Hand Out

Lesson 1
Recombinant DNA
Genetic engineering is a field in biotechnology which involves the use of
molecular techniques or method to modify the traits of a target organism. It is
also a process of altering or changing the part of a DNA of an organism to
modify its trait.
The DNA of an organism serves as the blueprint of its life: it dictates the
structure, functions and characteristics of the organism. To change its DNA
means to change its traits.
Scientists and researchers have been very busy producing new traits from
different organisms to be used in medicine, agriculture, and industry.
Why would altering DNA affect our characteristics or traits?
Remember that DNA (deoxyribonucleic acid) codes for the proteins that
determine our trait. The central dogma of molecular biology explained that DNA
provides the code that is transcribed in the RNA and then will be translated or
expressed as traits in proteins.
The central dogma states that if transcription and translation of a fragment of

the DNA lead to some traits.
WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

then the insertion of a new fragment of the DNA in a given organism may
provide it with new traits. This is the basis for the development of genetic
engineering.
The fragment of the DNA that is being used and modified in genetic engineering
is the gene. What is a gene?
A gene is a sequence of DNA on a chromosome that codes for a specific trait or

one protein. A chromosome is a thread-like structure found inside the nucleus
of the cell; it is made up of DNA. Part of that DNA is the gene.

How is DNA modified? (BASIC STEPS OF GENETIC ENGINEERING)
1. Scientists targets and identify specific gene.
2. They cut the targeted gene with restriction enzyme.

3. The targeted gene is “spliced” to the DNA of another organism using ligase.
4. The gene will be inserted in the host cell. Once inside the new cell, the new
instruction from the spliced DNA will direct the cell to make new proteins for
new function or characteristics.
Restriction enzymes are “scissor-like” enzymes that recognize and cut specific
sequences in the DNA. Ligases are enzymes that act like glue to join two
fragments of DNA. The process of attaching fragments of DNA from different
sources is known as gene splicing. The resulting “spliced” gene is termed as
the Recombinant DNA.
What is Recombinant DNA and what is its application?
Recombinant DNA is the resulting DNA formed through the process of

recombinant DNA technology, which involves combining DNA fragments from

different organisms or insertion of a foreign DNA fragment to the original
organism as discussed in the process of genetic engineering above.
This technology had been around since the late 1960s and early 1970s when
scientists learned that a broken DNA can be repaired by the cells by
recombining the broken pieces. Since then, various researches were made to
mimic this recombination in laboratories, and nowadays, the application of the
said technology is numerous and is seen across agriculture, medicine
advancement, and industry among others.

Lesson 1
Evolution and Origin of Biodiversity
Evolution and Origin of Biodiversity: History of Life on Earth and

Mechanism of Evolution
The Earth is around 4.5 billion years old. What was Earth like million years
ago? When did the first living organism evolved? By studying the Earth’s
geological timeline, we will be able to trace the processes by which fossils and
living organisms have evolved since the time that life started until the present
day.

The Earth’s history is divided into eons, eras, periods and epochs. The geologic
time scale is a record of the life forms and geological events in Earth’s history.
Scientists developed the time scale by developing by studying the rock layers
and fossils worldwide. Radioactive dating was used to determine the absolute
divisions in the time scale.

The Earth’s geological life may simply be subdivided this way;
1. The Precambrian life (Hadean, Archean and Proterozoic eras)
The Precambrian life covers approximately 88% of the Earth’s history. It is
during this time that the Earth was transformed from a ball of gas and dust to
liquid rock enveloped with hot, non-breathable gases mostly composed of
carbon dioxide, nitrogen, and sulfur. The molten rock cooled down to form the
earth’s crust and with that, the gases also changed providing a cooler
temperature composed mostly of nitrogen. The Earth become more conducive
to life and allowed single-celled cyanobacteria to exist.
The earliest life comprising Precambrian (Ediacaran) biota was long believed to
include only tiny, sessile soft-bodied sea creatures. But recently, there has
been scientific evidence suggesting that more varied and complex animal
species lived during this time, and possibly even before the Ediacaran period.
Fossils Coronacollina acula, date back as far as 560 million years were recently
discovered in South Australia (which was conducted by the university of
California geologist team headed by Professor Mary Droser), a sponge-like
fossils that show the existence of hard body parts and spicules that extended
20-40 cm from the main body (estimated about 5-cm long). It was believed that
soft bodied creatures lived during Precambrian but with this discovery, an
organism with individual skeletal body parts possibly appears before the
Cambrian. It is therefore the oldest animal with hard parts-they would have
been structural supports. This also signals that initiation of skeletons was not
sudden in the Cambrian as was thought, that Ediacaran animals are part of
the evolutionary lineage of animals. This recent discovery shows that
Ediacaran animals were not extinct just before the Cambrian. Another recent
fossil discovery may represent the earliest animal species ever found. While the
validity of this claim is still under investigation, these primitive
fossils appear to be small, one-cm long, sponge-like creatures. These fossils

