BIOLOGY REVIEWER Ø A suitable cloning vector is selected most

commonly use vectors are plasmids and

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bacteriophages
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LESSON 1: RECOMBINANT DNA
TECHNOLOGY/ GENETIC ENGINEERING
What is Recombinant DNA Technology?
Ø A series of procedures that are used to join
together (recombine) DNA segments
Ø A recombinant DNA molecule is constructed
from segment of two or more different DNA
molecules. Under a certain conditions, a
recombinant DNA molecules can enter a cell
and replicate there, either on its own or after it
has been integrated into a chromosome.
What is Recombinant DNA? Step III. Introduction of DNA – insert into vector to
Ø Recombinant DNA molecule are DNA form recombinant DNA molecule
molecules formed by the combination of at Ø The DNA insert which has been extracted and
least two strands. cleaved enzymatically by the selective
Ø Recombinant DNA is possible because DNA restriction endonuclease enzymes are now
molecules from all organisms share the same ligated (joined) by the enzyme ligase to vector
chemical structure, and differ only in the DNA to form a recombinant DNA molecule
nucleotide sequence. which is often called as cloning – vector –
insert DNA construct.
Ø Recombinant DNA molecules are sometime
called chimeric DNA.
Steps in Recombinant DNA Technology

Step I. Selection and isolation of the gene of interest

Step IV. Cell transformation
Ø Select a piece of DNA (gene) from a donor cell
Ø Suitable host cells are selected and the
which is it be cloned
recombinant DNA molecule is introduced into
Ø Cut the piece of DNA with a restriction enzyme these host cell.
and then isolated and enzymatically
Ø This process of entry of recombinant DNA into
Ø This DNA segment of interest is termed as host cell is called transformation
DNA insert or foreign DNA
Ø Usually selected is called hosts are bacterial
Step II. Selection of suitable cloning vector cells like E. col; however yeast – fungi may
also be utilized.
Ø A cloning vector is a self – replicating DNA
molecule, in to which the DNA insert is to be
integrated

Step V. Expression and multiplication of the gene
introduced into the host
Ø Production of the desired product
Ø Recombinant DNA works when the host cell
expresses protein from the recombinant genes
Ø Protein expression depends upon the gene
being surrounded by a collection of signals
which provide instruction for the transcription
and translation of the gene by the cell.
Applications of Recombinant DNA
Health & Medicine
Ø Production of antibiotic
Ø Production of hormones
Ø Production of vaccines
Ø Biosynthesis of interferon
Ø Modification of enzymes
Ø Gene therapy
Ø Prevention and diagnosis of diseases
Agriculture/ Food Production
Ø Production of transgenic plants
Ø Production of transgenic animals
Forensic Science

