(1) PROCESSES INVOLVED IN GENETIC techniques.
There are several steps in the process
ENGINEERING
The process of genetic engineering is not a
simple task, it requires complex machinery and
innovative minds. Since farming began, humans
have been selectively breeding different plants,
doing so provided more food and better food for all.
This process is genetic engineering in much
simpler terms than we think of it today.
In simple perspective, genetic engineering
is the process of manually transferring genetic
information from one organism to another. But,
when one thinks of the processes in genetic
engineering they are more likely to picture a
complicated science which involves altering the
very building blocks of life.
Genetic engineering is accomplished in
three basic steps:
(1) The isolation of DNA fragments from a
donor organism;
(2) The insertion of an isolated donor DNA
fragment into a vector genome and
(3) The growth of a recombinant vector in an
appropriate host.
The Process of Genetic Engineering
Genetic engineering is the process of using
recombinant DNA (rDNA) technology to alter the
genetic makeup of an organism. Traditionally,
humans have manipulated genomes indirectly by
controlling breeding and selecting offspring with
desired traits. Genetic engineering involves the
direct manipulation of one or more genes. Most
often, a gene from another species is added to an
organism's genome to give it a desired phenotype.
One of the most amazing things about life
on earth which we often take for granted is that all
life uses the same DNA code to store its
information and create proteins. Because all of life
uses the same DNA code, we are now able to
combine DNA from one species with another in
order to produce proteins in new and different ways
which is revolutionizing science and medicine. The
bacterial plasmids which you already know about
are often very crucial for these genetic engineering
of genetic engineering. Scientist follow a step-by-
step process in order to alter the DNA of an
organism.
As shown in Figure 1, the first stage of the
process is to identify the section of DNA that
contains required gene from the source
chromosome. Second stage, extract the required
gene. Third stage, bacterial plasmid is removed
from the bacterial cell and cut open using enzymes.
Fourth stage, insert plasmid into host cell and
sealed using enzymes. Fifth stage, grow
transformed cells to produce a genetically modified
organism (GMO).
Genetic engineering involves the direct
manipulation of one or more genes. Most often, a
gene from another species is added to an
organism's genome to give it a desired phenotype.
Application of Recombinant DNA
The introduction of recombinant DNA
technology paved the way in developing different
concepts and interventions in the field of biology.
Because of the different problems occurred in the
society, people began to discover many things to
lessen the problems encountered. This is the
reason why such developments were done. Below
are the important applications of recombinant DNA
technology. It includes (1) applications in crop
improvement, (2) applications in medicines and (3)
industrial applications.
Applications in Crop Improvement
In crop improvement, development of
different genetically modified crops improved both
yield and resistance to pests and weeds.
1. Distant Hybridization. Due to genetic
engineering, it is now possible to transfer
genes between distantly related species.
The barriers of gene transfer between
species or even genera have been
overcome. Through the recombinant DNA
technology, the desirable genes can be
transferred even from lower organisms to
higher organisms.
2. Development of Transgenic Plants.
Transgenic plants are genetically
transformed plants which contain foreign
genes. Resistance to diseases, insects and
pests, herbicides, drought; metal toxicity
tolerance; induction of male sterility for plant
breeding purpose; and improvement of
quality can be achieved through this
recombinant DNA technology.
3. Development of Root Nodules in Cereal
Crops. Rhizobium (nitrogen fixing bacteria)
found in the root-nodules of leguminous
plants converts the free atmospheric
nitrogen into nitrates in the root nodules.
The bacterial genes responsible for this
nitrogen fixation can be transferred now to
 cereal crops like wheat, rice, maize, barley
etc. through the techniques of genetic
engineering thus making these crops too
capable of fixing atmospheric nitrogen.
4. Development of C4 Plants. Improving the
photosynthetic efficiency of crop plants can
improve its yield. The photosynthetic rate
can be increased by conversion of C3
plants into C4 plants, which can be
achieved either through protoplasm fusion
or recombinant DNA technology C4 plants
have higher potential rate of biomass
production than C3 plants. Most C4 plants
(sorghum, sugarcane, maize, some
grasses) are grown in tropical and
subtropical zones.
Applications in Medicines
Genetic engineering plays an important role
in the production of antibiotics, hormones, vaccines
and interferon in the field of medicines.
1. Production of Antibiotics. Antibiotics
produced by microorganisms are very
effective against different viral, bacterial or
protozoan diseases. Some antibiotics are
tetracyclin, penicillin, streptomycin,
novobiocin, bacitracin, etc. Improving the
microbial strains through modification of
genetic characteristics helps in increasing
the production of antibiotics.