from south Australia date back 650 million years, actually placing the putative
animal before the great ice age extinction event that marked the transition
between period and the Ediacaran period. Until this discovery, most scientists
believed that there was no animal life prior to the Ediacaran period. Many
scientists now believed that animals may in fact have evolved during the
Cryogenian period. The latter part of Precambrian life, the Proterozoic era, was
greatly affected by the movement of tectonic plates forming the supercontinent
Rodinia. The Earth’s core and atmosphere cooled down and brought about the
Ice Ages. The production of oxygen of the primitive cyanobacteria cause a
drastic change in the chemical composition of the Earth’s atmosphere. Many
species of bacteria and protists were killed by the presence of higher
concentration of oxygen. New types of organisms evolved using biochemical
adaptations enabling them to survive the presence the presence of oxygen. This
allowed the domination of aerobic eukaryotes, the first multicellular organisms.
2. Paleozoic Era
This era known as “Old Life”, started more than 540 million of years ago and
lasted for more than 300 million years. This era is divided into six periods:
Cambrian, Ordovician, Silurian, Devonian, Carboniferous and Permian.
Geological processes during this era began with the break-up of supercontinent
Rodinia into continents Gondwana and Laurentia. These two continents were
located near the equator that subsumed much of the current day landmasses
in a different configuration. At this time, sea levels were very high, probably at
a level that hasn’t been reached since. As the Paleozoic progressed, glaciations
created a global climate, but conditions warmed at the end of the first half of
the Paleozoic, the landmasses began moving together. Eventually a single
supercontinent Pangaea, was formed in latter third of the Paleozoic. Glaciations
then began to affect Pangaea’s climate, affecting the distribution of animal life.
The characteristics of the different periods under Paleozoic era is described
from the geologic time scale on the previous page.
Towards the latter part of Paleozoic era, however, the largest mass extinction in
history also occurred, wiping out approximately 90% of all marine animal
species 70% of land animals. When the continents were rejoined as Pangaea,
lower sea levels increased volcanic activity, and climate change are the possible
causes of the
mass extinction during this era.
3. The Mesozoic Era or the “middle life”
It started 245 million years ago and lasted for 180 million years. It is
subdivided into three periods; Triassic, Jurassic and cretaceous periods. These
are the major geological events that happened during this era; movement of the
tectonic plates like the gradual rifting of the supercontinent Pangaea. This split
Pangaea into two northern continent (North America and Eurasia) and
Laurasia and a southern continent. Gondwana (South America, Australia,
Antarctica and the Indian continent. During the Triassic period, Pangaea still
formed one massive continent. Without much coastline to moderate the
continent’s interior temperature, Pangaea experienced major temperature
swings and was covered with large swaths of desert. The Jurassic period saw a
rise in sea levels which flooded coastal regions and hastened the break-up of
supercontinent. With more coastlines, many areas experienced warmer, more
stable temperatures, and a wetter climate. By the cretaceous era, carbon
dioxide levels in the atmosphere had risen, trapping the planet’s heat. As a
result, the planet was hotter- possibly up to 10 degrees Celsius warmer. This
era is known also as the era of dinosaurs because its predominated by reptiles
because of their ability to withstand dry climates. Small mammals and birds
also thrive d in this era because of being warm-blooded and hair or feathers to
protect them from the changing climate. Gymnosperms were most abundant
during this era because their seeds were protected to endure the dry weather.
Cretaceous period ended with a mass extinction event thought to be brought
about by the collision of an asteroid or comet with Earth.
4. The Cenozoic Era or ‘recent life’
This era started 65 million years ago and continues up to the present time. It is
divided into three periods: Paleogene, Neogene and Quaternary. The world’s
great mountain ranges were built during this era. The main Alpine orogeny,
which produced the Alps and Carpathians in southern Europe and the Atlas
Mountains in northwestern Africa, began roughly between 37 to 24 million
years ago. The Himalayas were formed during sometime after the Indian plate
collided with the Eurasian plate. The formation of these mountain ranges
contributed to the cooling down of the climate in this era.
Animals during this era had to adapt with the rise and fall of the oceans
caused by melting glaciers. Among marine life-forms, the mollusks became
highly diversified. Planktonic Foraminiferans underwent two major radiations-
during Paleocene and Miocene punctuated by a long (15-20 million years) mid-
Cenozoic reduction in diversity possibly related to global cooling. This era is
also known as the Age of Mammals. Mammals began to increase
and evolve in adaptation that allowed them to live in many different

environmentsland, air and sea. Marsupials developed a diverse array of
adaptive types in Australia and South America free from the predations of
carnivorous placentals. The placental mammals make up more than 95% of
known mammals today because of its rapid rate in reproduction.
This era is the development and proliferation of perissodactyls and artiodactyls.

During the later of this era, perissodactyl diversity declined markedly,
but artiodactyls continued to diversify. Many giant placental forms, like the
sabertoothed tiger, giant ground sloths, woolly mammoths, inhabited the
forests and the plains in the Pliocene epoch. It was also about this time that
the first hominids appeared. Early modern humans, however, did not emerge
until the Pleistocene epoch. The Cenozoic era was significantly affected by the
major extinction event that occurred between 10,000 and 8,000 years ago. This
event involved the sudden disappearance of many Ice Age mammals was linked
to these two factors- climate change following the melting of the most recent
Pleistocene glaciers or overkill by Paleolithic hunters.
Paleolithic hunters are considered by the scientists as more likely the cause of
the disappearance of these mammals. The rapidly improved technology of

Paleolithic humans produced more efficient tools for hunting. As climatic
differentiation increased over the course of Cenozoic era, flora became more
and more provincial. Deciduous angiosperms, for instance, came to
predominate in colder regions, whereas evergreen varieties prevailed in the
subtropics and tropics. Grasses also increased and provided food to the grazing
animals allowing them to increase in population.
Changes in the environment often creates new niches (living spaces) that
contribute to rapid speciation and increased diversity. On the other hand,
cataclysmic events, such as volcanic eruptions and meteor strikes that
obliterate life, can result in devastating losses of diversity. Such periods of
mass extinction as shown in the figure above have occurred repeatedly in the
evolutionary record of life, erasing some genetic lines while creating room for
others to evolve into the empty niches left behind. The end of the Permian
period and Paleozoic era was marked as the largest mass extinction event in
the Earth’s history with a loss of roughly 95% of the extant species at time. The
disappearance of Permian reptiles made it possible for a new of reptiles to
emerge, the dinosaurs. Another mass extinction event occurred at the end of
Cretaceous period that ends this era and was believed that is due to meteor
collision that ends the dominance of dinosaurs and plant species. In the
following Cenozoic era, mammals radiated into terrestrial and aquatic niches
once occupied by dinosaurs. The appearance and dominance of flowering
plants in the Cenozoic era created new niches for insects, as well as for birds
and mammals.

