Biology 2

Quarter 3 – Weeks 1 - 4
General Biology 2
Quarter 3 – Module 1:
Genetic Engineering
General Biology
Alternative Delivery Mode
Quarter 3 – Module 1: Genetic Engineering

Second Edition, 2021

Republic Act 8293, section 176 states that: No copyright shall subsist in any work of the
Government of the Philippines. However, prior approval of the government agency or office
wherein the work is created shall be necessary for exploitation of such work for profit. Such
agency or office may, among other things, impose as a condition the payment of royalties.

Borrowed materials (i.e., songs, stories, poems, pictures, photos, brand names,
trademarks, etc.) included in this module are owned by their respective copyright holders. Every
effort has been exerted to locate and seek permission to use these materials from their respective
copyright owners. The publisher and authors do not represent nor claim ownership over them.

Published by the Department of Education

OIC-Schools Division Superintendent: Carleen S. Sedilla CESE
OIC-Assistant Schools Division Superintendent: Dr. Jay F. Macasieb, DEM CESE

Development Team of the Module

Writers: Princess Ibron
Editor: Randy O. Salentes

Reviewer: Hernan L. Apurada

Layout Artist: Arnold G. Chan

Management Team: Neil Vincent C. Sandoval

Chief Education Supervisor, Curriculum Implementation Division

Hernan L. Apurada
Education Program Supervisor

Printed in the Philippines by the Schools Division Office of Makati City through the
support of the City Government of Makati (Local School Board)

Department of Education – Schools Division Office of Makati City

Office Address: Gov. Noble St., Brgy. Guadalupe Nuevo

City of Makati, Metropolitan Manila, Philippines 1212
Telefax: (632) 8882-5861 / 8882-5862
E-mail Address: makati.city@deped.gov.ph

1
 What I Need to Know
This module was designed and written with you in mind. It is here to help you master the
introduction to General Biology II. The scope of this module permits it to be used in many
different learning situations. The language used recognizes the diverse vocabulary level of
students. The lessons are arranged to follow the standard sequence of the course. But the order
in which you read them can be changed to correspond with the textbook you are now using.
The module is divided into two lessons, namely:
● Lesson 1 – Genetic Engineering

After going through this module, you are expected to:

1. Compare classical breeding with modern genetic engineering techniques;
2. Enumerate the steps in molecular cloning;
3. Describe some methods to introduce DNA into cells; and
4. Explain the selection and screening of transformants / genetically modified organisms
(GMOs)

What I Know
Answer the following questions. Write the chosen letter on a separate sheet of paper.
1. There are many plants and animals that have successfully domesticated by people. Some
organisms were modified and enhanced. Give some examples of “enhanced” animals and
plants. Explain your answer.
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
2. Can genetic engineering change our society? What will be the consequences if organisms
undergo this process? Support your idea/s.
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________

Lesson
Genetic Engineering
1

What’s In

Direction. Complete the table below. Use a separate sheet of paper.

Word Check Description Source

Recombinant DNA

Classical breeding

Genetic engineering

Biolistics

Genetically Modified
Organisms (GMOs)

1
 What is It

What is Genetic engineering?

● It involves the use of molecular
techniques to modify the traits of
a target organism. The
modification of traits may involve:
I. introduction of new traits into
an organism
II. enhancement of a present trait
by increasing the expression of
the desired gene
III. enhancement of a present
trait by disrupting the inhibition
of the desired genes’ expression.
● Classical breeding practices
focus on the mating of organisms
with desirable qualities.

What is the general outline of

recombinant DNA?

I. cutting or cleavage of DNA by

restriction enzymes (REs)

II. selection of an appropriate vector

or vehicle which would propagate
the recombinant DNA ( eg. circular
plasmid in bacteria with a foreign
gene of interest)

III. ligation (join together) of the

gene of interest (eg. from animal)
with the vector ( cut bacterial
plasmid)

IV. transfer of the recombinant plasmid into a host cell (that would carry out
replication to make huge copies of the recombined plasmid)

V. selection process to screen which cells actually contain the gene of interest

VI. sequencing of the gene to find out the primary structure of the protein

What are the ways in which these plasmids may be introduced into host
organisms?

● Biolistics- In this technique, a “gene

gun” is used to fire DNA-coated pellets
on plant tissues. Cells that survive the
bombardment, and are able to take up
the expression plasmid coated pellets
and acquire the ability to express the
designed protein.

2
 ● Plasmid
insertion by Heat
Shock Treatment-
Heat Shock
Treatment is a
process used to
transfer plasmid
DNA into bacteria.
The target cells are

pretreated before the procedure to increase the pore sizes of their plasma
membranes.
● Electroporation- This technique follows a similar methodology as Heat Shock
Treatment, but, the expansion of the membrane pores is done through an
electric “shock”. This method is commonly used for insertion of genes into
mammalian cells.
What are some methods to screen recombinant cells?
● Selection of plasmid DNA containing cells
- A selection marker within the inserted plasmid DNA sequence allows the
selection of “transformants”. Usually, an antibiotic resistance gene (e.g. AMP
ampicillin resistance gene) is included in the plasmid DNA.
● Selection of transformed cells with the desired gene
-Certain inserted genes within the plasmids provide visible proof of their
presence. These include the antibiotic resistance genes that allow for the
selection of the transformed cells within the solution.
● PCR detection of plasmid DNA
-Alternatively, the presence of the desired gene in the inserted plasmids may be
confirmed using PCR amplification. PCR reactions specific for the desired gene
may be done using DNA from cells. Amplification of the expected product would
confirm the presence of the gene within the samples.
What are Genetically Modified Organisms (GMOs)?
With the ability to insert gene sequences, comes the possibility of providing new traits
for these target organisms. This has allowed the development of GMOs. Some of these
genetic modifications promise higher product yields for their targets. These include the
Flavr-Savr Tomato and Bt-Corn.