2. Production of Hormone Insulin. The
insulin which is a hormone used by
diabetics is usually extracted from pancreas
of cows and pigs. This insulin is slightly
different in structure from human insulin. It
leads to allergic reactions in about 5%
patients. Human gene for insulin production
has been incorporated into bacterial DNA
and such genetically engineered bacteria
are used for large scale production of
insulin.
3. Production of Vaccines. Vaccines are now
produced by transfer of antigen coding
genes to disease causing bacteria. Such
antibodies provide protection against the
infection by the same bacteria or virus.
These include vaccines for polio, malaria,
cholera, hepatitis, rabies, smallpox, etc.
4. Production of Enzymes. Recombinant
DNA technique can produce some useful
enzymes like enzyme urikinase which is
used to dissolve blood clots. It has been
produced by genetically engineered
microorganisms.
5. Diagnosis of Disease. Recombinant DNA
technology has provided a broad range of
tools to help physicians in the diagnosis of
diseases. Most of these involve the
construction of probes: short Segments of
single stranded DNA attached to a
radioactive or fluorescent marker. Such
probes are now used for identification of
infectious agents, for instance, food
poisoning Salmonella, Pus forming
Staphylococcus, hepatitis virus, HIV, etc. By
testing the DNA of prospective genetic
disorder carrier parents, their genotype can
be determined and their chances of
producing an afflicted child can be
predicted.
6. Production of Transgenic Animals.
Animals which carry foreign genes are
called transgenic animals. Cow, sheep, goat
– therapeutic; human proteins in their milk.
Fish like common carp, cat fish, salmon and
gold fish contain human growth hormone
(hGH)
Industrial Applications
Biofuels derived from biomass and these
are renewable and cost effective. Genetic
engineering plays an important role in a beneficial
and large scale production of biofuels. It also helps
in improving the organisms for obtaining higher
product yields and improve tolerance.
Recombinant DNA technique will help in the
production of chemical compounds of commercial
importance, improvement of existing fermentation
processes and production of proteins from wastes.
This can be achieved by developing more efficient
strains of microorganisms. Specially developed
microorganisms may be used even to clean up the
pollutants.
(2) HISTORY OF LIFE ON EARTH
One of the great mysteries in the Universe
is the origin of creation. Biologists rely primarily on
dating the rocks in which fossils are contained and
looking at the "molecular clocks" in living
organisms' DNA to do this. Based on the most
accepted propositions, life started at least 3.5
billion years ago, since that's the age of the
world's oldest rocks with fossil proof of life. These
rocks are rare because the surface of our planet
has been reshaped by subsequent geological
cycles, sometimes crushing older rocks while
creating new ones.
Scientists have broken the Earth's 4.56-
billion-year history into units that represent unique
periods of time based on their interpretations of the
rock record. Taken together, the geologic time
scale is made up of these time periods.
Eons represent the greatest expanses of
time. Eons are divided into eras. Each era is
subdivided into periods. Finally, periods are
divided into smaller units called epochs. Each
period within an era is characterized by somewhat
lesser profound changes in life forms as compared
with the changes that occur during an era. The
periods of the Cenozoic era are divided into still
smaller units called epochs, during which even
lesser profound changes in life forms occur. During
Precambrian time, there were fewer life forms.
These life forms are more difficult to identify and
the rocks have been disturbed often.
The eon where life began was during the
Phanerozoic eon. There are three eras within the
Phanerozoic eon: the Paleozoic, which means
“ancient life,” the Mesozoic, which means “middle
life,” and the Cenozoic, which means “recent life.”
For ease in discussion and remembering,
the eras will be the basis of division of the history of
life. The following are the four eras of the origin of
life: Precambrian, Paleozoic, Mesozoic and
Cenozoic chronologically.
Precambrian History
The Precambrian encompasses immense
geological time, from Earth’s distant beginnings
4.56 billion years ago until the start of the Cambrian
period, over 4 billion years later. Earth’s original
atmosphere was made up of gases similar to those
released in volcanic eruptions today—water vapor,
carbon dioxide, nitrogen, and several trace gases,
but no oxygen.
The oldest fossils of single-celled organisms
date from 3.5 billion years ago. Some single-celled
organisms may be feeding on methane by this time.
At 2 billion years ago, Eukaryotic cells – cells with
internal “organs” (known as organelles) – come into
being. One key organelle is the nucleus: the control
center of the cell, in which the genes are stored in
the form of DNA. Eukaryotic cells evolved when
one simple cell engulfed another, and the two lived
together, more or less amicably – an example of
“endosymbiosis”. The engulfed bacteria eventually
become mitochondria, which provide eukaryotic
cells with energy. The last common ancestor of all
eukaryotic cells had mitochondria – and had also
developed sexual reproduction.