Early in Cenozoic era, new ecosystems appeared due to continuous geological
processed including the evolution of life forms as grasses and coral reefs
flourished.
Late in the Cenozoic, further extinction followed by speciation occurred during

ice ages that covered high latitudes with ice and then retreated, leaving new
open spaces for colonization.

Lesson 3
Mechanisms of Evolution
GENETIC VARIATION: YOU ARE ‘YOU-NIQUE’
Have you ever wondered why do people look the same, but also look different
from each other? Like how you look like some of your relatives, but still, you
are unique and recognizable. To some extent, even twins may look exactly alike
but still, there will be some traits that will make them different from each
other, such as the way they talk or the way they walk.
No two persons are exactly similar. Hence, no two persons have the same codes
of DNA. This is because as an individual, you carry a unique set of genes. The
differences between the genes of each individual and the differences between
genes of the different populations are termed as GENETIC VARIATION.
GENE FREQUENCY and EVOLUTION
As an individual, you carry a unique gene of traits, so as the other people in

the world. But there are parts of that gene in which you may find similarities
with others. For example, you may be unique because you are the only person
with tan skin and three moles beneath an eye within your community, but you
may also be the same with other people in your community because the
majority of you have tan skin.
The number of times at which the common gene appears in everyone within a
population is called GENE FREQUENCY. In a simpler context, gene frequency
refers to how common a specific gene is in a group of specie within a specific
area.
You can even solve gene frequency by dividing the actual occurrence of a
specific gene with the total number of populations. It is like solving for the
percentage of the population with a specific common gene.
Any change in the gene frequency of a species or population is EVOLUTION.

Evolution is the change in the genetic materials of organisms, it is a change
manifested in their traits. It is also a change that started deep within the cells
of individuals, in their genes, in their DNA, in their chromosomes.
MECHANISMS OF EVOLUTION: What causes a change in gene frequency?
Gene and the DNA don’t change overnight and don’t change with no cause.
There are various mechanisms that bring forth changes to the gene frequency,
let us investigate and explain them one by one:
1. Artificial Selection
This is also termed as selective breeding. One of the causes of change in the
gene frequency of some species specifically domesticated plants and animals is
artificial selection or selective breeding. It is when humans selectively choose to
breed animals and plants with specific traits that they deemed beneficial for
different purposes.
Examples are the modern corn and modern chicken; as time passed by, the
gene frequency of the original traits of corn and chicken, which are smaller

have evolved into bigger sizes to suit the needs for better market value for these
goods.
2. Natural Selection
It is the process which is also known as “Survival of the Fittest.” Fittest means
NOT the person or organism with the “body-goal” or “fitspiration” body type.
Fittest in the ground of survival means the organism with traits that are most
adaptive to its environment. Nature or the environment dictates which among
the organism will survive, this organism has a certain variety of traits or
characteristics that will be passed on to the next generation.
An example is the June bug or beetle which is well known as “salagubang” in

Filipino; you can always find a dark-colored salagubang within the
neighborhood especially during wet seasons in the Philippines. But in rare
instances, you may see that there are also green colored salagubang. Natural
selection is a major reason for this, green beetles are easily spotted by birds
that may feed on them. Since salagubang usually lives on logs and warm dark
areas or part of a tree, over the course of time those with green colors became
scarce after being easily eaten by prey such as birds. The surviving brown
salagubang passed on their genes to their.
offspring which is why most of the salagubang that you see around are brown
or dark-colored.
3. Gene Flow or Migration

Another mechanism of evolution is gene flow or migration. This occurs when a
group or individual specie migrated from one place to another affecting the
gene pool of the place that they left and the place where they arrive.
An example of gene flow is when a brown beetle migrated to the population of

green beetle because of certain reasons, when this brown beetle interbreeds
with a green beetle the gene of their offspring will be different from the rest of
the original population. As time goes by, continuous interbreeding will result in
hybrids offspring and will in turn make the gene frequency of the said
population significantly different from before.
4. Genetic Drift
Genetic drift is a mechanism that may bring change to the gene frequency in a
population because of “chance” events. It is a result of an incident or accident
which may have brought significant and palpable change to the gene frequency
or common traits in a given population.
Catastrophic events such as floods, volcanic eruptions, and a pandemic or

epidemic may greatly affect the gene pool of a given population, especially if the
population is small enough to be impacted by some “chance” events.
An event that significantly reduces the number of populations is called the

bottleneck effect. As you can see in the illustrative analogy on the left, the
original population is once filled with more variety of genes from different
unique individuals; but the bottleneck hinders some other individuals to

survive or continue reproducing, leaving only the chance survivors to
reproduce and pass on their traits.
5. Non-Random Mating
It occurs when some species choose a partner with preferred characteristics.

Some female species only allow certain male characteristics to be their partner,
making the genes of the chosen male species to reproduce in the next
generation. Some male species with less preferred traits may not be able to
reproduce and pass their genes on the next generation. This event may also
happen in male to female circumstances, wherein some male species choose or
look for specific traits in a female.
The given scenario above may result in less variation in the gene frequency of a
population; non-sexual reproduction, which is done by some species of plants
is also a type of non-random mating because it uses its variety of genes to
reproduce hence no mixing of traits will occur. Another example may observe
when humans choose whom to date, some men and women have certain
preferences in whom they will choose as a partner, it may also be dictated by
cultural preferences. These preferred characteristics may be manifested in the
genetic pool of a certain population as time will show how these characteristics
are more commonly observed than others.
6. RecombinationRecombination or gene shuffling is life’s way of bringing