3
Examples:

● Flavr-Savr (“Flavor
Savor”) tomato was the
first genetically modified
organism that was
licensed for human
consumption. The trait
modified in this tomato is
its ripening process. A
gene for an enzyme that
causes the degradation of
pectin in the cell walls (i.e.
polygalacturonase)
normally softens the fruit
as it ripens.

● Bt-Corn was developed to

incorporate the production of a
toxin (i.e. Bt-endotoxin) from
Bacillus thuringensis in corn
plants. This toxin results in the
death of pests that feed on these
plants like the corn borer larvae.
The toxin has been shown to be
selective for Lepidoptera larvae and
is non-toxic to humans, mammals,
fish and birds. The selective
toxicity of the toxin allows its use
in food crops.

What could be the possible concerns of some people in GMO’s regarding the
consumption of these modified foods?

● While most of the products are tested for safety, concerns are raised for the
possibility of not being able to detect hazards that are present, but are currently
undetectable by today’s current technology.

● Because of these issues, manufacturers are urged to provide labels that notify
consumers of GMO presence in their products.

● While GMOs are believed to be safe when licensed by the food regulatory
agencies, it is believed that the consumers must be provided with enough
information to make their own choices regarding their use.

4
 What’s More

Direction. Illustrate the steps and other methods involved in recombinant DNA.

What I Have Learned

Direction. Encircle the letter of your choice.

A. Are you confident that you learn the important lessons in this module?

1. I can easily explain the meaning and processes involved in genetic engineering.
a. I can't do this. c. I can do some of this
b. I can do most of this d. I can do all of this

2. I can describe the examples of genetically modified organisms.

a. I can't do this. c. I can do some of this

b. I can do most of this d. I can do all of this

3. It is easy for me to explain and describe the genetic engineering techniques.

a. I can't do this. c. I can do some of this

b. I can do most of this d. I can do all of this

5
 What I Can Do

Direction. Do the following activity. Use a separate sheet of paper. Research and make
a concept map on the pros and cons of genetic engineering.

Assessment

A. Multiple Choice. Choose the letter of the best answer. Write your answer in a
separate sheet of paper.
1. It involves mating two members of a species (plant, yeast, or animal), each of whom
possesses one or more different and desirable traits in order to create a hybrid
individual possessing both traits.

A. Classical breeding C. Recombinant DNA Technology

B. Genetic Cloning D. Electroporation

2. What is the expansion of the membrane pores that is done through an electric
“shock”?

A. Electroporation C. Selection of plasmid DNA containing cells

B. Biolistics D. Selection of transformed cells with the desired
gene

3. This technique is used to fire DNA-coated pellets on plant tissues.

A. Electroporation C. Selection of plasmid DNA containing cells

B. Biolistics D. Selection of transformed cells with the desired
gene

4. It is a technique in which target cells are pre-treated before the procedure to

increase the pore sizes of their plasma membranes.

A. Electroporation C. Heat Shock Treatment

B. Biolistics D.Genetic Cloning

6
5. Genetically Modified Organisms (GMOs) is the ability to insert gene sequences,
comes the possibility of providing new traits for these target organisms. Which of the
following examples does not belong to the group?

A. Insulin C. Bt-Corn
B. Flavr-Savr D. Genetic Diseases

B. Answer the following question briefly.

1. Which of the techniques discussed can be used to detect if GMOs were used in
a certain food product?

______________________________________________________________________________

______________________________________________________________________________

______________________________________________________________________________

2. What has been the impact of GM crops on pesticide use?

______________________________________________________________________________

______________________________________________________________________________

______________________________________________________________________________

3. Do you agree or disagree with genetic engineering and GMO? Support your
idea/s.

______________________________________________________________________________

______________________________________________________________________________

______________________________________________________________________________

______________________________________________________________________________

______________________________________________________________________________

7
 General Biology 2
Quarter 3 – Module 2:
Applications of Recombinant DNA
General Biology
Alternative Delivery Mode
Quarter 3 – Module 2: Applications of Recombinant DNA

Second Edition, 2021

Republic Act 8293, section 176 states that: No copyright shall subsist in any work of the
Government of the Philippines. However, prior approval of the government agency or office
wherein the work is created shall be necessary for exploitation of such work for profit. Such
agency or office may, among other things, impose as a condition the payment of royalties.

Borrowed materials (i.e., songs, stories, poems, pictures, photos, brand names,
trademarks, etc.) included in this module are owned by their respective copyright holders. Every
effort has been exerted to locate and seek permission to use these materials from their respective
copyright owners. The publisher and authors do not represent nor claim ownership over them.

Published by the Department of Education

OIC-Schools Division Superintendent: Carleen S. Sedilla CESE
OIC-Assistant Schools Division Superintendent: Dr. Jay F. Macasieb, DEM CESE

Development Team of the Module

Writers: Mary Joy Bertos
Editor: Randy O. Salentes

Reviewer: Hernan L. Apurada

Layout Artist: Arnold G. Chan

Management Team: Neil Vincent C. Sandoval

Chief Education Supervisor, Curriculum Implementation Division

Hernan L. Apurada
Education Program Supervisor

Printed in the Philippines by the Schools Division Office of Makati City through the
support of the City Government of Makati (Local School Board)

Department of Education – Schools Division Office of Makati City

Office Address: Gov. Noble St., Brgy. Guadalupe Nuevo

City of Makati, Metropolitan Manila, Philippines 1212
Telefax: (632) 8882-5861 / 8882-5862
E-mail Address: makati.city@deped.gov.ph

1
 What I Need to Know

This module was designed and written with you in mind. It is here to help you
master the introduction to General Biology II. The scope of this module permits it to be
used in many different learning situations. The language used recognizes the diverse
vocabulary level of students. The lessons are arranged to follow the standard sequence
of the course. But the order in which you read them can be changed to correspond with
the textbook you are now using.
The module includes the following lesson, namely:
● Lesson 1 – Applications of Recombinant DNA
After going through this module, you are expected to:
1. Give examples of products from recombinant DNA technology
2. Explain how genes may be cloned and expressed

What I Know

Answer the following questions. Use a separate sheet of paper.