Tools of Recombinant DNA Technology Ø Production of industrial products

1. The enzyme Ø Environmental protection

Ø Restriction enzyme – help to cut Ø Energy production – biofuel

Ø The polymerases – help to synthesize ——————————————————————

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Ø The ligases – help to bind or joined together
LESSON 2: HISTORY OF LIFE ON EARTH
Ø The desired gene and the vectors are cut by the
same restriction enzymes to obtain the The Geologic Time Scale
complimentary sticky notes, thus making the
work of the ligases easy to bind the desired
gene to the vector.
2. The vectors
Ø Help in carrying and integrating the desired
gene
Ø They are the ultimate vehicles that carry
forward the desired gene into the host organism
Ø Plasmid and bacteriophages are the most
common vector used as they have very high
copy number
3. Host organism
Ø The standard method used to divide the Earth’s
Ø Into which the recombinant DNA is introduced long natural history into manageable parts
Ø The host is the ultimate tool of recombinant Ø Divided into eon, era, period, and epoch which
DNA technology are characterized by the type of organisms that
dominated the Earth at that time.
Ø There are a number of ways in which the
recombinant DNA’s are inserted into the host, Precambrian Time
namely – micro injection, biolistic or gene gun,
alternate cooling and heating, use of calcium Hadean
ions, etc. Ø 4.6 bya to 4 bya
 Ø Formation of the Earth
Ø Meteorites, intense radiation from the sun
Ø Atmosphere are composed of non – breathable
gas: carbon dioxide, nitrogen, sulfur, methane
and ammonia
Archaean
Ø 3.58 bya
Ø The beginning of rock record
Ø Life first appeared on Earth, single – celled
bacteria (prokaryotes)
Ø Chemoheterotrophs
Ø Stromatolites – colonies of photo synthetic
bacteria (cyanobacteria or blue green algae)
Proterozoic (age of first life)
Ediacaran
Ø 2.5 bya
Ø Stable continent first appeared
Ø First abundant fossils of living organism mostly
bacteria and Archean's • Oxygen build up in the
atmosphere
Ø Aerobic eukaryotes dominate
Ø First animal appear soft bodied sea creature
like sponges and jellyfish
Ø Continents had merge into a single
supercontinent Rodina
Phanerozoic (revealed or visible life)
-age of muticellullar animal life
Paleozoic (ancient life)
Ø The longest and most diverse era
Ø Divide into six period based on the dominant
forms of life
Ø Multicellular animals underwent a dramatic
“explosion” in diversity called Cambrian
explosion
Ø Almost all living animal phyla appeared within
a few millions of years
Ø Mass extinction in history happened 90% of all
marine animal species are wiped out 70% of
land animals.
Ø Possible causes increased volcanic activity
climate change – cooler climate
Cambrian
Ø The Cambrian explosion pf life occurs, all
existing animal phyla develop
Ø First vertebrate, earliest primitive fish
Ø Supercontinent Rodina began to break into
smaller continent Gondwana and Laurentia
Ordovican
Ø First vascular plants appeared on land and have
spread through the continents
Ø Remarkable time in the evolution of fishes
Ø Rapid spread of jawless fish
Ø Appearance of first jawed fish and freshwater
fish
Devonian (the age of fishes)
Ø Fish and land plants become abundant and
diverse
Ø First tetrapod's (four limb or leg – like
appendages) appear
Ø First amphibians appear
Ø Ferns, horsetails, and seed plants have also
appeared
Carboniferous
Ø The term “carboniferous” or “carbon –
bearing” comes from
Ø England, in reference to the rich deposit of coal
that occur there
Ø Evolution of amniotic egg
Ø First winged insects
Ø First reptiles
Permian
Ø Largest mass extinction recorded in the history
of life on Earth due to climate change
Ø Land masses began moving together,
supercontinent called “Pangea” was formed
Ø Glaciation decrease continents become drier
Ø Reptiles diversify
Ø Forest of fern – like plants shifted to
gymnosperm
Mesozoic (middle life)
Triassic
 Ø Climate is generally hot and dry Ø Marked by the continued uplift of the rocky
mountains in western north America
Ø Modern gymnosperms such as conifers
Ø Growth of the mountain may have helped to
Ø first appeared
cool down the climate
Ø Dinosaur evolved
Ø Paleocene mammals were mostly small
Ø First true mammals appeared herbivores

Ø Reptiles become the most abundant because of Ø Prosimian primates (tree shrew and tarsiers)
their ability to adapt to the drier climate • also increase in number
Supercontinent Pangea began to break apart
Eocene Epoch
Ø Triassic period ended with mass extinction
Ø Oldest known fossils of most of the modern
accompanied by huge volcanic eruption
orders of mammals appear
Jurassic
Ø Both group of modern ungulates (Artiodactyl
Ø Age of dinosaur including bird – like dinosaur and Perissodactyl) became prevalent mammals
and flying reptiles at this time

Ø Flowering plants (Angiosperm) evolved Ø Rocky mountains grow and the alps and
Pyrenees are formed
Ø Early mammals were developing and
diversifying Oligocene Epoch

Ø Separation of the continent Laurasia and Ø Relatively short span of time

Gondwana was almost complete
Ø Appearance of the first elephant with trunks,
Cretaceous early horses • Appearance of many grasses

Ø Extinction of the dinosaurs Ø Origin of primates

Ø This mass extinction is the secondmost Miocene Epoch

extensive in the history of the Earth
Ø Was a time of warmer global climates than
Ø Flowering plants outnumbered the other plants those in the preceding Oligocene

Ø Mountain ranges where formed including Ø Expansion of grass land is correlated to a

California Sierra Nevada and the European drying of continental interior
Alps
Ø Mammals and angiosperm continue to diversify
Ø The age of reptiles came to end
Pliocene Epoch
Ø The age of mammals is about to begin
Ø Was a time of warmer global climates than
Cenozoic Era (modern life) those in the preceding Oligocene

Ø Is the most recent era in the history in life of Ø Expansion of grass land is correlated to a
Earth drying of continental interior