variety in similarity. It occurs during meiosis, the cell replication process used
for reproduction. Recombination is also the reason behind gene variation
between siblings and twins and makes genetic diversity possible. During
meiosis, crossing over happens where homologous chromosomes line up to
prepare for cell division. In this instance, chromosomes exchange information
and shuffle parts of the DNA which resulted in a very random variation yet the
same copy of the original gene.
7. Mutation
A Mutation occurs when an insertion, deletion, or any change in the codes of

the DNA takes place. Changes in the DNA codes may result from internal or
external factors. Internal factors happen when the DNA fails to copy or
duplicate the DNA correctly; while the cell has many mechanisms to prevent
this from happening. There are still times when this occurs and became
undetected by the cells. External factors are usually caused by radiation; this
is because excessive radiation causes ionization in the cellular level of the body
which may result in the breaking of the DNA. The break in the DNA will cause
faulty replication and mutation. Not all mutations are seen and manifested in
the physical characteristics of organisms, some mutations are not even passed
on from the parents to the offspring. Somatic mutation is when mutation
takes place in the somatic cells or regular cells of the organisms; hence will not
be replicated during meiosis. If the mutated DNA is not replicated during
meiosis, it will not pass on to the next generation.
The Mutation on the sex cells or gametes is the only type of mutation that may
affect the gene frequency of a population in the long run, this is called a

germline mutation. An example of this is the antibiotic resistance of some
bacteria.

Lesson 4
Patterns of Descent and

Evolutionary Thoughts
Patterns of Descent along Development of Evolutionary

Thoughts
“We are all connected with each other.” A line which is always used to signify
that our actions as human beings will affect every living organism on Earth,
even the planet itself.
Observe the illustration above. Birds are one of the most observable animals on
the planet; they may be found on different areas around the Earth, from the icy
caps of the Earth to the deserted and tropical parts of it. There are also tens of
thousands of species of Birds. Species refer to a group of organisms or
individuals under the same classification which has similar characteristics and
is capable of reproduction. It is important to take note that these organisms
may be under the same family of organisms but still possess key differences in
characteristics. An example is the species of birds called Finches; finches are
under one family (Fringillidae) but there are still observable differences between
them. One of these differences is their beaks.
Questions: Why do birds develop differences in their beaks? Why do some birds
of the same family which look exactly like each other developed different type of
beaks?
Hypotheses: Birds’ beaks are one of the most observable adaptation traits used
by an organism. The differences in their beaks resulted from natural selection.
Birds of the same family with different types of beaks can indicate that all birds
came from one single type of bird. We can hypothesize that during Jurassic
Period when birds first appeared there is only one specie or type of bird; as
these birds adapt to the kind of environment that they live and to some other
factors like the kind of food that is abundant in their environment they develop
different beaks for survival.
Can we prove these hypotheses?
Investigation: One of the good things among us living today is the availability of
information from previously done studies and investigation. In the questions
that we have today in this module, the following will be most helpful:
Charles Darwin’s Investigation and Voyage
Charles Darwin is a famous Naturalist of his time; it means that he has gained
knowledge to look at different natural phenomena involving plants and
animals. But before he became a well-known naturalist, he was first considered
as a Collector. He collects different fossils and specimens of animals and plants
from different places on Earth.

His most famous collection was collected from his Voyage during 1831. Darwin
was only 22 years old when he started his 5 years voyage aboard the ship
called HMS Beagle. During this voyage, he had seen and collected various
specimens and fossils of plants and animals. The ship HMS Beagle had
surveyed the coast of South America, for five years he was able to check on
different islands and to collect numerous samples of animals and plants
specimens.
It was like a long field trip. During his trip, he observed key differences among
animals that help him develop his famous idea about speciation which made
him the Father of Evolution. He spent his last 5 weeks on the voyage in the
Galapagos Islands. In this group of islands, he observed that tortoises have
different shell structure depending on the island where it came from. He
noticed that while some of the animal species found in the islands can also be
found in the nearby mainland, the species found on Galapagos islands are
unique and have unique adaptations.
One of these animals is the Finches. He collected samples of this bird because
he was very curious as to how these birds seem to be of the same species with
such observably different types of beaks. Later after his voyage, he found out
that these birds are different subspecies of Finches, yet they almost look the
same except for a few key structural differences such as their beaks. The
finches that he observed on the islands are unique because they have adapted
to feed on cacti.
Along with his observation and investigation of different plant and animal
species from his voyage, the notable differences between these closely related
finches’ beaks made him realize one of the most revolutionary facts about
species.
The Conclusion: For Darwin, and for us who have followed his journey, shortly,
there is one logical reason why these birds although have similar traits
developed into different species. Once in their life’s history, they are birds of
the same species, later as they adapt to their environment, they have developed
changes in their characteristics through the process of Natural Selection. In
which they adapt changes to suit their capability of surviving in their habitat.
Patterns of Descent with Modification

As we continue to follow Darwin in his fascinating adventure to discover the
mystery of the origin of species, you may see him having the “eureka” or
enlightened moment of his life as he arrived at one logical explanation for the
analyzation of data that he had gathered from his voyage: species diverge from
an old species and gave rise to new species.
On the left is an image of Charles Darwin’s penmanship “I Think” along with
his first diagram of an evolutionary tree, where we can observe that point 1 is
our common ancestor which have branched out to different species and a
group of species until we have arrived from the diversity of organisms that we
have today.
Image source: Wikimedia Commons
File name: Darwin Tree.png
The similarities among organisms of different species and the few