B. Guide Questions

1. What is genetic cloning? What could be the advantages and disadvantages of it?
______________________________________________________________________________
______________________________________________________________________________

1
 What are genetically modified organisms and how are they
created?______________________________________________________________________
______________________________________________________________________________

Lesson
Applications of Recombinant DNA
1

What’s In

Direction. Complete the table below. Use a separate sheet of paper.

Word Check Description Source

Insulin Production

Chymosin Production

PCR Amplification

Gene Cloning

Pest Resistance

What is It

What are examples of modified traits using cloned genes and their applications?

MODIFIED TRAIT GENE RECIPIENT APPLICATION (FIELD)

MODIFICATION ORGANISM

Insulin Production Insertion of Human Bacteria (Medicine) Production of

Insulin Gene Human Insulin in Bacteria

Pest Resistance Insertion of Bt- Corn / (Agriculture) Production of

toxin gene Maize corn plants with increased
resistance to corn boxer

Delayed Ripening Disruption of a Tomato (Agriculture) Production of

gene for a ripening plant plants with fruits that have
enzyme (e.g. delayed ripening fruits. These
polygalacturonase) fruits will survive longer
transport time, allowing their
delivery to further locations
(i.e. export deliveries)

2
 Chymosin Insertion of a gene Bacteria (Industry) Enhance large scale
Production for chymosin production of chymosin. This
enzyme serves as a substitute
for rennet in the coagulation
of milk. Rennet has to be
harvested from calves. The
large scale production of this
enzyme in bacteria provides
an abundant supply of this
important component for the
cheese production industry.

What is PCR (Polymerase Chain Reaction) Amplification?

● A technique that allows the detection of specific genes in target organisms

● Once a desired trait is chosen, information must be acquired for either its
detection or expression in a given organism.
● It is an in-vitro method that simulates DNA replication in vivo. It utilizes a
thermostable (heat-resistant) DNA polymerase that builds single stranded DNA
strands unto unwound DNA templates.

❏ Detection

Some researchers may be interested in determining if a given gene/trait is available in

a particular organism. If no previous research provides this information, researchers
may test the DNA of different organisms for the presence of these specific genes.

PCR Applications

● PCR may be used to detect the presence of a desired gene in an organism.

3
 ● The first case is useful for detection of the gene, or the detection of organisms
with that specific gene within a sample.
● The second case is useful for the amplification of the entire gene for eventual
expression in other organisms.
● The direct amplification/copying of a full gene is part of the process for
“cloning” that gene.

What is Cloning and Expression?

Cloning

-Cloning is the process of

producing individuals with
identical or virtually identical
DNA, either naturally or
artificially. In nature, many
organisms produce clones through
asexual reproduction.

● Some genes provide

economically, and industrially
important products (e.g. insulin-
coding genes; genes for collagen
degradation).
● In some cases, scientists would
want to put these genes into
organisms for the expression of their products.
● One example would be the insertion of an insulin coding gene from the human
genome into bacteria. This allows the “transformed” bacteria to now produce
human insulin as a product.
● Certain types of bacteria are capable of this process since they are able to take
genes within their cell membranes for eventual expression.
● The genes are normally in the form of small, circular DNA structures called
plasmids.
● The genes found in the inserted plasmid DNA sequence will be expressed as
proteins that provide specific traits to the transformed bacteria.

What are other applications of recombinant DNA technology?

● is used to make microbes, plants, and animals that carry genes from other
species.
● can be used in the prenatal diagnosis of human genetic disease.
● Bioremediation- Pseudomonas putida and Nitrosomonas europaea are the
organisms which are typically utilized in bioremediation. The objective is to
isolate the original genes located in these bacteria that promote bioremediation,
then modify and incorporate them into a suitable host to be used as a
bioremediation agent usually E. coli.
● Biotechnology- An appreciable biotechnological success and novel commercial
application is the production of genetically modified fluorescent zebrafish, Danio
rerio, and similar species using genes encoding glowing characteristics.

4
 What’s More

Direction. Make an essay related to the impacts of applications of recombinant DNA.

And illustrate some examples of it in a separate paper.

_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________

What I Have Learned

Direction. Encircle the letter of your choice.

A. Are you confident that you learn the important lessons in this module?

1. I can easily explain the applications of recombinant DNA.

a. I can't do this. c. I can do some of this
b. I can do most of this d. I can do all of this

2. I can describe PCR amplification and its applications.

a. I can't do this. c. I can do some of this
b. I can do most of this d. I can do all of this

3. It is easy for me to explain and describe cloning and expression.

a. I can't do this. c. I can do some of this
b. I can do most of this d. I can do all of this

What I Can Do

Direction. Do the following activity. Use a separate sheet of paper.

1. Discuss how PCR may be used for the detection of disease-causing pathogens
in a population. Give at least two examples.

5
 ______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________

2. Discuss how the cloning and expression of certain genes allows for massive
production of the desired product. Give at least two examples.

______________________________________________________________________________
______________________________________________________________________________
_____________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________

3. What do you think are the ethical issues related with genetic cloning? Explain.

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________

Assessment

A. Multiple Choice. Choose the letter of the best answer. Write your answer in a
separate sheet of paper.

1. It is an in-vitro method that simulates DNA replication in vivo.

A. Classical breeding C. Heat Shock Treatment

B. Cloning D. PCR amplification

6
 2. Organisms that produce a clone through asexual reproduction.

A. Electroporation C. Cloning
B. Classical breeding D. Heat Shock Treatment

3. What do you call the genes that are normally in the form of small, circular DNA
structures?

A. Antibiotic Resistance Gene C. Insulin-coding genes

B. Inserted Gene Sequence D. Plasmid

4. Which of the following applications of recombinant DNA technology does not

belong to the group?