Later, primary plants evolved that used
photosynthesis and released oxygen. Oxygen
began to accumulate in the atmosphere about 2.5
billion years ago. The most common Precambrian
fossils are stromatolites. Stromatolites are
distinctively layered mounds or columns of calcium
carbonate. They are not the remains of actual
organisms but are the material deposited by algae.
Many of these ancient fossils are preserved in chert
—a hard dense chemical sedimentary rock.
Early Paleozoic (Life Explodes)
Following the long Precambrian, the most
recent 540 million years of Earth’s history are
divided into three eras: Paleozoic, Mesozoic, and
Cenozoic.
Life in early Paleozoic time was restricted
to the seas. Laurasia is the continental mass that
formed the northern portion of Pangaea, consisting
of present-day North America and Eurasia. By the
end of the Paleozoic, all the continents had fused
into the supercontinent of Pangaea.
Some 400 million years ago, plants that had
adapted to survive at the water’s edge began to
move inland, becoming land plants. The
amphibians rapidly diversified because they had
minimal competition from other land dwellers.
The world’s climate became very seasonal,
probably causing the dramatic extinction of many
species. The late Paleozoic extinction was the
greatest of at least five mass extinctions to occur
over the past 500 million years.
Mesozoic Era (Age of Reptiles)
The gymnosperms quickly became the
dominant plants of the Mesozoic era.
Gymnosperms are seed-bearing plants that do not
depend on free-standing water for fertilization.
The development of the shelled egg
characterized the animal life of this era. Unlike
amphibians, reptiles have shell-covered eggs that
can be laid on the land. The elimination of a water-
dwelling stage (like the tadpole stage in frogs) was
an important evolutionary step. With the perfection
of the shelled egg, reptiles quickly became the
dominant land animals. At the end of the Mesozoic
era, many reptile groups became extinct.
Cenozoic Era (Age of Mammals)
The Cenozoic era is divided into two periods
of very unequal duration, the Tertiary period and
the Quaternary period. Plate interactions during the
Cenozoic era caused many events of mountain
building, volcanism, and earthquakes in the West.
Mammals—animals that bear live young
and maintain a steady body temperature—replaced
reptiles as the dominant land animals in the
Cenozoic era. Adaptations like being warm
blooded, developing insulating body hair, and
having more efficient heart and lungs allow
mammals to lead more active lives than reptiles.
Angiosperms—flowering plants with
covered seeds—replaced gymnosperms as the
dominant land plants.
Large mammals started to become extinct
at the later part of the era. In North America, the
mastodon and mammoth, both huge relatives of the
elephant, became extinct. In addition, saber-
toothed cats, giant beavers, large ground sloths,
horses, camels, giant bison, and others died out on
the North American continent. The reason for this
recent wave of extinctions puzzles scientists.
 (4) MECHANISMS OF CHANGE IN
POPULATION
Mechanisms that Produces Change in
Population
For a population to start evolving, members
of the population should possess variations, which
is the material on which agents of evolution act.
Any heritable trait is a characteristic of organism
that is influenced by the genes. Without any genetic
variation, the basic mechanism of evolutionary
change cannot activate.
1. Mutation
Very occasionally, little copying alteration or
change (mutations) occurs during the process of
DNA replication. This may because by a number of
factors, which include but not limited to radiation,
viruses, or carcinogens (cancer causing materials).
Since the blueprint of any cell function is dictated
by its genotype, even a minute mutation might
mean that the cells fail work properly.
2. Gene Flow
A result of migrating individuals that breed
in a new location is gene flow. Genes coming from
the immigrants may add new alleles to the existing
gene pool of the population, or they may modify the
allele frequencies already present if they come from
a population with different allele frequencies. Some
events that lead to gene flow may be in pollen or
spores being disperse by air in a new location,
animals hibernating and transferring to a new locale
due to changes in temperatures, or humans moving
to new cities or countries.
3. Recombination
Because of sexual reproduction, new gene
combination are introduced into a population; thus,
it can be an important source of genetic variation.
As what you might already know, even siblings are
not genetically identical to their parents or even to
each other because when organism reproduce
sexually, some genetic “recombination” on
homologous chromosomes occur during meiosis,
bringing together new combinations of genes.
4. Genetic drift
Any change in the allele frequencies in a
population due to random sampling is called
genetic drift. In every new generation, some
species, just by chance, may leave behind a few
more descendants than other individual. The genes
of these next generations will be genes of the
“luckier” individuals, but not necessarily mean the
healthier or “better” individuals. When a few
“original” individual settle in a new region, the
resulting population will not have all the alleles
found among the members of the populations. The
resulting patterns of genetic variation is what is
known as the founder effect.