Ø Age of mammals Ø Mammals and angiosperm continue to diversify

Ø Divided into two main subdivision: the tertiary Cenozoic Era (modern life)
and quaternary
Quaternary period
Tertiary Period
Ø The younger of the two period of Cenozoic era
Ø from 65 million years ago to 1.8 million years
Ø 2 million years ago to the present
ago
Ø Divided into: Pleistocene and Holocene
Ø Divided into five epochs: Paleocene, Eocene,
Oligocene, Miocene, and Pliocene • Mammals Ø Europe and North America were covered by
diversify quickly glacier
Paleocene Epoch Ø Marked by the rise and dominance of human
Pleitocene
Ø Large mammals characterized Pleistocene
Ø Evolution and expansion of Homo sapiens
Ø Human had spread through most of the world
Ø Pleistocene fossils are often abundant, well –
preserved and can be dated very precisel
Holocene (the age of man)
Ø The name given to the last 11,000 years of the
Earth’s history
Ø Holocene was witnessed all of humanity’s
recorded history and the rise and fall of all its
civilizations
Ø Holocene has also seen the great development
human knowledge and technology
Ø To observe a Holocene environment, simply
look around you
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LESSON 3: MECHANISMS OF EVOLUTION
What is evolution?
ü Evolution is change in the heritable
characteristics of biological populations over
successive generations.
ü Evolution is any change in the relative
frequencies of alleles in the gene pool of a
species
ü Evolution means that a population is changing
in its genetic makeup over generations
The population as the basic unit of evolution
ü Individual organisms of a species do not
evolve, but a population of organisms
ü Evolution is caused by changes in the gene
pool of a population as a result of changes that
occur to individual genes.
Two types of genetic drift
What then can cause the allele frequencies in a gene
pool to change?
Five forces or mechanisms of evolution that may have
caused changes in the gene pool
I. Natural Selection
ü Natural selection can only take place
if there is variation or differences
among individuals in a population.
These differences must have genetic
basis
ü Natural selection occurs when one
allele (or combination of alleles of
different genes) makes an organism
more fit, that is able to survive and
reproduce in a given environment. If
an allele reduces fitness its frequency
will tend to drop from one generation
to the next.
II. Mutation
ü Mutation is a source of new allele in a
population
ü Mutation is a change in a DNA
sequence of the gene
ü A mutation can change one allele into
another, but the net effect is a change
in frequency
ü The change in frequency resulting
from mutation is small, so its effect on
evolution is small unless it interacts
with one of the other factors, such as
natural selection.
III. Genetic Drift
ü Genetic drift involves changes in
allele frequency due to chance event –
literally, “sampling error” in selecting
alleles for the next generation.
ü Alleles may on may not made it to the
next generation due to chance events
including mortality of an individual,
events affecting finding a mate, and
even the events affecting which
gametes end up in fertilization.
ü Genetic drift can occur in any
population of non – infinite size, but it
has a stronger effect on small
population.
① Population bottleneck effect
that results in a large portion
of the genome suddenly
being wiped out for example
a disaster that kills a large
portion of the population, the
genetic structure of the
survivors becomes the
genetic structure of the entire
population, which maybe
 different from the pre –
disaster population.
② Founders effect occurs when
some portion of the
population leaves to start a
new population a new
location, or if a population
gets divided by a physical
barrier of some kind. This
new population does not
have the genetic diversity of
the previous one.
IV. Genetic Flow/ Migration
ü Gene flow or the flow of alleles in and
out of a population resulting from the
migration of individuals or gametes.
ü When the migrating individuals
interbreed with new population, they
contribute their genes to the pool of
the local population.
ü Gene flow may change the frequency
or the range of alleles in the
population.
ü The introduction of new alleles
increases variability within a
population and allows for new
combination of traits.
V. Recombination
ü production of new combination of
alleles occurs in three ways during
sexual reproduction..
ü During meiosis, homologous pairs of
chromosome are separated in parceled
randomly into gametes. As a result of
this segregation of homologues each
human (having 23 paired of
chromosomes) can produces 8 million
different combination of
chromosomes in his or her gametes
ü Recombination of alleles on
individual chromosomes also occurs
regularly as a result of crossing over
between pairs of homologous
chromosomes, adding to the
variability.
ü Then, during fertilization, gametes
join in random pairs. Together, these
events guarantee that each fertilized
egg bears a completely unique
combination of allele, or genotype.
Many of these new allele combination
produce measurable differences in
physiological traits (new phenotypes)
that in turn alter the fitness of the
individual in a particular environment.
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LESSON 4: EVOLUTION AND ORIGIN OF
BIODIVERSITY: PATTERNS OOF DESCENT
WITH MODIFICATION
What is Charles Darwin’s view of evolution?
ü Darwin propose that species undergo “descent
with modification” and that all living things
can trace their descent to a common ancestor
What Exactly is a Species?
① Species is a Latin word meaning “kind” or
“appearance”
② Species are group of interbreeding natural
populations that are reproductively isolated
from other such group.
③ Species are group similar – looking organisms
that can breed with one another and produce
fertile offspring.
④ Species is a collection of individual who share
a common gene pool and who regularly
interbreed with each other in nature to produce
viable and fertile offspring
ü When members of two different
species cannot interbreed, this is known as
reproductive isolation (no genetic
exchange)
ü When members of a species
interbreed, they share genes with one
another, therefore the individuals within a
species share a group of allele called gene
pool.
ü Because of that common gene pool, a