A. Chymosin Production C. Insulin Production

B. Delayed Ripening D. Pest Receptivity

5. This enzyme serves as a substitute for rennet in the coagulation of milk.

A. Chymosin C. Ligase
B. Endonucleases D. Polygalacturonase

B. Answer the following question briefly. Use separate paper.

1. Give at least 10 countries that used genetic cloning.

2. Why do you think they are practicing the cloning process?

7
 General Biology 2
Quarter 3 – Module 3:
Biodiversity and Evolution
General Biology
Alternative Delivery Mode
Quarter 3 – Module 3: Biodiversity and Evolution

Second Edition, 2021

Republic Act 8293, section 176 states that: No copyright shall subsist in any work of the
Government of the Philippines. However, prior approval of the government agency or office
wherein the work is created shall be necessary for exploitation of such work for profit. Such
agency or office may, among other things, impose as a condition the payment of royalties.

Borrowed materials (i.e., songs, stories, poems, pictures, photos, brand names,
trademarks, etc.) included in this module are owned by their respective copyright holders. Every
effort has been exerted to locate and seek permission to use these materials from their respective
copyright owners. The publisher and authors do not represent nor claim ownership over them.

Published by the Department of Education

OIC-Schools Division Superintendent: Carleen S. Sedilla CESE
OIC-Assistant Schools Division Superintendent: Dr. Jay F. Macasieb, DEM CESE

Development Team of the Module

Writers: Jose Mari J. Fontanilla
Editor: Hernan L. Apurada

Reviewer: Hernan L. Apurada

Layout Artist: Arnold G. Chan

Management Team: Neil Vincent C. Sandoval

Chief Education Supervisor, Curriculum Implementation Division

Hernan L. Apurada
Education Program Supervisor

Printed in the Philippines by the Schools Division Office of Makati City through the
support of the City Government of Makati (Local School Board)

Department of Education – Schools Division Office of Makati City

Office Address: Gov. Noble St., Brgy. Guadalupe Nuevo

City of Makati, Metropolitan Manila, Philippines 1212
Telefax: (632) 8882-5861 / 8882-5862
E-mail Address: makati.city@deped.gov.p
 What I Need to Know

This module was designed and written with you in mind. It is here to help you master the
Evolution and Origin of Biodiversity. The scope of this module permits it to be used in many
different learning situations. The language used recognizes the diverse vocabulary level of
students. The lessons are arranged to follow the standard sequence of the course. But the
order in which you read them can be changed to correspond with the textbook you are now
using.

The module is divided into three lessons, namely:

• Lesson 1 – Patterns of Descent with Modification
• Lesson 2 – Development of Evolutionary Thought
• Lesson 3 – Evidences of Evolution

After going through this module, you are expected to:

1. Show patterns of descent with modification from common ancestors to produce the
organismal diversity observed today.
2. Trace the development of evolutionary thought.
3. Explain evidences of evolution (e.g., biogeography, fossil record, DNA/protein
sequences, homology, and embryology).

What I Know

Choose the letter of the best answer. Write the chosen letter on a separate sheet of paper.
1. Where does hybrids between tigers and lions called tiglons occur only?
a. India
b. captivity
c. Madagascar
d. central Africa
2. The similarity of bone structure in the forelimbs of many vertebrates is an example of
a. analogy
b. convergence
c. digitality
d. homology
3. Darwin explained his theory of evolution in a book called
a. The Beagle
b. Survival of the Fittest
c. On the Origin of Species
d. Around the World in Population Eighty Days
4. Which is NOT a prezygotic isolating mechanism?
a. temporal isolation
b. geographical isolation
c. production of sterile hybrids
d. prevention of gamete fusion
5. As adults, humans have a vestige of a tail. It is called the
a. vermiform
b. placenta
c. lanugo
d. coccyx

1
 Lesson
Patterns of Descent with
1 Modification
In this lesson, we will discuss the Patterns of Descent with Modification. Patterns of Descent
with Modification is one of the primary components of the theory of evolution. We will learn
how it works at the genetic, individual, and population levels of different organisms.

What’s In
The fundamental principle of biological evolution is that, over time, populations and
types of organisms change. Today, when we think of evolution, we are likely to relate
this concept to one particular individual - Charles Darwin, the British naturalist.
In 1859, Darwin published an influential and controversial book, On the Origin of
Species by Means of Natural Selection. In this book, he proposed that species evolve
and that all living organisms can trace their descent to a common ancestor. But, what
exactly is a species?
Ernst Mayer an ornithologist defined a species as follows: "species are groups of
interbreeding natural populations that are reproductively isolated from other such
groups”.
Activity 1.1
Summarize Darwin’s observations that drive changes in species over time by matching
column A with column B. Write the letter before each number.

Column A Column B
(Observation) (Example)
1. Variations in traits exist. A. Not all dandelion seeds germinate
or survive to maturity
2. These variations (traits) are heritable. B. Dandelions produce thousands of
seeds.
3. Species overproduce. C. Variation in color and spot pattern
of Asian ladybird beetles
4. There is competition for resources; not D. Variation in closely related species
all offspring survive. of elephants; offspring resemble
close relatives more than other
members of a population.

What is It
Species are groups of interbreeding natural populations that are reproductively isolated
from other such groups.
The following are the types of reproductive isolating mechanisms that can lead to
speciation.
I. Prezygotic Isolating Mechanisms prevent formation of viable zygotes.
a. Ecological Isolation. Two closely related species may occupy different
ecosystems within a geographical region. They are ecologically isolated if
their habitat preferences lower their probability of mating.
b. Temporal Isolation. Two related species occupying the same geographical
range may have different periods of sexual activity or breeding seasons.
c. Behavioral Isolation. Species with complex courtship behaviors usually
exhibit stereotyped "call and response" signals between male and female
before actual mating takes place. These rituals prevent wasted mating
effort that would halt gene transmission by inviable or infertile hybrids.
d. Mechanical Isolation. Morphological differences between species prevent
hybridization.
2
 e. Gametic Isolation. In this case, sperm and ova of the two species are
chemically incompatible, and will not join to form a zygote.
II. Postzygotic Isolating Mechanisms prevent hybrids from passing on their genes.
a. Hybrid Inviability. Sperm and egg from the two species may combine, but
the genetic information is insufficient to carry the organism through
normal development. The embryo dies after a few cleavages, or some time
before birth/hatching.
b. Hybrid Sterility. Hybrids are sterile because gonads develop abnormally or
there is abnormal segregation of chromosomes during meiosis
c. Hybrid Breakdown. Two related species can hybridize, and their F1
offspring are fertile. But successive generations (F2 and beyond) suffer
lower viability or fecundity. Thus, they cannot become an established
population.
Modes of speciation
1. Allopatric speciation or geographic speciation. In this mode of speciation,
something extrinsic to the organisms prevents two or more groups from mating
with each other regularly, eventually causing that lineage to speciate. Isolation
might occur because of great distance or a physical barrier, such as a desert or
river.