Natural Selection
As what it expressed in Darwin’s Theory of
natural selection in species, it encompasses the
phrase, “when the environment changes, natural
selection often favors different traits in a species.”
Humans are significantly changing the environment
in a number of ways; we therefore should not be
flabbergasted to see biological species that try to
adapt to these new conditions.
The Peppered Moth case forwarded by the
biologist J.B.S. Haldane in 1924 is an excellent
example of Darwin’s Natural selection in action.
The gene that controls the color of the peppered
moth occurs as two alleles, a melanic allele (black
color), and a mottled allele (pale color). Pale moths
were dominant in the country side around
Manchester in the early 18th century.
However, the trees on which these moths
are resting get disturbed, altered, and were covered
in black soot during Industrial Revolution. Pale
mottled moths were poorly camouflaged on the
black tree trunks and especially eaten by birds as
food. In contrast, the black melanic moths were
better in avoiding predation. Natural selection acted
against the mottled moths while the melanic moths
were dominant. However, there was one final twist.
As the skies became cleaner in 20th century, the
pale-colored moths returned and displace the
melanic moths again.
Artificial Selection
Artificial selection is exactly the same
mechanism as natural selection but it is sort of
controlled by human purposes rather than natural
forces. Even if we have been successful in shifting
the frequency of alleles in various dog breeds, we
have not created new species.
The biological definition of species is a
population that can interbreed and produce fertile
offspring. Most dogs can effectively interbreed with
other dogs, and also with wolves, so technically all
dog breeds are just subspecies of the wolf (Canis
lupus). Breeding of dogs is hence an example of
what biologist called as microevolution, wherein the
frequency of alleles in the population has change
but not that great enough to produce an actual new
species.
What happens when a population will not
undergo evolution?
As we have discussed genetic frequencies,
it is also important to know the underlying principle
when a population will have a stable genetic
frequency. Thus, the Hardy-Weinberg
Equilibrium.
If a certain population has a constant
genetic stability, it is said to be at HardyWeinberg
equilibrium. This state is reached when allele and
genotype frequencies do not change from
generation to generation. In order to achieve such
equilibrium, five important criteria should be met:
 (1) random mating;
 (2) a very large population size;
 (3) migration between population did not
transpire;
 (4) no mutation occurred; and
 (5) gene pool is not affected by natural
selection.
If all the aforementioned criteria are met,
two result will follow. First, allele frequencies at a
locus will stay constant from generation to
generation. After one generation of random mating,
the genotype frequencies will stay the same.
Stating the second result in the form of an equation
produces the Hardy-Weinberg equation:
p2 + 2pq + q2 = 1
The most important principle of the Hardy-
Weinberg equilibrium is that unless some agents
act to change them, allele frequencies should not
change to generation to generation. More so, the
equilibrium shows the distribution of genotypes to
be anticipated for a population at genetic
equilibrium at any value p or q.
If the conditions set for the equilibrium to
hold are not found in nature, why is that necessary
for such equilibrium to be considered important?
This is simply because the Hardy-Weinberg
equilibrium allows biologists to determine whether
evolutionary agents are already operating together
with the probable agents (as evidence by the
pattern of nonconformity from the equilibrium).
(5) DESCENTS WITH MODIFICATION
Reproductive Isolation Mechanism
A. Pre-zygotic isolation mechanisms prevent
fertilization and zygote formation.
1. Geographic or habitat isolation
(Ecological) – potential mates occupy
different areas or habitats thus, they never
come in contact. Rivers change course,
mountains rise, continents drift, organisms
migrate, and what was once a continuous
population is divided into two or more
smaller populations.
2. Temporal or seasonal isolation
(Allochronic) – different groups may not be
reproductively mature at the same season,
or month or year. Example are individuals
that have bold behavioral types might be
more likely to feed, or to mate, during times
of high-predation risk than individuals with
shy temperament types that are less likely
to be active during risky periods.
3. Behavioral isolation (Ethological) –
patterns of courtship are different. Example
are some birds that construct elaborate
bowers and decorate them with different
colors in order to woo females. If two
incipient species evolved differences in this
mating ritual, it might permanently isolate
them and complete the process of
speciation.
4. Mechanical isolation – differences in
reproductive organs prevent successful
interbreeding. Lack of "fit" between sexual
organs: This is a big issue for insects with
variably-shaped genitalia. These damselfly
penises illustrate just how complex insect
genitalia may be.
