestry. There are more closely related species groups with more recent
common ancestors, and each group would appear to share the characteristics
that were present in their last common ancestor. If a particular physical
feature, such as a complex bone structure or a body plan, is shared by two or
more animals, they may all have inherited this feature from a common
ancestor. It is said that physical characteristics shared due to evolutionary
history (a common ancestor) are homologous. To give one example, the
forelimbs of whales, humans, and birds are homologous structures.

Not all physical traits that appear identical are indicators of shared
ancestors. Instead, some physical similarities are analogous: in different species,
they developed independently because the organisms lived in similar
environments or encountered similar selective pressures. A duck and a platypus
are similar in that they both lay eggs, however, the egg laying capability likely
developed independently rather than from a common ancestor.

Molecular biology
Structural homologies, similarities may reflect shared evolutionary
ancestry between biological molecules. Similarities and variations in various
species between the "same" gene (that is, a pair of homologous genes) will help
us decide how closely the organisms are related.

DNA evidence for evolutionary relationships

All living organisms share the same genetic
material (DNA), identical genetic codes, and the same
basic gene expression mechanism at the most basic
level (transcription and translation). The sequences
of associated (or homologous) genes are also
contrasted by biologists. If the "same" gene is found
in two animals, it is because they inherited it from a
shared ancestor. In general, the more DNA similarities
between the two species in homologous genes, the
more closely related the species is.
It is possible to examine segments of DNA
using gel electrophoresis, in which fragments of DNA
are separated by size. Fragments are represented by
horizontal bands. Bands between samples that are identical in size will be on the
same horizontal line and suggest that the sequence of DNA is shared. The more
fragments two samples share, the more related they are to each other (Figure 1.)
Taxonomy vs. Systematics
Systematics is the study of the diversification of life forms over time, both
past and present, and their relationships between other species. On the other
hand, taxonomy is the science of organizing and categorizing living organisms
into classes called taxa.
Both a systematist and a taxonomist provide scientific names; give
detailed descriptions of organisms; collects and keeps volumes of specimens;
offer classifications for the organisms by constructing identification keys and
data on their occurrence and distribution. However, it is the systematist that
investigates on evolutionary histories and considers environmental adaptation of
species.

Taxonomic Classification

The method of taxonomic classification (also referred to as the Linnaean

system after the Swedish botanist Carl Linnaeus, Zoologist, and doctor) uses a
hierarchical model. Moving from the point of origin, the groups become more
precise until the branch terminates as a single species. For a start, scientists
split species into three large groups after the usual beginning of all life.
Bacteria, Archaea, and Eukarya are groups called domains. After domains, the
following categories of increasing specificity are kingdoms: phylum, class,
order, family, genus, and species (Figure 2)

Figure 2. The taxonomic classification system uses a hierarchical model to

organize living organisms into increasingly specific categories. The common
dog, Canis lupus familiaris, is a subspecies of Canis lupus, which also includes
the wolf and dingo. (credit “dog”: modification of work by Janneke

Source:https://d3bxy9euw4e147.cloudfront.net/oscms-
prodcms/media/documents/Biology2e-WEB_ICOFkGu.pdf

Figure 3 demonstrates how the levels move with other species toward
specificity. Note how the dog shares a domain, like plants and butterflies, with the
largest diversity of species. At each sub-level, since they are more closely related,
the species become more similar. Scientists have traditionally categorized
organisms using characteristics, but as DNA technology has been developed, they
have determined more precise phylogenies.
Figure 3. At each sublevel in the taxonomic classification system, organisms become
more similar. Dogs and wolves are the same species because they can breed and
produce viable offspring, but they are different enough to be classified as different
subspecies. (credit “plant”: modification of work by "berduchwal"/Flickr; credit
“insect”: modification of work by Jon Sullivan; credit “fish”: modification of work by
Christian Mehlführer; credit “rabbit”: modification of work by Aidan Wojtas; credit
“cat”: modification of work by Jonathan Lidbeck; credit “fox”: modification of work
by Kevin Bacher, NPS; credit “jackal”: modification of work by Thomas A. Hermann,
NBII, USGS; credit “wolf”: modification of work by Robert Dewar; credit “dog”:
modification of work by "digital_image_fan"/Flickr)

Source:https://d3bxy9euw4e147.cloudfront.net/oscms-
prodcms/media/documents/Biology2e-WEB_ICOFkGu.pdf
The following table shows four species that are classified using the Linnaean
system of classification. Features are used as bases for classification.

DOMAIN Eukarya FEATURES

KINGDOM Animalia Organisms that are able to move on their own
PHYLUM Chordata Animals with a backbone
CLASS Mammalia Chordates with fur or hair and mammary
glands
ORDER Primata Mammals with grasping fingers
FAMILY Hominidae Primates with relative flat faces and three-
dimensional vision
GENUS Homo Hominids with upright position and large brain
SPECIES Homo Members of the genus homo with a high
sapiens forehead and notably thin skull
Common Human
name

DOMAIN Eukarya
KINGDOM Animalia Plantae
PHYLUM Chordata Arthropoda Magnoliophyta
CLASS Mammalia Insecta Lilopsida
ORDER Primata Carnivora Diptera Liliales
FAMILY Hominidae Canidae Drosophilidae Liliaceae
GENUS Homo Canis Drosophila Allium
SPECIES Homo Canis Drosophila Allium cepa
sapiens familiaris melanogaster
Common Name Human Dog Fruit fly Onion

Phylogeny
Phylogeny is the study of relationships and their evolutionary
development among different groups of organisms. A phylogeny is commonly
represented by a phylogenetic tree called a tree diagram. An early example of
a phylogenetic tree is the "Tree of Life" by Darwin (Figure 4).