2. Sympatric speciation occurs when

members of a population that
initially occupy the same habitat
within the same range diverge into
two or more different species. It
involves abrupt genetic changes
that quickly lead to the
reproductive isolation of a group of
individuals. Example is change in
chromosome number
(polyploidization).

3. Parapatric speciation. In parapatric

speciation, there is no specific
MODES OF SPECIATION
extrinsic barrier to gene flow. The Image from Spatial Aspects of Speciation by BenB4 (public domain)
population is continuous, but https://en.wikipedia.org/wiki/File:Speciation_modes.png
nonetheless, the population does
not mate randomly. Individuals are more likely to mate with their geographic
neighbors than with individuals in a different part of the population's range. In
this mode, divergence may happen because of reduced gene flow within the
population and varying selection pressures across the population's range.

What’s More
Activity 1.2
Identify the type of isolating mechanisms in the following examples.

Example Isolating
mechanism
1. Two species of garter snakes live in the same
region but one lives in water and the other on land
2. Two species of meadowlarks with different mating
songs
3. Two species of trout that breed in different seasons
4. Mule is the sterile offspring of a horse and a
donkey
5. Two species of plants flower at different months

3
 Lesson
Development of
2 Evolutionary Thought
What’s In
Evolution is the change in inherited traits over successive generations in populations of
organisms. The theory of evolution is based on the idea that all species are related and
gradually change over time.
The discovery of evolutionary principles first took place in western Europe and was made
possible by advances in scientific thinking that date back to the sixteenth century. In
this lesson we will understand the events, people and their contributions in the
development of evolutionary thought.
Activity 2.1
Define evolution broadly and then give a narrower definition, as discussed in the
overview.

What is It
People have long noted that organisms are well suited to their environments, that there
is a rich diversity of life on Earth, and that life shows a striking unity. Charles Darwin’s
fascination with what he called “endless forms most beautiful” led him to propose a
scientific explanation for these broad observations. On November 24, 1859, Darwin
published his hypothesis in a book called On the Origin of Species by Means of Natural
Selection, ushering in the era of evolutionary biology. Darwin defined evolution as
descent with modification, proposing that Earth’s many species have descended from
ancestors that were very different from those alive today.
At age 22, Charles Darwin set out on a sea voyage that
began his intellectual voyage toward the fundamental
concept of modern biology. His hypothesis had its roots
in the work of many other individuals, most notably
geologists of the day. Before Darwin’s voyage, the
predominant view of life was that species were fixed
and unchanging. This view can be traced as far back
as Aristotle (384–322 A.D.). The Old Testament’s
account of creation stated that species were
individually designed by God and, therefore, perfect. By
the 1700s, the adaptations of organisms were seen as
evidence that the Creator had designed each species for
a purpose. That said, people understood that some
organisms were less developed (i.e., more primitive) Charles Darwin, English naturalist
Image from Charles Darwin by Julius Jääskeläinen
than others and they used this as a way of organizing (public domain)
life forms. However, this did not imply any kind of https://commons.wikimedia.org/wiki/File:Charles_D
arwin,_English_naturlist,_colored.jpg
evolutionary relationship, but rather the order of their
creation.
Darwin’s views were influenced by fossils, remains or traces of organisms that have
become mineralized within sedimentary rocks. Sedimentary rocks form when mud and
sand settle to the bottom of seas, lakes, and marshes. New layers of sediment cover
older ones, creating layers of rock called strata. Erosion may later carve through
sedimentary rock to expose older strata at the surface. Fossils within layers of