differences of closely related species led Darwin to think about
the patterns of descent with modification. In simple words, it
means that we are descendants of one common ancestor, and we evolved into
different species through time as we change our heritable traits over a
generation.
That is: COMMON ANCESTOR → EARLIER SPECIES → PRESENT DAY
ANCESTOR
The Development of Evolutionary Thoughts
Patterns of descent with modification, as you have seen and read is another
way of putting how evolution works. This revolutionary idea of Charles Darwin
has not been the only available thought about evolution. There are also other
scientists who have contributed to the knowledge of evolution that we have
today. We will learn about some of these people in this lesson.
LAMARCK → DARWIN → WALLACE
1. Jean Baptiste Lamarck. Before Darwin, some notable people who have
already thought about the concept of evolution. One of them is Jean Lamarck,
a French Naturalist who has theorized on habits or the Principle of Use and
Disuse; he thought that organisms have evolved to change their characteristics
to fit in their environment through continuous use and disuse of their organs.
Examples are the giraffes that have developed long necks as they need to feed
on fruits from tall trees, while snakes, on the other
hand, have lost their legs as they continue to disuse or not use their legs.
However, later researchers showed that acquired characteristics may not be
simply inherited or passed on to offspring, an analogy for this is how people
who body-built may not pass the trait of the muscled body to their children in
that manner.
2. Charles Darwin. Darwin, an English Naturalist, as we have already learned,

had theorized on how species came from a common ancestor and how these
species may also give birth to another species in a long time as changes occur
in their characteristics via the process of Natural Selection. These organisms
change to adapt to their environment as time passed by until they have finally
evolved into a new species incapable of breeding with the original species. He
wrote the famous book: “On the Origin of Species” where he published his
discoveries and theories on how species evolved from a single ancestor.

3. Alfred Russel Wallace. He is a British Naturalist, had been a friend of
Darwin, and is of great significance to the development of evolutionary thought
because he had been a key person to Darwin’s Publication of the Origin of
Species. Darwin was first very hesitant to publish his theory about speciation
and evolution because he is afraid. During their time it is widely acknowledged
that species have been the same from the very beginning and will still be the
same to the end. Species do not change; this is the accepted concept during
their time. But, as Wallace get acquainted with Darwin, he had been inspired

to take another voyage to
also collect samples of
different species from Indian
and Malay Regions. On his
eight years journey, he had
collected samples of various
species of plants and
animals one of them is
different variations of
Birdwing butterflies. As he
had observed how these
butterflies differ from one
place to another, he also
arrived at the same
conclusion with Darwin
even though Wallace didn’t
have an idea that Darwin has the same theory because Darwin chose to keep it
secret at first. Wallace also thought that species that look almost the same
differ in key characteristics because they have been
modified through their struggle to survive. Through a letter, he sent this
thought to his friend Darwin, which made Darwin also work on his theory
further and publish the work together with Wallace’s work.
Wallace wrote a journal titled “On the Tendency of Varieties to Depart
Indefinitely from the Original Type” where he reasoned about how the
animals in the wild struggle for existence. He said that naturally, there are a
greater number of offspring born than can survive. That is because of different
factors such as food supply and environmental conditions or hazards. He also
said that offspring were born with different characteristics such as size and
color. Environment dictated which among these offspring will survive, and
these survivors will have a higher ability to reproduce and pass on their traits
to another generation. This process will continue until varieties of traits of
organisms became dominant in one place to another.
As these three given theories develop, we have arrived at the most accepted
theory of evolution today, which is Charles Darwin’s On the Origin of Species;
this is because, through his and Wallace’s observation, we can now conclude
that the giraffes on Lamarck’s theory of use and disuse did not develop long
necks simply because of frequent use of their neck. Giraffes have developed
their long neck because those who were born with slightly longer neck survive
and were able to pass on their traits to the next offspring. After a long time,
giraffes have developed longer necks because of their parents who have already
longer neck. This is the pattern of descent with modification along with the
development of evolutionary thoughts.

Lesson 5
Evidence of Evolution
THE CLAIM: DARWIN’S THEORY OF EVOLUTION
You have learned from the previous lesson how the thoughts about evolution
were developed, the prominent among the said thoughts is Charles Darwin’s
Theory of Evolution on which he stated that the organismal diversity today or
the present-day species descended from older species and a common ancestor;
this happens through the mechanism of natural selection on which organisms
developed a modified behavior, trait or characteristics as they adapt or become
“fit” to the living condition presented by their environment.
EVIDENCES: THE BRIDGE BETWEEN THE CLAIM AND THE FACTS

The pieces of evidences which consist of facts may be used to support a claim
or a theory or hypothesis, the evidence is used to check the relationship
between a scientific claim and the truth. They are data gathered through
observation, collection of specimens, or results of tests and experiments.
Without such pieces of evidence, a scientific claim must be revised or rejected.
EVIDENCES OF EVOLUTION AND HOW TO USE THEM TO INFER

EVOLUTIONARY RELATIONSHIP
1. FOSSIL RECORD

Fossils are the remains of a living organisms that lived in the past. These
remains may be in the form of fossilized or preserved bone structure, other
hard body parts aside from bones, imprinted activities such as footprints,
dungs, nests, or gastric stones. Scientists use these fossils to infer the
characteristics, structures, and lifestyle of the ancient organisms.
Fossils showed that organisms from the past look very different from the
organisms living today. An example is how the unearthed fossils of the horses
from different times
led scientists to infer
that the ancestors of
the modern horses
have looked different
from them. The
fossils showed that
ancient horses have
more toe-fingers
because they used to
feed on shrubs and
broad leaves plants
or trees which are
usually found on soft
marshy grounds. As
the land becomes drier and the grass becomes more available, horses evolved
to adapt and survive.
We may not have the complete records of fossils from different times in the
history of life on Earth, but scientists can still theorize based on the available
data using logical reasoning. It is also important to take note that fossils were
collected from different areas across the world so as time pass by and the
records from fossils became more available, the sequences of prehistoric events
made evolution clearer.
2. COMPARATIVE ANATOMY
Body structures of organisms may be compared to each other to investigate

more on evolution. Scientists have developed classifications for these body
structures as deemed useful in the study of evolution.
2.a. HOMOLOGOUS STRUCTURE
These are body structures from different organisms that may look somewhat
similar to each other or have the same component but may perform different
functions. Homologous structures suggest common ancestry or shared
descent. For example,
the human arm, the
cat’s foreleg, the whale’s
flipper and the bat’s
wings have different
functions but have the
same features or bone
structures. This
indicates that these
organisms inherited
this developmental
pattern from a common
ancestor.
2.b. ANALOGOUS STRUCTURE