Figure 4. Darwin’s Tree of Life. This branching diagram represents the evolutionary histories
of different species. It is the only diagram that originally appeared in Darwin’s famous 1859 book,
On the Origin of Species by Natural Selection.

Source: https://www.ck12.org/section/phylogenetic-classification/
 Darwin was attempting to explain in this diagram how he felt evolution
had happened.

The tree reveals how animals, from the bottom of the tree to the top,
developed over time. They developed new branches on the tree of life as species
evolved. Eventually, some of these species branched into more descendant
species. Others died without leaving any heirs, or went extinct.

To reflect evolutionary history, modern biologists still use phylogenetic

trees. Figure 5 shows a basic phylogenetic tree. Genetically related species
represent the tips of the branches. Common ancestors reflect the branching
points.
The ancestor to which
two descendant species shared
before they took separate
evolutionary paths is a common
ancestor. Species 1 and 2 have
shared a more recent common
ancestor with each other in the
tree than with species 3 (Figure
5). Species 1 and 2 are, thus,
Figure 5. Phylogenetic Tree. This
more closely related to each phylogenetic tree shows how hypothetical
other than to species 3. species 1, 2, and 3 are related to one another

Source: https://www.ck12.org/section/
phylogenetic-classification/

Ancestor species are like ancestors of your own. With any siblings you
may have, your most recent common ancestor is a shared relative. A shared
grandparent is the most recent common ancestor with a first cousin. A shared
great-grandparent is the most recent common ancestor with a second cousin.
In general, the more distant the relationship between you and relatives in
your own generation, the farther in the past you shared a common ancestor. The
same holds true for related species. The more distant the relationship between
two related species, the farther back in time they shared a common ancestor.
Many phylogenetic trees have a single lineage at the base representing
a common ancestor. Scientists call such trees rooted, which means there is a
single ancestral lineage (typically drawn from the bottom or left) to which all
organisms represented in the diagram relate. Notice in the rooted phylogenetic
tree that the three domains— Bacteria, Archaea, and Eukarya—diverge from
a single point and branch off. The small branch that plants and animals (including
humans) occupy in this diagram shows how recent and miniscule these groups
are compared with other organisms. Unrooted trees do not show a common
ancestor but do show relationships among species (Figure 6).
Figure 6. Both of these phylogenetic trees show the relationship of the three domains of
life—Bacteria, Archaea, and Eukarya—but the (a) rooted tree attempts to identify when
various species diverged from a common ancestor while the (b) unrooted tree does not.
(credit a: modification of work by Eric Gaba)

In a rooted tree, the branching indicates evolutionary relationships

(Figure 6). The point where a split occurs, a branch point, represents where
a single lineage evolved into a distinct new one. We call a lineage that evolved
early from the root that remains unbranched a basal taxon. We call two
lineages stemming from the same branch point sister taxa. A branch with
more than two lineages is a polytomy and serves to illustrate where scientists
have not definitively determined all of the relationships. Note that although
sister taxa and polytomy do share an ancestor, it does not mean that the
groups of organisms split or evolved from each other. Organisms in two taxa
may have split at a specific branch point, but neither taxon gave rise to the
other.

Figure 7. A phylogenetic tree's root indicates that an ancestral lineage gave rise to
all organisms on the tree. A branch point indicates where two lineages diverged. A
lineage that evolved early and remains unbranched is a basal taxon. When two lineages
stem from the same branch point, they are sister taxa. A branch with more than two
lineages is a polytomy.

Source:https://d3bxy9euw4e147.cloudfront.net/oscms-
prodcms/media/documents/Biology2e-WEB_ICOFkGu.pdf
Cladistics
The most common way to integrate information into phylogenetic trees is
called cladistics. Based on features of ancestor and descendant species,
cladistics explains theories about how organisms are linked. In the 1950s,
a scientist named Willi Hennig
established cladistics. It became
very popular over the next few
decades, and is still used widely
today.
Cladistics is derived from the
term clade. A clade is a collection
of organisms that include an
ancestor species and all of their
descendants. A diagram showing
evolutionary relationships is
called a cladogram within one or
more clades.
A clade is a relative concept. Figure 8. Clade
How a clade is described depends Source:
on the species that you are https://www.chino.k12.ca.us/site
interested in classifying. Small /handlers/filedownload.ashx?mod
clades may have as few as two uleinstanceid=4464&dataid=41803
species and a shared ancestor. &FileName=LAB%20Review%20Cla
Many more species and their
shared ancestors may be found
in the larger clades (Figure 8 and 9).