genetic change that occur in one member
of a species can spread through the
population.
ü On the other hand, because members
of different species do not share genes,
each species evolves as a separate units.
What processes lead to genetic differences sefficient
to crete a new species? (Mechanism of Speciation)
ü For speciation to occur two new population
must be form from one original population, and
 they must evolve in such a way that it becomes
impossible for individuals from the two new
population to interbreed
ü The key to one species diverging into 2 or more
different species is establishing a barrier to
gene flow, in this way, geographic isolation
may lead to reproductive isolation and the
formation of new species. In other words, two
or more population of a species must be
prevented from sharing the same pool of genes.
Mechanism of Speciation
I. Allopatric Speciation or geographic speciation
(allo – other, patric – place; ‘other place’) –
occurs when some members od a population
become geographically separated from the
other members thereby preventing gene flow.
Over time the populations may acquire their own unique
genetic changes. After enough changes have been
introduce, the two population may no longer be able to
interbreed even if they become reunited geographically.
In this way, geographic isolation may lead to
reproductive isolation and the formation of new species.
Examples of geographic barriers are bodies of water and
mountain ranges.
II. 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 involve abrupt
genetic changes that quickly lead to the
reproductive isolation of a group of individuals.
Two population become reproductively isolated
while they live in the same geographic location.
Many new plant species do emerge through
sympatric speciation by simply duplicating
their set of chromosomes and becoming
polyploid. Plants with different numbers of
chromosome cannot make with their parents
species to produce fertile offspring and are
therefore distinct species. Example is change in
chromosome number (polyploidization).
Reproductive Isolating Mechanisms
ü Four kinds of isolation – geographic, biological
sexual and genetic are influential in the
evolutionary process and the formation of new
species from older ones, a process known as
speciation. Speciation occurs when small
mutation, overtime, gradually change the
characteristics of a group of organisms, so that
the group is different from its ancestors. If a
group is isolated in some way, the development
of a new species is enhanced.
I. Geographic Isolation
The physical separation of two or more groups of the
same population. When the two groups are isolated, they
cannot interbreed, and mutations that occur in one of the
group may caused the group to evolve quite differently
from the other group.
II. Biological Isolation
Occurs when two groups living in the same area do not
meet so they are no longer able to interbreed. It is one
way to obtain the isolation essential to the development
of a new species. Biological isolation can result when
two group occupy different habitats and thus do not
normally come in contact with one another.
III. Sexual Isolation
Groups of organisms become unable to interbreed
because of certain characteristics of their reproductive
processes. Animals, for example, may be unable to
interbreed of they have develop different meeting
seasons or as in plant they have different pollen –
producing season.
IV. Generic Isolation
Occurs when mating between two different organisms
results either in the failure to produce any offspring or in
the production of sterile offspring .Once genetic
isolation has occurred,a new species has been
created ,because the new species can breed only with its
own kind.
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LESSON 5: DEVELOPMENT OF
EVOLUTIONARY THOUGHT
Greek Philosophers Belief About Evolution
Ø Plato believed in two worlds: a real world,
ideal and eternal and an illusionary world of
imperfection that we perceive through our
senses. The variations that we see and plants
and animals population were to Plato merely
imperfect representation of ideal forms and
only the perfect forms were real.
Ø Aristotle believed that species are fixed, or
permanent and do not evolve.
Evolutionary Thought
Ø Erasmus Darwin
Charles Darwin's grandfather, Erasmus Darwin, was one
of the leading intellectuals of eighteenth century
England, a man with a remarkable array of interests and
pursuits. Erasmus Darwin was a respected physician, a
well known poet, philosopher, botanist, and naturalist. (Darwin's first book dealing with natural selection was
As a naturalist, he formulated one of the first formal published in 1859): If an organism changes during life in
theories on evolution in Zoonomia, or, The Laws of order to adapt to its environment, those changes are
Organic passed on to its offspring.
Life (1794-1796). He also presented his evolutionary Ø Thomas Robert Malthus
ideas in verse, in particular in the posthumously
Thomas Robert Malthus, an English cleric, and scholar,
published poem The Temple of Nature. Although he did
published this theory in his 1798 writings, An Essay on
not come up with natural selection, he did discuss ideas
the Principle of Population. He believed that through
that his grandson elaborated on sixty years later, such as
preventative checks and positive checks, the population
how life evolved from a single common ancestor.
would be controlled to balance the food supply with the
Organic life beneath the shoreless waves Was born and population level.
nurs'd in ocean's pearly caves; First forms minute,
Malthus was a political economist who was concerned
unseen by spheric glass, Move on the mud, or pierce the
about, what he saw as, the decline of living conditions in
watery mass; These, as successive generations bloom,
nineteenth century England. To combat this, Malthus
New powers acquire and larger limbs assume; Whence
suggested the family size of the lower class ought to be
countless groups of vegetation spring, And breathing
regulated such that poor families do not produce more
realms of fin and feet and wing. -Erasmus Darwin. The
children than they can support.
Temple of Nature. 1802.
Ø George Cuvier
Ø Carolus Linnaeus
The most important contribution of Cuvier was his
best known for his innovative classification system