5. Gamete Viability isolation (Gametic) –
incompatibilities between egg and sperm
prevent fertilization. Example are foxes
which cannot interbred with coyotes,
wolves, and domestic dogs,
B. Post-zygotic isolation mechanisms allow
fertilization but nonviable or weak or sterile
hybrids are formed.
1. Hybrid inviability – fertilized egg fails to
develop past the early embryonic stages.
2. Hybrid sterility – hybrids are sterile
because gonads develop abnormally or
there is abnormal segregation of
chromosomes during meiosis. The ability to
participate in hybridization is not equally
distributed in the populations and frequently
is restricted to a small proportion of cross-
compatible genotypes.
3. Hybrid breakdown - F1 hybrids are normal,
vigorous and viable, but F2 contains many
weak or sterile individuals. There are genes
contributing to genetic incompatibilities, and
therefore it results to the evolution of
intrinsic reproductive isolation (hybrid
sterility and inevitability).
Note: Remember the different genetic mechanisms
that can change gene frequencies. In the presence
of a reproductive isolating mechanism, genetic drift,
natural selection, mutation and gene flow are free
to operate on the population. These will lead to
genetic divergence and ultimately to species
formation or speciation.
Speciation – Diversity of Organisms
Modes of Speciation
A. Allopatric speciation or geographic
speciation (allo – other, patric – place; ‘other
place’) - occurs when some members of a
population become geographically separated
from the other members thereby preventing
gene flow. Examples of geographic barriers are
bodies of water and mountain ranges. Dispersal
occurs when a few members of a species move
to a new geographical area. Vicariance occurs
when something in the environment separates
organisms of the same species into groups.
 Allopatric speciation may be by subdivision of
the species range or by a peripheral isolate - a
small population which becomes cut off at the
edge of the species range.
B. Parapatric speciation (para – beside, patric –
place; ‘beside each other’) –occurs when the
groups that evolved to be separate species are
geographic neighbors. Gene flow occurs but with
great distances is reduced. There is also abrupt
change in the environment over a geographic
border and strong disruptive selection must also
happen. Parapatric speciation could happen if a
steep cline evolved into a hybrid zone and
barriers to interbreeding then evolved.
C. Sympatric speciation (sym – same, patric –
place; ‘same place’) - 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). Sympatric speciation is most
likely if selection first establishes a stable
polymorphism and then favors assortative
mating within each polymorphic type.
Reinforcement is the enhancement of
reproductive isolation by natural selection: forms
are selected to mate with their own, and not with
the other, type. Sympatric speciation requires
reinforcement to happen; parapatric speciation
usually requires it; allopatric speciation can take
place with or without reinforcement.
(6) EVOLUTIONARY THOUGHTS
The Origins of Evolutionary Thought
There are many different theories which
explain how different life forms exist. In the mid-
18th century, most people believed in creationism.
Creationism held the idea that all forms of life were
created in its present form and they remain
unchanged since the beginning. Even the famous
Carl von Linnaeus, the Father of Taxonomy,
believed in the fixity of species George Louis
Leclerc, known as Count Buffon, was a French
naturalist who first described descent with
modification such as environmental influences,
migration, geographical isolation and the struggle
for existence. However he was hesitant in sharing
his idea to the public.
In the late 18th century, Georges Cuvier, a
vertebrate zoologist and paleontologist proposed
the theory of catastrophism. One day he had
observed that a particular region showed a
succession of life forms in the soil layers. His
observation seemed to contradict with his belief in
special creation of each species. Cuvier explained
that there might have been violent and sudden
natural catastrophes such as great floods, tectonic
earthquakes, and rapid formation of mountain
chains, which resulted to death and extinction of
most plants and animals. After each catastrophe,
God created new sets of life forms.
In contrast to catastrophism, James Hutton
and Charles Lyell believed that natural forces now
changing the shape of the earth’s surface have
been operating in the past much the same way.
This idea is known as uniformitarianism - large
geological changes occurred not in catastrophic
events but by gradual accumulation of small
geological changes over long period of time.
Jean Baptiste de Lamarck was the first
biologist to believe that life forms evolve. He
proposed the Inheritance of Acquired
Characteristics, which is also called Lamarckian
Evolution. He believed that every organism has the
will to survive, and that will has allowed us to
change to more advantageous traits that suit us to
the environment. The acquired traits are then
inherited by the next generation. One example that
Lamarck gave is the elongation of giraffes’ necks
over time because animals stretched their necks to
reach for food and then passed on a long neck to
their offspring. Today, Lamarck’s idea was proven
to be incorrect. Phenotypic changes acquired
during an organism’s lifetime cannot pass onto next
generation’s common ancestor. Because we all
share a common ancestor, we are all related to one
another no matter how different we are. The
relationships among organisms can be illustrated
on a family tree.