These are body
structures that look
the same and have
the same function
but have different
structures or
features. Analogous
structures suggest
that organisms of
different descent or
close common
ancestor have
evolved the same structure with the same function because of the same
needs.
Examples are the wings of bats, birds , and insects; the differences from the
bone structures and features of their wings indicate that even if they have
wings to serve a common function, they still evolved independently from two
distantly related groups of ancestors. Bones are the frameworks of the birds’
wings, meanwhile, chitin, a tough material like bones is what composed the
wings of the insects. Therefore, the wings of birds and insects evolve
independently with each other in two distantly related groups of ancestors.
2.c. VESTIGIAL STRUCTURE
These are body structures that are still present in some life forms but have no
clear functions. Vestigial structures suggest that organisms have once had
them, but evolution took place and they were no longer needed, so they have
shrunken in size and appear to be remnant from their common ancestor.
Examples are the human’s tailbone and appendix. Indicatively, vestigial
structures were once useful to the ancestor organisms, but due to changes in
different mechanisms of evolution, these structures no longer serve their
original purpose yet are still inherited by the descendant organisms as part of
the body plan.
3. EMBRYOLOGY
Early development stages or

organisms were studied and
compared. Embryology
suggests that organisms
that are closely related
seems to have similarities
or common traits during
their embryonic stage
because they have
evolved from a common
ancestor.
For example, the embryo of a human showed vestigial structures such as gill
slits and longer tail bone. These are indicative of the shared common descent of
humans from other living organisms such as fishes.
4. MOLECULAR BIOLOGY
Technological advancement provided a new line of knowledge and evidence to
prove common descent or evolution. New equipment and technique in the field
of molecular biology allowed researchers to map the DNA sequence of different
organisms. You have already learned from the previous modules that the DNA
serves as the blueprint or instruction of the life of an organism. Molecular
biology studies showed that the more similar the DNA sequences of
organisms are, the more relevant they are with one another.
An example is the 99.6% shared DNA sequence between humans and
chimpanzees which indicated that humans and chimpanzees are closely
related to each other in the tree of life. It also showed the complexity of DNA
because the 0.4% difference makes humans so much different from
chimpanzees in behavior and characteristics.
5. BIOGEOGRAPHY
Scientists study the

geographical
distribution of
organisms on Earth.
Their findings
suggest that some
living organisms are
unique to specific
places because they
have evolved to adapt on certain conditions present in those places; it
may also be noted that specie which seems similar despite different
geographical location is an indication that those places were once connected
before that massive island of the Earth, the Pangaea divided.
THE RESULT: INTERPRETING THE EVIDENCES

The pieces
evidence
presented above
are not only used
to prove the
claim of the
theory of
evolution but
also showed how
they may be used
to infer the
evolutionary
relationship
between different biological organisms. Evolutionists or scientists used these
pieces of evidence to complete the PHYLOGENETIC TREE or the TREE OF
LIFE. This tree or diagram is used to present the evolutionary relationship
between the organisms using different pieces of evidence of evolution.

Lesson 5
Systematics
Amidst diversity, there is a system. Nature, as beautiful and wonderful as it
is, offers a myriad of different life forms. 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. And together, we will explore how

systematics work! The system unto which the living things were put into order
by the scientists and researchers underwent revisions and numbers of
collaboration before it had been the way it is today. In this module, 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 this module is
still 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.
DATA: WHAT DO WE HAVE ON HANDS?
Scientists have long begun the quest to understand life forms; we can
summarize this study in a specialized subject that you have been learning ever
since you first loved science as a STEM student, that is BIOLOGY. Because of
the hard works of our experts in this field we have huge data at our hands,
which are all a result of the quest that started hundreds of years ago.
What are those data? Let us explore each in the following section.
 Biodiversity
Bio means life and diversity
means variety. We have a diverse
collection of life forms at hand,
they vary from sizes, shapes,
body structures, lifestyle, and
habitats. We also have data
about organisms that are already
dead and extinct through various
fossil records analyses efforts of
experts in the field. We have
millions of different kinds
of living organisms found on
Earth.
 Evidences of Evolution
We also have collected data that serve as evidence of evolution. We have
at our hands’ different ways to prove that evolution of organisms took place;
fossil records showed clear differences between the structures of organisms
living in the past and the present, comparative anatomy allowed us to compare
the homologous and analogous body structures of organisms, biogeography
indicates that environmental factors made organisms to evolve unique
characteristics to those living in a the same place, embryology revealed how
some organisms look similar to each other during their early development and
technology-aided in a new development at molecular biology to help compare
and map the similarities between the DNA of various organisms found on
Earth.
 Evolutionary Relationship
Evidence of evolution lead to the
inference data of evolutionary descent and
relationship between the diverse
life forms
that we have at hand. Correlating
our data
from biodiversity and evidences of
evolution (hence evolution), we
have
another data at hand and that is
the evolutionary relationship
between organisms.
STUDIES: WHERE DO WE PUT OUR DATA?
Having those data at hands, it calls for a need to organize. It is now essential
that these data be organized in a manner that will be beneficial for data
management, further investigation, and communication between experts in the
field as well as to the students studying Biology.
A need for systemization arouses from the continuous collections of these
data. Hence, here comes the various field of specialization that makes sense of
the data at hands, to create order in the diversity of living organisms.
To bring order or to systematize the given data, experts have arrived at the
following field of study, let us explore each of them on the following section.