theory of catastrophism. Through his fossil study, he
called taxonomy. He published Systema Naturae in
came to notice that some layers (strata) differed from
1735, in which he outlined his way of classifying plants.
other layers. Cuvier's theory of catastrophism is
The classification system was primarily based on his
important to evolution because it gave other scientists a
expertise of plant sexuality, but it was met with mixed
basis to work from.
reviews from traditional botanists of the time.
Ø James Hutton
Linnaeus' desire to have a universal naming system for
living things led him to the use of binomial James Hutton (1726 - 1797) is best known for his
nomenclature to organize the botanical collection at important contributions to the science of geology
Uppsala University. He renamed many plants and (uniformitarianism and the great age of the earth).
animals in the two-word Latin system to make scientific However, Hutton was also the first person to propose a
names shorter and more accurate. His Systema Naturae mechanism of natural selection to account for
went through many revisions over time and came to evolutionary change over time. In his book,
include all living things. Investigation of the Principles of Knowledge (1794), he
lays out a clear argument for a process of transmutation
In the beginning of Linnaeus' career, he thought species
by natural selection, and does so through analogy with
were permanent and unchangeable, as was taught to him
the process of artificial selection. Hutton argues that
by his religious father. However, the more he studied
members of species vary, and that when the environment
and classified plants, he began to see the changes of
changes over time, those individuals best adapted to the
species through hybridization. Eventually, he admitted
new environment will survive, while those poorly
that speciation did occur and a sort of directed evolution
adapted will perish. Thus, a process of natural selection
was possible. However, he believed whatever changes
(Hutton did not use this term) inevitably leads to change
that were made were part of a divine plan and not by
within species over time.
chance.
Ø Charles Lyell
Ø Jean - Baptiste Lamarck
Lyell's version of geology came to be known as
Jean-Baptiste Lamarck (1744 - 1829), a French
uniformitarianism, because of his fierce insistence that
naturalist, did not get much credit for his scientific
the processes that alter the Earth are uniform through
contributions until he was dead. Lamarck is best known
time. Like Hutton, Lyell viewed the history of Earth as
for his contributions to evolution, or Lamarckism, which
being vast and directionless. And the history of life was
suggests organisms acquire or lose traits based on how
no different.
much they use them in their lives.
Lyell had an equally profound effect on our
Lamarck is best known for his Theory of Inheritance of
understanding of life's history. He influenced Darwin so
Acquired Characteristics, first presented in 1801
deeply that Darwin envisioned evolution as a sort of
biological uniformitarianism. Evolution took place from
one generation to the next before our very eyes, he
argued, but it worked too slowly for us to perceive.
Ø Alfred Wallace
Alfred Russel Wallace was born in Wales in 1823. He
has been described variously as a naturalist, a
geographer, and a social critic. He even weighed in on
the debate as to whether or not life could exist on Mars.
However, what he is best known for is his work on the
theory of natural selection.
Like fellow naturalist and colleague Charles Darwin,
Wallace traveled the world, observing and collecting
samples of species. He traveled to Brazil and various
islands of the Malay Archipelago that make up modern-
day Indonesia and the Philippines, where he collected
thousands of specimens of insects, birds, and other
animals. After four years in Brazil, Wallace fell ill and
decided to return home to England. But 26 days into
their voyage home, his ship caught fire and sank in the
Atlantic. Wallace’s team and the ship’s crew spent 10
days adrift before being picked up by a passing ship, and
all of Wallace’s notes and samples were lost at sea.
Ø Charles Darwin
Species keep on evolving or changing with time. As the
environment changes, the requirements of an organism
also change and they adapt to the new environment. This
phenomenon of changing over a period of time as per
the natural requirements is called adaptation.
As per Darwin’s theory, only the superior changes are
naturally selected and the inferior ones are eliminated.
Thus, not all adaptations contribute to progressive
evolution. For example, people living in tropical
countries have more melanin in their body to protect
them from the sunlight.
Almost all organisms share common ancestry with some
organism. According to Darwin, all organisms had one
common ancestor at some point in time and kept on
diverging ever since. His evolutionary theories support
the convergent theory and divergent theory of evolution
with examples.
He also studied that the birds of Galapagos Island
(Darwin’s finches) developed different beaks as per the
availability of the food. This proved adaptive radiation.
Similarly, he also observed the Australian Marsupials
which showed a number of marsupials emerging from
an ancestor.
According to Charles Darwin, evolution is a very slow
and gradual process. He concluded that evolution took
place over a very long period of time. As we talk about
the time period in evolution we usually refer to billions
of years. The generation of a species from another takes
a long period of time. It is a very steady process as the
changes and adaptation take a long time to stabilize and
give rise to a new species.
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LESSON 6: EVIDENCES OF EVOLUTION
Fossil Record
ü Fossils are relics or impressions of organisms
that lived from the ancient times
ü Most fossils are found in sedimentary rocks
ü Fossil record displays graphic evidence that
earth has had a succession of floras (plant life)
and faunas (animal life)
ü From stratum to stratum (layer by layer of
rocks), new species appear and other disappear
ü The appearance of species in younger strata
were not present in older rocks
ü Chronological appearance of animals from fish,
followed by amphibians, reptiles, mammals
and birds show a progression of evolution