Charles Darwin
Charles Darwin was only 22 years old when
he got a chance to set sail aboard the Beagle, to
travel around the world and map the coasts of
South America. He was an assistant for Captain
Robert Fritz Roy. His Beagle voyage allowed him to
develop a theory that would contradict the special
creation of every organism and imply that all
species evolve from common ancestors through a
process called natural selection.
While on his visit to Galapagos Islands, he
had observed that organisms are geographically
distributed and isolated on the separate islands. He
noted that similar animal types show distinct
differences in body form and functions from island
to island. He explained that these differences
represent adaptations to differing environment
living organisms sit like leaves at the tips of the
branches of the Tree of Life. Living things share a
common ancestor. All organisms are related to one
another no matter how different they seem.
Theories Related to Evolution
Creationism is the idea that living things are
created and remains unchanged since the
beginning.
Catastrophism is the idea that violent and
sudden natural catastrophes have resulted to death
and extinction of most plants and animals. After
each catastrophe, God created new sets of life living organisms. Organisms usually arise in areas
forms. where similar forms already exist. Similar
organisms may also be found in different locations
Uniformitarianism claims that large
which could mean that the two places were
geological changes occurred not in catastrophic
previously connected.
events but by gradual accumulation of small
geological changes over long periods of time. (8) INVESTIGATIVE FILES: INTO THE
DEPTHS OF EVOLUTION
Evidences of Evolution
Differentiating Phylogeny
Fossils are remains of ancient organisms
trapped in rocks, tar pits, frozen in ice or embedded The world is highly diversified. Living things,
in amber. The activities and behavior of ancient life not just the plants and animals that are common or
forms also left behind fossil traces (such as easily seen but also the species that are not well
footprints, dungs, gastric stones, nests and known, such as microorganisms or invertebrates
burrows) which scientists can study. The records are included. Biodiversity refers to life on land, in
found in the rocks show a gradual evolutionary the water, in the air, in deserts and caves—even in
descent from simpler to more complex life forms. hot springs or glaciers. Scientist work hard to
Paleontologists use the fossils found in rocks to organize living things into groups as they are
track the evolutionary history of many organisms. identified. This is the field of study called taxonomy
which come from a Greek word ‘taxis’ that means
As the climate changed to drier conditions,
Order or arrangement .Taxonomist is a biologist
foliage plants were replaced by grass fields. Those
who studies taxonomy. They decide how to classify
with the characteristics suited for this (tooth
species, explore how they fit in their ecosystem and
structure fit for eating hard, dry grass) survived
categorize relationship with others in their habitat
better. The forced grazers also became runners
before giving them names according to
(with longer leg bones and lesser toes) to be able
standardized system, the binomial naming. This is
run more efficiently in the hard ground and to
consists of the genus and specie.
escape from predators.
The hierarchical taxonomic classification
Evidences from Structure
helps scientists understand and organize the
Structures in different organisms can be diversity of life in our planet. Basically, it means
compared to infer common lineage. groups are classified within larger groups. Each
level of hierarchy is called the taxonomic level
HOMOLOGOUS STRUCTURES are wherein the kingdom is the highest and specie the
structures with the same set of bones that lowest. It means from general to specific.
presumably evolved from a common ancestor.
They appear different and may have varied Specie is the basic unit of classification.
functions. They are organisms that share many features and
can breed with each other producing fertile
ANALOGOUS STRUCTURES are offspring. During the time of Linnaeus the kingdoms
structures that perform the same function but have were only the plants and animals.
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.
Evidences 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 After the discovery of microscope where
juvenile or adult form. other organisms and cells can be seen, it became
six, the plants, animals, protists, fungi,
Evidences from Molecular Biology archaebacteria and eubacteria.
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. Biogeography is
the study of geographical distribution of fossils and
 KPCOFGS, for Kingdom, Phylum, Class,
Order, Family, Genus, Specie which means ‘Keep
Ponds Clean Or Frogs Get Sick’.
A sample phylogenetic tree showing
relationship between organisms based on shared
anatomical features:
Phylogenetic Tree and Evolutionary
Relationship
Phylogenetic Tree
A phylogenetic tree is a branching diagram
that represents hypotheses about the evolutionary
relationship among organisms. The pattern of
branching reflects how specie or other groups
evolved from ancestors. It is showing the inferred
relationship between various biological species.
Two species are more closely related if they have a
more recent common ancestor and less related if
they have a less recent common ancestor.