4
sedimentary rock present an ordered succession of organisms that have populated
Earth throughout time.
Paleontology, the study of fossils, was largely developed by the French anatomist
Georges Cuvier (1769–1832). In examining rock strata in the Paris Basin, Cuvier realized
that the older the strata, the more different the fossils were from modern life. Cuvier
began to understand that extinction had been a common occurrence in the history of
life. Instead of evolution, Cuvier advocated catastrophism, speculating that boundaries
between strata were due to local floods or droughts that destroyed the species then
present. He suggested that areas stripped of life due to some catastrophe were later
repopulated by new species immigrating from neighboring areas.
In contrast to Cuvier’s catastrophism, Scottish geologist James Hutton (1726–1797)
proposed a theory of gradualism, which held that profound geologic changes took place
through the cumulative effect of slow but continuous processes identical to those
currently operating. Thus, valleys were formed by rivers flowing through rocks, and
sedimentary rocks were formed from soil particles that eroded from land and were
carried by rivers to the sea.
Later, geologist Charles Lyell (1797–1875) proposed a theory of uniformitarianism,
which held that geologic processes had not changed throughout Earth’s history. That
is, geological changes that occurred in the past were still occurring and that the same
rules were in effect. Hutton and Lyell had a strong influence on Darwin. First, if geologic
changes result from slow, continuous processes rather than sudden events, then the
Earth must be far older than the 6,000 years estimated by Biblical scholars. Second,
slow and subtle processes that last for long periods of time can also act on living
organisms, producing substantial changes in them over a long period of time.
In 1809, French biologist Jean-Baptiste de Lamarck (1744–1829) published a theory of
evolution based on his observations of fossils. By comparing fossils and current species,
Lamarck found what appeared to be several lines of descent. Each line of descent was
a chronological series of older to younger fossils, leading to a modern species. Lamarck
explained his observations with two principles: use and disuse of parts and the
inheritance of acquired characteristics. Use and disuse was the concept that body parts
that are used regularly become larger and stronger, while those that are not used
disappear. The inheritance of acquired characteristics stated that modifications
acquired during the life of an organism can be passed on to offspring. A classic example
is the long neck of the giraffe. Lamarck reasoned that the long, muscular neck of the
modern giraffe evolved over many generations as the ancestors of giraffes reached for
leaves on higher branches and passed this characteristic on to their offspring.
Lamarck thought that evolutionary change was driven by a deep-rooted drive of
organisms to become more complex. Lamarck’s theory was a visionary attempt to
explain the fossil record and the current diversity of life with recognition of gradual
evolutionary change. However, modern genetics has provided no evidence that acquired
characteristics can be inherited. Acquired traits
such as a bodybuilder’s bigger muscles do not
change the genes transmitted through gametes
to offspring.
The Origin of Species
Darwin never used the word evolution in the
first edition of The Origin of Species, although
the final word of the book is evolved. Instead
Darwin used the phrase descent with
modification. All living organisms are related to THE TREE OF LIFE
Image from 122 [Study Guide] 22-1 Descent with Modification
each other due to their descent from a common https://massasoit.instructure.com 1
ancestor that lived in the distant past. Over evolutionary time, the descendants of that
common ancestor have accumulated diverse modifications, or adaptations, that allow
them to survive and reproduce in specific habitats. Over long periods of time, descent
5
with modification has led to the rich diversity of life we see today If we try to visualize
descent with modification, the history of life resembles a tree, with multiple branches
from a common trunk. Closely related species, the twigs on a common branch of the
tree, shared the same line of descent until their recent divergence from a common
ancestor.

What’s More

Activity 2.2
Describe how each of the following play into Darwin’s mechanism for evolution by
natural selection.
1. over reproduction 2. survivability 3. variable traits 4. inheritance

Lesson

3 Evidences of Evolution

In this third lesson we will discuss pieces of evidence of evolution. Understanding evolution
helps us solve biological problems that impact our lives. It explains the striking similarities
among vastly different forms of life, the changes that occur within populations, and the
development of new life forms.

What’s In

The evidence for evolution is compelling and extensive. Looking at every level of
organization in living systems, biologists see the signature of past and present evolution.
Darwin dedicated a large portion of his book, On the Origin of Species by Means of
Natural Selection, identifying patterns in nature that were consistent with evolution and
since Darwin our understanding has become clearer and broader.
Activity 3.1
List the traits of the following organisms below that help them to survive or reproduce
better than others of that same species.
a. rabbit: b. turtle c. oak tree d. bacterium

What is It

EVIDENCES OF EVOLUTION

Evidence from Fossils

Fossils are remains of ancient organisms trapped in
rocks, tar pits, frozen in ice or embedded in amber.
The activities and behavior of ancient life forms also
left behind fossil traces (such as footprints, dungs,
gastric stones, nests and burrows) which Ammonite fossil from Kilve beach in Somerset England
Image from Ammonite fossil by Becks (public domain)
scientists can study. The records found in the https://commons.wikimedia.org/wiki/File:Ammonite_fossil_
(8606998286).jpg
6
 rocks show a gradual evolutionary descent from simpler to more complex life forms.
Paleontologists use the fossils found in rocks to track the evolutionary history of many
organisms.
Evidence from Structures
Structures in different organisms can be
compared to infer common lineage.

Homologous structures are structures with

the same set of bones that presumably
evolved from a common ancestor. They
appear different and may have varied
functions.

The principle of homology: The biological derivation relationship (shown by

colors) of the various bones in the forelimbs of four vertebrates is known as
homology and was one of Darwin’s arguments in favor of evolution.
Image from the Homology of vertebrates by Волков Владислав Петрович
(public domain)
https://commons.wikimedia.org/wiki/File:Homology_vertebrates-en.svg

Analogous structures are structures that perform the same

function but have very different embryological
development or set of structures like bones.
Vestigial structures are structures or attributes that have
lost most of its ancestral function in more recent species.
Image courtesy analogous wings

Evidence from Embryology

Embryology is the study of the development
of an organism from an embryo to its adult
form. Common structures are shared in the
embryo stage and disappear by the time the
embryo reaches the juvenile or adult form.

In humans the vermiform appendix is a vestigial structure;

it has lost much of its ancestral function.
Image from haustration by Henry Gray (1918) Anatomy of the
Human Body (public domain)
https://commons.wikimedia.org/wiki/File:Gray536.png

Evidence from Molecular Biology

Many organisms have similar molecules of life
(RNA, DNA, proteins) that suggest descent from
a common ancestor with modifications. The
near universality of the genetic code reflects an
evidence of common ancestry and relatedness
and can be inferred from the similarities in the Comparisons of animal embryos
DNA sequences between and among organisms. Image from Embryo comparisons by Starlarvae (public domain)
https://commons.wikimedia.org/wiki/File:Embryo_comparisons.jpg
Many organisms have similar molecules of life
(RNA, DNA, proteins) that suggest descent from a common ancestor with modifications.
The near universality of the genetic code reflects an evidence of common ancestry and
relatedness and can be inferred from the similarities in the DNA sequences between and
among organisms.
2
Many organisms have similar
molecules of life (RNA, DNA, proteins)
that suggest descent from a common
ancestor with modifications. The near
universality of the genetic code
reflects an evidence of common
ancestry and relatedness and can be
inferred from the similarities in the
DNA sequences between and among
Sequence Alignment of DNA from Two Species
organisms. Image from Gene Comparisons
https://ib.bioninja.com.au/standard-level/topic-3-genetics/31-genes/gene-
comparisons.html
Evidence from Biogeography
Biogeography is the study of geographical distribution of fossils and living organisms.
Organisms usually arise in areas where similar forms already exist. Similar organisms
may also be found in different locations which could mean that the two places were
previously connected.