ü George Cuvier speculated that the boundaries
between the fossils strata correspond in time to
catastrophic events that caused mass extinction
Biogeography
ü The geographical distribution of species on
earth follows patterns that are best explained by
evolution
ü Island have many species of plants and animals
that are endemic (native, found nowhere else )
but closely related to species of the nearest
neighboring island
ü Two island with similar environment in
different part of the world not populated by
closely related species but by species
taxonomically affiliated with the plants and
animals of the nearest mainland, where the
environment is often quite different
ü The great diversification of marsupials in
Australia and the absence of other mammals
reflect that island continent’s long isolation.
Australia has an abundance of endemic species
which is typical of island whose isolation by
expanses of water prevents migration of species
to other regions. Over time , these species
diverge evolutionarily into new species that
 look very different from their ancestors that
may exist on the mainland.
ü The Darwinian interpretation is that we find
modern species where they are because they
evolved from ancestors that inhabited those
regions
Comparative Anatomy/ Homology
ü Homology means similarity in characteristics
resulting from common ancestry
ü Homologous structure -physical features shared
due to evolutionary relationship (common
ancestry)
ü Analogous structure -are similar adaptation that
result from convergent evolution (no
evolutionary relationship)
ü If two or more species share a unique features,
such as complex bone structure or a body plan ,
they may all have inherited this features from a
common ancestors
ü Comparative anatomy is consistent with all
other evidence in testifying that evolution is a
remodeling process in which ancestral
structures that functioned in one capacity
become modified as they take a new function.
ü Examples Forelimbs of human, whale, bats,
and cats they have the same skeletal elements,
although these appendages have different
functions
Comparative Embryology
ü Closely related organisms go through similar
stages in their embryonic development
ü Examples: All vertebrate embryos go through a
stage in which they have gill pouches on the
sides of their throats and have tail.
ü Inspired by the Darwinian principle of decent
with modification, biologist proposed that
“ontogeny recapitulated phylogeny” which
means that the development of an individual
organism (ontogeny) is a replay of the
evolutionary history of the species(phylogeny).
Molecular Biology
ü Like anatomical structures, similarities between
biological molecules can reflect shared
evolutionary ancestry. At the most basic level,
all living organism share:
² Same genetic materials (DNA)
² Same or highly similar genetic codes
² Same basic processes of gene expression
(transcription and translation)
ü Same molecular building blocks, such as amino
acids
ü These shared features suggest that all living
things are descended from a common ancestor
ü Recently, molecular biologist developed
techniques to read information coded in DNA.
As information on DNA sequence
accumulated, they realized that many genes
where shared by a wide range of organisms.
The more closely two organisms are related,
the more closely their genes resemble each
other.
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LESSON 7: EVOLUTIONARY RELATIONSHIP
How do we study evolutionary relationship?
ü In its search for evolutionary relationship
among diverse organisms, systematics (the
study of biological diversity in an evolutionary
context) encompasses taxonomy, the
identification and classification of species and
phylogenetics
ü As a component of systematics, taxonomy has
two main objectives
² First is to sort out closely related organisms and
assign them to species, describing the
diagnostic characteristics that distinguish the
species from one another
² Second the arranging of species into the
broader taxonomic categories from genus to
family up to domain.
ü Taxonomy focuses on classifying, naming and
grouping of organisms based on similarities of
characteristics
Phylogenetics
ü There is more to systematics than taxonomy,
the naming and classification of species
ü Systematics has a goal beyond simple
organization: to have classification that reflect
the evolutionary affinities of species
ü Phylogenetics is the study of determining
evolutionary relationships or patterns of
descent of organism or evolutionary line of
descent.
 ü Classification of organisms based on their
assumed evolutionary history and relationship.
Phenetics
ü Phenetics (Greek word “phainein” which
means to appear) (same root word of
Phenotype) decides taxonomic affinities
entirely on the basis of measurable similarities
and differences
ü As many anatomical characteristics as possible
are compare. Phenetic classification are based
on overall similarities of characters and makes
no attempt to reflect evolution.
ü However, critics of phenetics argue that overall
phenotypic similarity is not a reliable index of
phylogenetic proximity
ü It may be easy to assume that more closely
related organisms look more alike, and while
this is often the case, it is not always true
ü If two closely related lineages evolved under
significantly varied surroundings or after the
evolution of a major new adaptation, it is
possible for the two groups to appear more
different than other groups that are not closely
related.
Cladistics
ü Cladistics ( Greek word “clados” which means
branch) classifies organisms according to the
order in time that branches arise along a
cladogram
ü Cladistic approach compares homologous
traits, also called characters , which may exist
in two or more organisms
ü Each branch point in a cladogram is defined by
novel homologous unique to the various
species on that branch
ü However, critics of cladistics pointed out that
cladistics does not consider the degree of
evolutionary divergence between the organism
represented in the cladogram
Molecular Systematics
ü Analysis of genetic data, such as DNA and
amino acid sequences, to identify and study
genetic homologies and propose phylogenetic
trees
ü DNA and amino acid sequences from closely
related species are more similar to each other
than to sequences from more distantly related
species