 SYSTEMATICS: the order in
biodiversity!
Systematics (a field of study under
Biology) aims to identify, compare, analyze, and document the biodiversity of
Earth through Phylogenetics.
 What is PHYLOGENETICS? Phylogenetics is a field of study under
systematics which employ techniques and scientific processes to synthesize the
data into Phylogeny.
 What is PHYLOGENY?
Phylogeny is the pattern of evolutionary relatedness of living organisms based
on data from fossil records, comparative anatomy, molecular or comparative
biology, embryology, and biogeography.
ANALYSES: HOW DO WE PROCESS OUR DATA?
To process the data that we have at our hands, there are various techniques
and methods that have been developed by different discipline under
systematics.
What are these methods? We will explore two of the most famous methods
used
in analyzing data under systematics, first is PHENETICS and second is
CLADISTICS.
 PHENETICS vs CLADISTICS
1. PHENETICS is a method that aims to classify, or group organisms based on
their similarities, through this method, scientists were able to create a
phenogram which is a diagram that represents the similarities between a
group of organisms.
PROS: It is easy to classify organisms based on their physical attributes and
similarities. Organisms tend to have similarities if they are relative to each
other.
CONS: Phenetics did not take into consideration that we have two types of
similar body structures, as we have discussed from the previous module
similar body structures of organisms may be based on descent or maybe just
a result of same adaptation to the environment. If the similarity is homologous
it will be useful to systematics as it tries to group organisms based on their
evolutionary relationship. If the similarity is analogous, it may not represent
the real evolutionary relationship between organisms.
2. CLADISTICS is another method used by scientists to group or classify
organisms; unlike phenetics, this method reflects phylogeny or the pattern of
evolutionary relatedness of organisms. This method will result in the creation
of a cladogram, a diagram that represents the group of organisms with shared
derived characteristics.
PROS: Since this method focuses on grouping organisms with hared derived
characteristics, its result will easily represent organisms from the same
descent or common ancestor. Its analyses will fit with the objective of
systematics which is to classify organisms based on phylogenetics or
evolutionary relationship.
CONS: It is more difficult to make. Sometimes the method will also require
several hypotheses or versions of 1 cladogram before arriving at the most
probable result.
 CLADOGRAM FOR THE WIN!
After we have explored the two given methods of analyzing data under
systematics, it is easy to conclude that cladistics or making cladogram is the
more favored method. This method is systematic and will present more
relevant information when it comes to studying phylogeny or evolutionary
relationships.
HOW TO INTERPRET A CLADOGRAM?
What is in a cladogram? As you have learned from the previous section, a

cladogram is very useful in deducing evolutionary relationships. To do that,
you
need to be able to interpret a cladogram. A cladogram consists of a root which
represents the common ancestor of all the organisms represented in the
cladogram, a node which represents the hypothetical younger common
ancestor of organisms within the branch, the hypothetical common ancestor
typically is the organism where of new species or daughter taxa originated, taxa
(A, B and C in the diagram above) are the smallest unit of classification of
organisms in biology, taxa may represent species, clade consists of branches or
organisms with the same common ancestor, a clade represents an ancestor
and all of its known descendant, lastly, an outgroup is a taxon (singular for
taxa) is a species which is distantly related to other organisms within the
group, but they are still included in the cladogram to serve as a reference
group to trace the root/early common ancestors of the organisms present
within the given cladogram.
Morphology: structural and developmental characteristics as a basis in a

cladogram. As you have observed in the given example of diagrams a cladogram
may be presented both horizontally and vertically if the needed parts
and information were provided. Above is an illustration of how we may use the
shared derived characteristics of organisms for classification.
Morphology: structural and developmental characteristics as a basis in a

cladogram. As you have observed in the given example of diagrams in this
module, a cladogram may be presented both horizontally and vertically if the
needed parts and information were provided. Above is an illustration of how we
may use the shared derived characteristics of organisms for classification.
Understanding and deducting data from a cladogram: we can deduct from the
given cladogram above that the eukaryotes found at the root of the cladogram
are the common ancestor in the diagram, there are also nodes between reptiles
and birds as well as between rodents and primates, each node represent
hypothetical common ancestors of the daughter taxa reptiles and birds which
share a common characteristic of having eggshells to protect their embryonic

offspring, while the daughter taxa rodents and primates share common
characteristics of fur/hair.
Furthermore, as represented by the diagram, the development of these
characteristics happen chronologically, the characteristics closer to roots first
appear and observable or present to all organisms in the cladogram; for
example, the characteristics or having a backbone is shared characteristic that
can be found on fish, amphibians, reptiles, birds, rodents, and primates. The
rest of the characteristics showed later along with evolution and are only
present on organisms from the given point when it was developed towards the
end of the cladogram. For example, four limbs are only seen on amphibians up
to the primates and not on ; another example is the amniotic egg, which is only
present on reptiles up to the primates and not on fishes and amphibians. We
can also deduce from the cladogram that fishes first evolved from eukaryotes
and primates were last to evolve as is also evident in the geographic timescale.

Image source: bioninja.com
Molecular biology: DNA and protein sequences as basis for cladogram.
Scientists have also developed a way to compare the DNA and protein
sequences of organisms from one another and infer phylogeny from the
analysis. Computing machines and new techniques were used to map the DNA
and protein sequences of organisms. After having laid the part of those
sequences, scientists can easily point out the most related organisms in terms
of their DNA structure. You have already learned from Module 1 that DNA
codes for the structure and characteristics of organisms, hence it is fit to say
that if the DNA or protein synthesis of organisms share a great number of
similarities, the organisms’ development and structure will also follow. It is also
theorized that the DNA sequences of one organism carry mutations from the
previous species where they evolve, and this process is true to and pro the
evolutionary line of descent of that said organism.
Putting DNA and protein sequences data on a cladogram. In putting and using
the data from DNA connection
analyses to the cladogram, the
organisms with a more shared
number of similar odes of DNA will
be put closer to each other. I
terms of time frame where we can
indicate when does a certain
species appear and evolve in the
cladogram, scientists employ
various methodologies in trying to
count the number of mutations
present in the DNA: less mutation
means the organism is an older species and will be put closer to the root of the
cladogram depending on the correlation of data from all of the present
organisms in the clade or within the whole cladogram.
CLASSIFICATION: THE RESULT OF OUR DATA ANALYSES