Several evidences are employed such as
external morphology, internal anatomy, biochemical
pathways, behavior and DNA. It also includes
evidence of fossils during the generation of a
phylogenetic tree. There are two forms of
phylogenetic tree, the phylogram and cladogram.
They differ based on whether the branches are
scaled or unscaled. The phylograms are scaled
while cladograms are unscaled so lines in this tree
are of the same size.
Homologous and analogous structures
provide evidence for common ancestry.
Homologous structure shared similar embryonic
origin like the bone of the flipper of whale and the
human arm. Analogous structures have similar
function like the wings of butterfly and of a bird.
Homologous structures share common ancestry but
the analogous structures do not share a common
ancestry.
How to Read a Phylogenetic Tree
Important features that help in
understanding a phylogenetic tree are described
below.
1. A phylogenetic tree is a branching diagram,
showing the evolution of closely-related species
from their ancestor.
2. It is composed of lines that represent the
branches of trees.
3. The root or basal node of the tree represents
the common ancestor.
4. A line shows the propagation of a particular
species over time. The length of a line
represents the existence of the species over
time.
5. The branching of the line at a particular point
called external node shows the split of a lineage
or speciation or formation of new and distinct
species in the course of evolution.
6. The internal node is the one connecting the
branches of the tree.
7. The distance of the branches in the
phylogenetic tree represents the amount of
inferred evolutionary change.
8. Each tip of the phylogenetic tree represents a
unique species. They are called the
descendants.
9. From root to tips, the branching represents the
descendant of species from the common
ancestor.
10. The phylogenies traces show the uniqueness of
a particular species and the parts that it share
with the other related-species during evolution.
11. Each species has its own ancestor every time it
splits; the organisms are closely related if they
have common ancestor.
12. Monophyletic groups are organisms descended
from the same common ancestor
13. Polyphyletic group are organisms composed of
unrelated organisms descended from more
than one ancestor.
14. An ingroup is the clade that is the focus of a
phylogenetic analysis while an outgroup is the
distantly related group of organisms that serves
as reference group, nearest to the root.
Phylogenetic tree is constructed based on a
given evidence of evolution. Organisms that share
similar physical features and genetic sequences
tend to be more closely related than those that do
not.
 (9) THE EXPLANATION BEHIND EVERY
TRANSFORMATION
What makes one unique and what makes
one similar to another” is the leading question not
only to systematists but for all of us. A systematist
is a specialist of taxonomy who has two major
functions:
1. to determine by means of comparison
what the unique properties of each
species and higher taxon are
2. to determine what properties certain
taxa have in common and the biological
causes of the differences or shared
characters.
With these information, one can start to
understand the relatedness of organisms. Using the
data from fossils to molecules and genes help
systematist to create a comprehensive tree of life.
A tree where one can infer the relationships
among organisms. Systematics has been used in
creating the evolutionary relationship of the various
kinds of life forms.
2. HOMOLOGIES
Systematics is the study of the many kinds
and diversity of organisms and all the relationships Homologies mean similar characters due to
among them. This traces phylogeny which is one of relatedness. This can be shown by comparing the
its goal. A phylogeny is the study of evolutionary anatomies or structures of different living things,
history of a species or group of species. comparing their cellular similarities and differences,
Systematics is also considered as the study of studying embryological development and studying
biological diversity in an evolutionary context. On the vestigial structures within individual organisms.
the other hand, a phylogenetic tree is a diagram
that represents evolutionary relationships. Anatomical/Structural Evidence
Diverse species of plants are widespread on
Lines of Evidence to Infer Evolutionary
Relatedness earth. They have leaves that vary in shape, size
and functions. For example, the pitcher plant and
1. FOSSIL EVIDENCE Venus’ flytrap use leaves to trap and digest insects.
Nevertheless, all are homologous structures came
Knowledge about the life’s history was
from the same origin. The same with the picture
based on the study of fossils which are remains of
below, homologous structure of vertebrate.
ancient organisms. Scientists compared the fossils
in the different rock layers to enable them to
understand the changes happened in the
characters of the organism through years.
Fossils provide evidence that organism had
undergone changes as the time passed by. One
example is the Cyanobacteria Imprint. This gives
evolutionist a hint that life today had evolved from a
single celled organism called bacteria.
Fossils also provide the structural The forearm of human, horse, dolphin and
similarities shown by fossilized plants and animals bat have common structure but functions
with the present plants and animals. In human differently. Likewise, the forelimbs of frogs, birds,
evolution for example, the commonality of the skulls rabbits and lizards are different, telling the
of ape men and the skull of man (Homo sapiens) differences the way they live. But those different
are very evident as shown in figure 1. So, one forelimbs all share the same set of bones – the
could assume that ape men be the ancestors of humerus, radius and the ulna. Although those
man that endured 4.5 billion years ago. structures function differently but have evolved from
similar ancestral structure. Therefore, organisms
that are closely related to one another share many
anatomical or structural similarities.