ü A smaller number of differences corresponds to
more related species
ü A larger number of differences corresponds to
less related species
The Evolutionary Timescale
ü A Molecular Clock tells time on an
evolutionary timescale. Changes in the
molecular sequences of our DNA, mutation,
maybe random, but they take place at a relative
predictable rate. Thus, we can estimate how
long ago two species branched off from each
other by counting how many differences there
are in their gene sequences.
Gene Conservation
ü Genes are sequences of DNA that code for
polypeptides (which constitute proteins)
ü With the sequencing of a variety of organismal
genomes, it has been found that many
organisms that are not closely related, still
retain particular genes in common
ü These genes are said to be conserved and
typically serve a critical role in controlling
organismal development
ü Examples of such genes that are ultraconserved
include:
² Regulatory genes (e.g. coding for protein-based
hormones)
² Genes encoding for tRNA (needed for
translation to occur)
² Genes involved in ATP production (e.g. coding
for the cytochrome proteins in the electron
transport chain)
ü The number of conserved genes can be used to
show evolutionary relationships between
organisms
DNA Sequencing
Over the course of millions of years, mutations will
accumulate within any given segment of DNA
ü The number of differences between comparable
base sequences can be used to demonstrate the
degree of evolutionary divergence
ü Non-coding sequences of DNA provide the
best means of comparison as mutations will
occur more readily in these sequences
² Gene sequences mutate at a slower rate, as
changes to base sequence can potentially have
 detrimental effects on protein structure and have been used to divide the human population
function into distinct haplogroups
² Protein similarity (based on amino acid ü All humans are thought to be able to trace their
sequence) can also be used for comparison, but origins back to one of seven super-haplogroups
will have the slowest rate of change due to derived from an original haplogroup - the
codon degeneracy 'mitochondrial Eve'
ü Some genes or protein sequences may Genome Phylogeny
accumulate mutations at a relatively constant
ü The term phylogeny describes the evolutionary
rate (e.g. a 1% change per million years)
development of a species
ü If this rate of change is reliable, scientists can
ü This evolutionary divergence can be
calculate the time of divergence based on the
represented in a branching diagram called a
number of differences between two species
phylogeny tree (or cladogram)
ü This concept is called the molecular clock, and
ü These diagrams can be used distinguish
is limited by a number of factors:
between, and trace the evolutionary history of,
² The rate of change can differ for different biological taxa or even groups of taxa (clades)
groups of organisms (e.g. animals and plants) o
ü The branching of the phylogeny tree can be
The rate of change can vary between different
based on structural features, protein similarities
genes and different proteins
or, more commonly, genome comparisons
² Over long periods, earlier changes may be
ü Species that have fewer branching points
reversed by later changes
between them are more closely related to one
Mitochondrial Evolution another
ü Mitochondrial DNA (mtDNA) is an important ——————————————————————
tool for tracing evolutionary relationships ————
within a species
LESSON 8: TAXONOMY, CLAIDSTICS AND
ü Mitochondria DNA is structurally identical to PHYLOGENY
nuclear DNA, but differs in a number of
What is Taxonomy?
important ways:
² Descent via maternal line: mtDNA is inherited
from the mother only, providing a much more
direct genetic lineage
² Lack of recombination: As mtDNA is passed
directly from the mother, no recombination
occurs, maintaining fidelity of the maternal
sequence
² Higher mutation rate: Mitochondria produce
reactive oxygen species which cause non-
conserved sequences to mutate at a faster rate
² High copy number: As every cell has multiple Ø Is the science of classifying organism
mitochondria, larger amounts of mtDNA can
be gathered for sampling Ø The taxonomic classification system uses a
hierarchical model to organize living organism
ü Because of these differences, mtDNA
sequencing is ideal for comparing organisms Ø It was developed by Swedish physician and
within a species or those who have diverged in botanist Carl von Linnaeus in the 18th century
a relatively short time (~20 million years)
Ø Linnaeus’s system is also useful for scientific
ü Distinctive human mtDNA sequences have naming
been found in different global populations and
 Ø The two main features of this taxonomic The domain system was developed by Carl Woes and
system are binomial nomenclature and places organisms under the three domains
categorical classification
I. Archae
Ø Scientist classify organisms using
² This domain includes prokaryotic
characteristics
organisms (which lack nucleus) that
Ø Taxonomist decide which are the most. differ from bacteria in membrane
significant or “important” characteristics composition and RNA
Binomial Nomenclature ² They are extremophiles capable of
living in some of the most
Ø The first feature of Linnaeus ‘s taxonomy,
inhospitable conditions on earth , such
which makes naming organisms uncomplicated
as hydrothermal vents
Ø The naming system devises a scientific name
II. Bacteria
for an organism based on two terms: the name
of the organisms’ genus and the name of its ² This domain includes prokaryotic
species organisms with unique cell wall
compositions and RNA types
Ø These terms are unique and ensure that no two
organisms have the same scientific name. It is ² As part of the human microbiota,
written in LATIN. bacteria are vital to life. However,
some bacteria are pathogenic and
Ø This universal naming system is recognized
cause disease
worldwide and avoid confusion over the
naming of organisms III. Eukarya
Classification Categories ² This domain includes eukaryotes or
organisms with a true nucleus
The second feature of Linnaeus’s taxonomy, which
simplifies organism ordering is categorical ² Eukaryotic organisms include plants,
classification. This means narrowing organism types animals, protist, and fungi
into categories:
Hierachy of Taxonomy
I. KINGDOM
II. PHYLUM
III. CLASS
IV. ORDER
V. FAMILY
VI. GENUS
VII. SPECIES
Domain System