The analyses of our data resulted in the comprehensive data about the
evolutionary relatedness of the organisms. Through systematics, we will be able
to put organisms on their correct classification based on their relativeness to
one another in terms of the phylogeny.
Hence the creation of the “THE TREE OF LIFE”. The tree of life is like a family
tree of all the organisms found on earth, including those that lived on the past
that we have available information from fossil records. The tree is based on the
systematics of the biodiversity of life on Earth. It puts all the organisms into
their own branches, those which are closely related to each other were placed
closer to
each other in the tree. The tree of life represents the great evolution of life as
well as the history of life on Earth because the tree also uses information from
the geologic timescale where organisms were put into the time when they first
appear. Organisms found on the root and lower part of the tree are the early
ancestors of all the organisms on Earth.
As you observe the following tree of life, where researchers worked hard to put
all of the studied and available data together so that making sense of the given
data will be more systematic and convenient, you may notice that the tree of
life contains numerous cladograms and clades which were put together as a
whole. At the end of each branch is a taxon which has unique distinctive
characteristics from other taxa.
Image
TAXONOMY and ITS PRESENCE in the TREE OF LIFE
At the bottom-most part of the tree of life is the origin of life which we have
already explored from module 2 after that is the three domain classification of
life forms on Earth namely the Archaea, Bacteria and Eukarya.
Archaea and bacteria are among the oldest living organisms on earth, together
they were comprised of the prokaryotes. Prokaryotes are single-celled
microorganism, they have simple cell structures and minimal specifications for
survival. The difference between a bacterial prokaryote and archaean
prokaryote lies on their cell wall, bacterial
prokaryotes have developed peptidoglycan in their
cell wall while archaea do not. Peptidoglycan is a
chain of protein that gives strength and
protection to the cell wall of the bacteria, it also
serves a function in binary fission,
the bacterial cell division.
Eukarya are organisms that have evolved to
have eukaryotic cells or cells which are more
complex and have several of organelles, they also
have a nucleus, unlike prokaryotes. Eukarya
consists of a different kingdom, namely the
Animalia, Plantae, Fungi, and Protista. Animalia
are the animals, Plantae are the plants, fungi are
plants like organisms but have DNA structures
that are far related to plants, their DNA is more related to that of animals
examples of fungi are molds and mushrooms, protists, on the other,

hand are microorganisms which cannot be considered
as plants or animals and were also distinguishable with
bacteria because of the more intricate cell structures
such as the nucleus. These kingdoms will be further
subdivided into phylum, and each phylum into class,
each class into order and family, which is further
subdivided into genus and species. This way of
grouping organisms is based on the principles of
Taxonomy which is fathered by Carl Linnaeus, the first
man to group organisms into a set of hierarchy.
Taxonomy precedes systematics, but both fields of
study under Biology have been working together to
make a comprehensive collection and the Earth’s biodiversity.
Taxonomy has long been naming and categorizing
organisms before systematics arrive, but systematics
help taxonomy to reclassify some organisms.
based on phylogeny rather than phenetics, molecular biology also paved the
way to make reclassification of organisms more concrete by using DNA and
protein
sequence analyses.

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Lesson 1

Why would altering DNA affect our characteristics or traits?

The central dogma states that if transcription and translation of a fragment of

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

A gene is a sequence of DNA on a chromosome that codes for a specific trait or

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

1. Scientists targets and identify specific gene.

2. They cut the targeted gene with restriction enzyme.

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

What is Recombinant DNA and what is its application?

Recombinant DNA is the resulting DNA formed through the process of

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

Evolution and Origin of Biodiversity

Evolution and Origin of Biodiversity: History of Life on Earth and

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

1. The Precambrian life (Hadean, Archean and Proterozoic eras)

The Precambrian life covers approximately 88% of the Earth’s history. It is

fossils appear to be small, one-cm long, sponge-like creatures. These fossils

mass extinction during this era.

3. The Mesozoic Era or the “middle life”

4. The Cenozoic Era or ‘recent life’

and evolve in adaptation that allowed them to live in many different

This era is the development and proliferation of perissodactyls and artiodactyls.

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

Late in the Cenozoic, further extinction followed by speciation occurred during

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

GENE FREQUENCY and EVOLUTION

As an individual, you carry a unique gene of traits, so as the other people in

Any change in the gene frequency of a species or population is EVOLUTION.

MECHANISMS OF EVOLUTION: What causes a change in gene frequency?

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

An example is the June bug or beetle which is well known as “salagubang” in

3. Gene Flow or Migration

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

An example of gene flow is when a brown beetle migrated to the population of

Catastrophic events such as floods, volcanic eruptions, and a pandemic or

An event that significantly reduces the number of populations is called the

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

It occurs when some species choose a partner with preferred characteristics.

6. RecombinationRecombination or gene shuffling is life’s way of bringing

A Mutation occurs when an insertion, deletion, or any change in the codes of

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

Patterns of Descent and

Patterns of Descent along Development of Evolutionary

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

Patterns of Descent with Modification

The similarities among organisms of different species and the few

2. Charles Darwin. Darwin, an English Naturalist, as we have already learned,

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

EVIDENCES: THE BRIDGE BETWEEN THE CLAIM AND THE FACTS

EVIDENCES OF EVOLUTION AND HOW TO USE THEM TO INFER

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

Body structures of organisms may be compared to each other to investigate

WRITTEN WORKS GENERAL BIOLOGY 2 QUARTER 3 AMOR C. DELA CRUZ, MED

Early development stages or

Scientists study the