What’s More

Activity 3.2
These are embryos at their most advanced stage, shortly before birth.

Source: http://www.starlarvae.org

Describe how the embryos developed from the earliest stage to the latest stage in the
following organisms.
Species Anatomical Changes from Early to Late Stages

Human
Chicken

Rabbit

Tortoise

1. Look again at the six embryos in their earliest stages. Describe the patterns you
see. What physical similarities exist between each of the embryos?

3
 2. Does this suggest an evolutionary relationship? Explain how, these embryos
can be used as evidence of a common ancestor between each of these six
organisms.

What I Have Learned

1. Species are groups of interbreeding natural populations that are reproductively

isolated from other such groups.
2. Reproductive isolation can occur by preventing individuals of separate species
from mating (prezygotic isolation) or by selecting against hybrids (postzygotic
isolation).
3. The theory of evolution is based on the idea that all species are related and
gradually change over time.
4. Charles Darwin’s theory of evolution states that evolution happens by natural
selection.
5. Individuals with characteristics best suited to their environment are more likely
to survive, finding food, avoiding predators and resisting disease. These
individuals are more likely to reproduce and pass their genes on to their offspring.
6. Individuals that are poorly adapted to their environment are less likely to survive
and reproduce. Therefore, their genes are less likely to be passed on to the next
generation.
7. Multiple types of evidence support the theory of evolution (Evidence from
Fossils, Evidence from Structures, Evidence from Embryology, Evidence from
Molecular Biology, and Evidence from Biogeography)

What I Can Do
Activity 3.3 (Natural Selection in Action)
1. Choose two of the island environments from the four described below.
2. Design a squirrel for each island that has adapted to that island’s specific
environmental conditions. Include at least 5 adaptations.
3. Draw each squirrel with its adaptations in its island environment.
4. Include labels of the adaptations and why they are beneficial to the squirrel. Explain
how natural selection resulted in the traits of your different squirrel populations.

4
 Assessment
Multiple Choice. Choose the letter of the best answer. Write the chosen letter on a separate
sheet of paper.

1. During their early stages of development, the embryos of reptiles, birds, and
mammals look very similar. This suggests that reptiles, birds, and mammals
a. have a common ancestor
b. live in the same types of environments
c. have undergone parallel evolution
d. have gotten rid of all their vestigial structures
2. Behavioral isolating mechanisms may occur when two species have different
a. sized and shaped copulatory organs
b. courtship displays
c. times of the day that they are sexually active
d. habitat ranges
3. Two species of wild lettuce grow in the same areas, but one flowers in early spring
and the other flowers in summer. This is an example of a
a. geographical isolating mechanism
b. behavioral isolating mechanism
c. mechanical isolating mechanism
d. temporal isolating mechanism
4. Using the molecular record to determine phylogenetic relationships is based on the
assumption that
a. nucleotide sequences do not change over time
b. nucleotide sequences change at a fairly constant rate over time
c. nucleotide sequences change randomly and erratically over time
d. evolutionary changes occur in phenotypes but not in genotypes
5. The sperm of species A dies when it comes in contact with the female reproductive
tract of species B. This is an example of
a. a prezygotic isolating mechanism
b. a postzygotic isolating mechanism
c. sexual selection
d. polyploidy

5
General Biology 2
Quarter 3 – Module 4:
Evolutionary Relationships
of Organisms
General Chemistry
Alternative Delivery Mode
Quarter 3 – Module 4: Evolutionary Relationships of Organisms

Second Edition, 2021

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 What I Need to Know

This module was designed and written with you in mind. It is here to help you master the
Evolutionary Relationships of Organisms. The scope of this module permits it to be used in
many different learning situations. The language used recognizes the diverse vocabulary
level of students. The lessons are arranged to follow the standard sequence of the course.
But the order in which you read them can be changed to correspond with the textbook you
are now using.

The module is composed of lesson below, namely:

• Lesson 1 – Evolutionary Relationships of Organisms

After going through this module, you are expected to:

1. Infer evolutionary relationships among organisms using the evidence of evolution
2. Explain how the structural and developmental characteristics and relatedness of DNA
sequences are used in classifying living things

What I Know

Choose the letter of the best answer. Write the chosen letter on a separate sheet of paper.
1. Which pairs are the best examples of homologous structures?
a. bat wing and human hand
b. owl wing and hornet wing
c. porcupine quill and cactus spine
d. bat forelimb and bird wing
2. If this evolutionary tree is an accurate depiction of relatedness, then which of IS
CORRECT?
(1) The entire tree is based on maximum parsimony.
(2) If all species depicted here make up a taxon, this taxon is monophyletic.
(3) The last common ancestor of species B and C occurred more recently than the
last common ancestor of species D and E.
(4) Species A is the direct ancestor of both species B and species C.
(5) The species present at position 3 is ancestral to C, D, and E.
a. 2 and 5
b. 3 and 4
c. 2, 3, and 4
d. 1, 2, and 3
3. Shared derived characters are most likely to be found in taxa that are
a. paraphyletic
b. polyphyletic
c. monophyletic
d. diphyletic
4. When using a cladistic approach to systematics, which of the following is
considered most important for classification?
a. shared primitive characters
b. analogous primitive characters
c. shared derived characters
d. overall phenotypic similarity

1
 5. Cladograms (a type of phylogenetic tree) constructed from evidence from molecular
systematics are based on similarities in
a. the pattern of embryological development.
b. biochemical pathways.
c. habitat and lifestyle choices.
d. mutations to homologous genes.

Lesson
Evolutionary Relationships
1 of Organisms

In this lesson we will discuss the evolutionary relationship of organisms. Scientists gather
data that enables them to create evolutionary relationships between species. Similar to
detective work, scientists must use evidence to uncover the facts. In the case of phylogeny,
evolutionary investigations focus on two types of evidence – morphology and genetics.