Cytological/Cellular Evidence
Organisms having the same cellular
organelles are believed to share common
ancestors. Plants for example contain chloroplast to
perform the process of photosynthesis. In like
manner, the three domains of life was categorized
based on the cellular structures of the organisms.
The Eukarya or Eukaryotes have nucleases and
membrane bound organelles, while the Archaea
and Bacteria do not have distinct nucleus but differ
from each other in some attributes.
Developmental Body
Figure 3 shows the different stages of
embryological development of different vertebrates.
Similarities are evident at the early stage of
embryonic development among human, pig,
chicken and fish. This implies a common ancestor.
These organisms are said to be closely related
since the embryos display similar patterns of
development.
Biochemical Evidence
One of the many lines of evidences is the
same four (4) DNA bases existence in all living
things. This suggests that all life evolved from one
common ancestor. Organisms having similar amino
acids and genetic arrangement have close
evolutionary connections. By comparing amino acid
sequences can possibly estimate the evolutionary
distances and relationships between different
species.
As time goes by, inherited characters (like
DNA sequences) change as Evolutionary Theory
states. Thus, organisms that are closely related will
have more similar DNA sequences than those
organisms who are related distantly, and the DNA
sequences will differ more if two species will be
separated far from a common ancestor. Example,
human DNA sequences are about 97.7 % identical
to a chimp’s DNA sequences while only 85.7%
identical to a mouse DNA sequences.
When organisms are closely related, they
have more the same appearance or morphology
than those of distantly related organisms. For
example, humans and chimps. However, how
closely related organisms are can be hard to
determine. The same appearance can be
misleading when trying to identify organisms. In
that case, DNA can be used by the scientists as aid
to explain the relationships between organisms.
DNA sequences are used by the scientists to
create a phylogenetic tree.
According to Dowell, 2008, evolutions of
living organisms is a molecular process based on
genetic information encoded in the DNA, RNA, and
protein.
3. BIOGEOGRAPHY
Biogeography means the geographic
distribution of species in time and space as
influenced by many factors, including continental
drift and long distances dispersal. Evidence
supporting continental drift was the discovery of
fossils with similarities found in different continent.
While long distance dispersal is a characteristically
extreme event that propagate movement in any
plant or animal population.
4. MOLECULAR CLOCK HELPS TRACK
EVOLUTIONARY TIME
Molecular clock tells time – on an epoch.
(Epoch, a unit of geological time during which a
rock series is deposited). It measures the number
of changes, or mutations, which accumulate in the
gene sequences of different species over time
(Hedges, Penn State Professor of biology).
Connection of Classification to Phylogeny
Biologist use phylogenetic tree for many
purposes, including:
I. Testing hypothesis about evolution
II. Learning about the characteristics of
extinct species and ancestral lineages
III. Classifying organisms
Commonly accepted evolutionary
relationships are shown in a phylogenetic tree. This
shows how organisms are closely related or
distantly related. The taxa are being represented as
branches that are divided into two nodes. Nodes
represent the hypothetical common ancestor of the
taxa and the taxonomic unit (order, family, genus,
etc.) that contains the branches represented.
Organisms in the same clade or branch are more
closely related while those in different clade are
distantly related. DNA sequences predict the
evolutionary relationship of an organism (Rea and
Dagamac).
Hierarchical classification is shown on the
phylogenetic tree’s progressively fine branching
that exhibits a connection between classification
and phylogeny. Evolutionary relationships between
various biological organisms are shown on the
branches, it also shows that from a series of
ancestors, species are transformed.
In some cases, the hierarchical
classification of groups match the branching
patterns nested within more inclusive groups. In
other situations, taxonomist may lead to a place of
species within group of organisms (for example
genus or family) other than the group to which it is
closely related by just using certain similarities
among organisms. Is such mistake has occurred
and was concluded by systematics, to accurately
reflect it evolutionary history, organisms may be

reclassified (that is placed in a different genus or

family). Let us take order carnivore as an example
The tree traces possible evolutionary
relationships between some of the taxa within the
order Carnivora, itself a branch of Class Mammalia.
The branch point (1) represents the most recent
common ancestor of all members of the weasel
(Mustelidae) and dog (Canidae) families. The
branch point (2) represents the most recent
ancestor of coyotes and gray wolves.