I. KINGDOM – it includes all organisms who

share a set of distinguish common characters
II. PHYLUM – it includes all organisms
belonging to different classes having a few
common characteristics
Organism are grouped primarily according to
III. CLASS – it represents organisms of related
differences in ribosomal RNA structure, not physical orders
properties
 IV. ORDER – it is an assemblage of families
resembling one another in a few characteristics
V. FAMILY- it is represented by a group of
related genera that are more similar to each
other than with the genera of other families
VI. GENUS- it is a group of species which are
related and have less characteristics in common
as compared to species
VII. SPECIES- is a group of individuals with
similar morphological characteristics
Cladistics
Is a classification system that categorizes organism
based on shared traits as determined by genetic,
anatomical, and molecular analysis
This system sorts organisms into clades: groups of
organisms that descended from a single ancestor
The main assumption of cladistics is:
① all organisms descended from a common
ancestor
② new organisms develop when existing
population split into two groups
③ over time, lineage experience changes in
characteristics
Phylogeny
Ø Is the study of relationships among different
groups of organisms and their evolutionary
development
Ø It attempts to trace the evolutionary history of
all life on the planet
Ø It is based on the hypothesis that all living
organisms share a common ancestry
Ø The relationships among organisms are
depicted in what is known as phylogenetic tree
Ø Relationships are determined by shared
characteristics, as indicated through Phylogeny
and Taxonomy the comparison of genetic and
anatomical similarities are two system for
classifying organisms
Ø While the goal of phylogeny is to reconstruct
the evolutionary tree of life, taxonomy uses a
hierarchical format to classify, name and
identify organism
Phylogenetic Tree (Cladogram)
Ø Is a schematic diagram used as a visual
illustration of proposed evolutionary
relationships among taxa
Ø Phylogenetic tree is diagrammed based on
assumptions of cladistics or phylogenetic
systematics
Parts of Phylogenetic Tree
① Nodes- these are points on a phylogenetic tree
where branching occurs. A node represents the
end of the ancestral taxon and the point where a
new species splits from its predecessor
 ② Branches – these are the lines on a What about our remaining traits of fur and feathers?
phylogenetic tree that represent ancestral These traits are derived, but they are not shared, since
and/or descendant lineages. Branches arising each is found only in a single species. Derived traits that
from nodes represent descendant species that aren't shared don't help us build a tree, but we can still
split from a common ancestor place them on the tree in their most likely location. For
feathers, this is on the lineage leading to the bald eagle
③ Clade- this group is a single branch on a
(after divergence from the alligator). For fur, this is on
phylogenetic tree that represent a group of
the antelope lineage, after its divergence from the
organisms that are descended from a most
alligator and bald eagle.
recent common ancestor
——————————————————————
④ Taxon(taxa) – are specific groupings or
————————————
categories of living organism. The tips of
branches in a phylogenetic tree end in a taxon. R.T. Reuval
Taxa that share a more recent common ancestor
are more closely related than taxa with a less
recent common ancestor
⑤ Derived traits- traits that arise during the
evolution of a group and differ from the traits
of the ancestor of the group
⑥ Ancestral traits – the characteristics which is
found in the ancestor of a group, all of the
organism in the taxon or clade have that trait
Constrcting a Phylogenetic Tree
A good place to start is by looking for the derived trait
that is shared between the largest number of organisms.
In this case, that's the presence of jaws: all the
organisms except the outgroup species (lamprey) have
jaws. So, we can start our tree by drawing the lamprey
lineage branching off from the rest of the species, and
we can place the appearance of jaws on the branch
carrying the non-lamprey species.

Next, we can look for the derived trait shared by the

next-largest group of organisms. This would be lungs,
shared by the antelope, bald eagle, and alligator, but not
by the sea bass. Based on this pattern, we can draw the
lineage of the sea bass branching off, and we can place
the appearance of lungs on the lineage leading to the
antelope, bald eagle, and alligator.
Following the same pattern, we can now look for the
derived trait shared by the next-largest number of
organisms. That would be the gizzard, which is shared
by the alligator and the bald eagle (and absent from the
antelope). Based on this data, we can draw the antelope
lineage branching off from the alligator and bald eagle
lineage, and place the appearance of the gizzard on the
latter.