What’s In

Activity 1
Use the following word bank to identify the descriptions by writing the correct term on
the line. Not all words will be used:
Cladogram Cladistics Phylogeny Derived characters
___________________1. Characteristics that appear in recent parts of a lineage but not in
its older members.
___________________2. A diagram of the evolutionary relationships among organisms
___________________3. The study of evolutionary relationships among organisms

What’s New

Humans have been attempting to properly classify living things since Aristotle made the first
attempt during the 4th century BC. Aristotle’s system was improved upon during the
Renaissance and then, subsequently, by Carolus Linnaeus in the mid 1700’s. These more
formal classification and organization systems grouped species by their physical similarity
to one another. For example, all vertebrates have a backbone, but invertebrates do not.

Traits like the backbone are called synapomorphies, which are traits that are shared by a
group of organisms, presumably because they were derived from a common ancestor. As we
will explore, this method has been shown to have limitations and has more recently been
amended to include genetic analysis. Still, scientists construct trees called dendrograms to
create a visual representation of how species are related to one another and share common
ancestors. These dendrograms can aid in our understanding of the evolutionary processes
that drive these relationships. Genetic comparisons have added an important tool guiding
the analysis of evolutionary relationships.
2
 What is It

Dendrogram

A type of dendrogram, called a cladogram, depicts the hypothetical genealogical

relationships between species with the tips (or leaves) of the tree representing a species and
the branches showing how species are related to each other.

A slightly more complicated type of tree, called a phylogram, differs from a cladogram in that
the branches leading to the species are of different lengths. The length of a branch in this
type of tree represents the degree of change between species: the longer the branch, the
more time since the species have diverged from a common ancestor.

In both types of tree, the common ancestor of a group of species is indicated by a node,
which is the point where a series of branches meet. Species that are more closely related to
each other (most recently shared a common ancestor) will be located closest to the node.
The two species that share a node are called a sister group

Constructed cladograms all typically share certain key features:

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

Key Features of a Cladogram

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

Constructing Cladograms

1. Using Structural Evidence

a. Organize selected organisms according to defined characteristics
i. Use characteristics that are developmentally fixed (i.e. innate) and not
influenced by environmental pressures
b. Sequentially order organisms according to shared characteristics to
construct a cladogram
i. Grouping of organisms may be facilitated by constructing a Venn
diagram prior to developing a cladogram
ii. Each characteristic will be represented by a node, with more common
characteristics representing earlier nodes
iii. The species with the least number of characteristics in common will
represent the outgroup (establishes baseline properties)

3
Rectangular and diagonal cladogram formats
Image from An Introduction to Tree Thinking
https://my.vanderbilt.edu/lauranovick/treethinking/

2. Using Molecular Evidence

a. Select a gene or protein common to a range of selected organisms
b. Copy the molecular sequence (DNA or amino acid) for each of the selected
organisms
c. Run a multiple alignment to compare molecular sequences (DNA or amino
acid)
d. Generate a phylogeny tree (cladogram) from multiple alignment data

Multiple Alignment of a Protein Sequence from Various Species

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

Cladograms focus on characteristics at the macro and molecular level that indicate
relatedness. A cladogram suggests likely evolutionary relationships between groups of
organism or taxa that can be small or large in number:
Monophyletic taxon. A clade of organisms that includes their most recent common
ancestor and all the living and extinct descendants.
Paraphyletic taxon. A group of organisms that includes the most common ancestor of
all members but leaves out some of the descendants that trace back to that same
common ancestor.
Polyphyletic taxon. A group of organisms that don’t have much in common other than
some similar traits.

4
 What’s More

Activity 2
Use the following cladogram to answer the questions below.

Image courtesy blogs.ubc.ca

1. What separates rabbits/primate from the crocodiles on this cladogram?

2. Which organism is most related to the rodents and rabbits on this cladogram?
3. What 5 traits do the bird and its closest relative share?
4. Which organism will have DNA most similar to the bird? Why?
5. Which organism’s DNA will differ the most from the bird? Why?

What I Have Learned

1. Derived characters are characteristics that appear in recent parts of a lineage but
not in its older members.
2. Cladogram is a hypothetical genealogical relationship between species with the tips
(or leaves) of the tree representing a species and the branches showing how species
are related to each other.
3. A taxon (pl. taxa) is any group of organisms that is given a formal taxonomic name.
4. The most direct evidence for evolutionary relationships is similarity in base
sequences of the nucleic acids DNA and RNA. The more similar the base sequences
of two species, the more closely related the species are assumed to be.

5
 What I Can Do

Fill out the following character matrix. Put a ✓ if an organism has the trait.

Cells Legs Antenna Wings 2 sets of

wings
Worm
Spider
Carpenter
ant
House fly
Dragonfly

In the box below, create a cladogram based on your matrix.

6
 Assessment

Multiple Choice. Choose the letter of the best answer. Write the chosen letter on a separate
sheet of paper.

1. A researcher compared the nucleotide sequences of a

homologous gene from five different species of
mammals with the homologous human gene. The
sequence homology between each speciesʹ version of
the gene and the human gene is presented as a
percentage of similarity.

What probably explains the inclusion of rabbits in

this research?
a. Their short generation time provides a ready source of DNA.
b. They possess all of the shared derived characters as do the other species
listed.
c. They are the closest known relatives of rhesus monkeys.
d. They are the outgroup.
2. What conclusion can be drawn validly from these data?
a. Humans and other primates evolved from rabbits within the past 10 million
years.
b. Most of the genes of other organisms are paralogous to human genes, or
with chimpanzee genes
c. Among the organisms listed, humans shared a common ancestor most
recently with chimpanzees.
d. Humans evolved from chimpanzees somewhere in Africa within the last 6
million years.
3. A common ancestor for both species C and E
could be at position number
a. 1
b. 2
c. 3
d. 4
4. The two extant species that are most closely
related to each other are
a. A and B
b. C and D
c. B and C
d. D and E
5. Which species are extinct?
a. A and E
b. A and B
c. C and D
d. D and E