Figure 9. Vertebrate Clade

Source: https://www.chino.k12.ca.us/site/handlers/
filedownload.ashx?moduleinstanceid=4464&dataid=
41803&FileName=LAB%20Review%20Cladistics.pdf
 A monophyletic group (clade) can be separated from the root with a single
cut, whereas a non-monophyletic group (not a clade) needs two or more cuts.
In Figure 9, grouping 1 is monophyletic; grouping 2 is paraphyletic while
gouping 3 is polyphyletic.

Figure 9. Monophyletic Group and Paraphyletic Group

Source:
https://www.chino.k12.ca.us/site/handlers/filedownload.ashx?modulein
stanceid=4464&dataid=41803&FileName=LAB%20Review%20Cladistics.p df

Enrichment Activity 1
Directions: Fill in the name of each missing taxonomic category in the chart below.
Enrichment Activity 2: Making of a cladogram
Directions: Using the example below as basis, create a Venn diagram and cladogram
for the given set of organisms. (20 pts.)

Example:
Given these characters and taxa:
Taxa
Characters Shark Bullfrog Kangaroo Human
Vertebrae X X X X
Two pairs of X X X
limbs
Mammary X X
glands
Placenta X

1. Draw a Venn diagram. Start with the character that is shared by all the taxa on
the outside. Inside each box, write the taxa that have only that set of
characters.

Placenta: Human
Mammary glands: Kangar oo
Mammary glands: Kangaroo
•

Two pairs of limbs: Bullfrog

Vertebrae: Shark

2. Convert the Venn diagram into a cladogram.

Human
Task: Convert the following data table into a into a Venn diagram, and then into a
cladogram

Characters Sponge Jellyfish Flatworm Earthworm Snail Fruitfly Starfish Human

Cells with X X X X X X
flagella
Symmetry X X X X X
Bilateral X X X X
symmetry
Mesoderm X X X
Head X X X
develops
first
Anus X X
develops
first

Grading Rubric
Excellent Good Fair Poor
10 8 6 4

Correctness of All details of the Most of the Some of the Details are
details illustrations are details are details are poorly
correct correctly correctly illustrated
illustrated illustrated.

Completeness Illustration Illustration Illustration Illustration

Of details contains all the lacks few of the lacks some of lacks most of
details details the details the details
 Gauge

Directions: Read carefully each question and select the correct answer from the
given choices. Use separate sheet of paper for your answers. Write the letter only.

1. Which of the following refers to the two-name classification system used to

organize living things?
A. Biodiversity B. binomial nomenclature
C. phylogeny D. systematics

2. What are the main levels of taxa in order?

A. domain, kingdom, phylum, class, order, family, genus
B. kingdom, phylum, class, order, family, genus, species
C. domain, kingdom, phylum, class, order, genus, family, species
D. domain, kingdom, phylum, class, order, family, genus, species

3. Which of the following scientific name is correctly written?

A. Musca domestica B. Musca domestica
C. Musca Domestica D. Musca domestica

4. What is defined as the study of the diversification of living forms, both

past and present, and the relationships among living things through time?
A. Phonetics B. systematics
C. systemics D. taxonomy

5. How important is DNA barcoding in systematics? DNA barcoding helps

determine
A. morphological similarities B. evolutionary relationships
C. physiological differences D. physical traits

6. Which of the following is NOT part of a taxonomist role?

A. Assigning a scientific name.
B. Classifying ornamental plants.
C. Identifying an unknown flowering plant.
D. Explaining the relatedness of plants in different locations.

7. To which category will two organisms with different correlated

morphological characters belong to?
A. one biological species B. two biological species
C. one taxonomic species D. two taxonomic species

8. What do you call the type of classification that reflects the evolutionary
inter relationships of organisms?
A. Phylogenetic classification B. Artificial classification
C. Natural classification D. Numerical classification
9. What is the characteristic of a rooted phylogenetic tree?
Phylogenetic tree is one .
A. that extends back to the origin of life on earth.
B. at whose base is located the common ancestor of all taxa
depicted on that tree.
B. that illustrates the rampant gene swapping that occurred early in
life’s history.
C. that indicates our uncertainty about the evolutionary
relationships of the taxa depicted in the tree.
D. That hides the evolutionary relationships among various
biological species.

10. Which of the following anatomical tree part is most analogous

to two species with a common ancestor?
A. the trunk
B. a node where two twigs diverge
C. a twig that branches with time
D. a single twig that gets longer with time

11. Which of the following is a characteristic of the best classification

system? A classification system that .
A. reflects evolutionary history.
B. conforms to traditional, Linnaean taxonomic practices.
C. unites organisms that possess similar morphologies.
D. corroborates the classification scheme in use at the time of
Charles Darwin.

12. Which level of classification within a lineage has the largest

number of shared derived characters?
A. Kingdom B. Class C. Domain D.

Family 13-15. Use the figure below to answer

questions 13-15.

13. Which number represents the common ancestor for both species C
and E? A. 1 B. 2 C. 3 D. 4
14. Which species are closely related?
A. A and B B. B and C C. C and D D.B and D

15. Which species are extinct?

A. A and E B. B and C C. C and D D.B and D