Recombinant DNA (rDNA) - With the advancement of genetic engineering, it is now possible to
transfer genes between distantly related species. The barriers of gene
A Brief History of Recombinant DNA
The use of recombinant (r)DNA technology to produce genetically
engineered organisms started in the early 1970s with the pioneering
transfer of genes between bacteria of the same Escherichia coli (E. coli)
species. Following these successful pilot experiments, in 1978 Cohen and
colleagues progressed to transfer an insulin synthesis gene into a plasmid
of E. coli, with that producing the first genetically modified organism
(GMO). By 1982, this protocol received full approval from national drug
regulatory authorities, notably the US Food and Drug Administration,
thereby enabling the economically viable mass production of human
insulin, a hormone that regulates blood sugar levels and is made naturally
by beta cells in the pancreas. This facilitated the widespread commercial
availability of insulin at a price affordable to patients with the metabolic
disorders’ types 1 and 2 diabetes mellitus, who either fail to produce or to
metabolize sufficient insulin.
This proof of principle demonstration of the translational medical benefits
of genetic modification pioneered a trend in biotechnology for molecular
cloning methods to transfer genes expressing desirable traits into another
host organism thereby producing favorable characteristics. This now
involves both prokaryotes such as bacteria (comparatively routine to
modify genetically by rDNA technology) and eukaryotes including yeast,
plants, insects, and mammals (comparatively complex to manipulate via
rDNA technology).
- Molecules of DNA from two different species that are inserted
into host organism to produce new genetic combinations that
are of value to science, medicine, agriculture, and industry.
- It is often shortened to rDNA.
- It is an artificially made DNA strand that is formed by the
combination of two or more gene sequences. This new
combination may or may not occur naturally but is engineered
specifically for a purpose to be used in one of the many
applications of recombinant DNA
Applications
The three important applications are:
1. agricultural applications (applications in crop improvement),
2. medicinal applications (applications in medicines), and
3. industrial applications.
Genetic engineering has several potential applications in crop
improvement, such as given below:
transfer between species or even genera have been overcome. The
desirable genes can be transferred even from lower organisms to higher
organisms through recombinant DNA technology.
- Genetically transformed plants that contain foreign genes are called
transgenic plants. Resistance to diseases, insects and pests, herbicides,
drought; metal toxicity tolerance; induction of male sterility for plant
breeding purposes; and improvement of quality can be achieved through
this recombinant DNA technology. BT-cotton resistant to bollworms is a
glaring example.
- Leguminous plants have root nodules which contain nitrogen-fixing
bacteria Rhizobium. These bacteria convert 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.
𝑪𝟒
Improvement in yield can be achieved by improving the photosynthetic
efficiency of crop plants. 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 𝐶3plants. Most 𝐶4 plants
(sorghum, sugarcane, maize, some grasses) are grown in tropical and
subtropical zones.
Biotechnology, especially genetic engineering, plays an important role in
the production of antibiotics, hormones, vaccines, and interferon in the
field of medicines.
- Penicillium and Streptomyces fungi are used for mass production of
famous antibiotics penicillin and streptomycin. Genetically efficient
strains of these fungi have been developed to greatly increase the yield of
these antibiotics.
- Insulin, a hormone used by diabetics, is usually extracted from the
pancreas of cows and pigs. This insulin is slightly different in structure from
human insulin. As a result, 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.
- 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.
- Interferons are virus-induced proteins produced by virus infected
cells. Interferons are antiviral in action and act as first line of defense
against viruses causing serious infections, including breast cancer and
lymph node malignancy. Natural interferon is produced in very small
quality from human blood cells. It is thus very costly also. It is now
possible to produce interferon by recombinant DNA technology at a
much cheaper rate.
- Some useful enzymes can also be produced by recombinant DNA
technique. For instance, enzyme urokinase, which is used to dissolve
blood clots, has been produced by genetically engineered
microorganisms.
- Genetic engineering may one day enable the medical scientists to
replace the defective genes responsible for hereditary diseases (e.g.,
hemophilia, phenylketonuria, alkaptonuria) with normal genes. This
new system of therapy is called gene therapy.
- Disputed cases of parentage can now be solved most accurately by
recombinant technology than by blood tests.
- 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 singlestranded DNA
attached to a radioactive or fluorescent marker. Such probes are now
used for the 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.
- Animals which carry foreign genes are called transgenic animals.
Examples: Cow, sheep, goat – therapeutic human proteins in their milk.
Fish like common carp, catfish, salmon and goldfish contain human
growth hormone (hGH).

In industries, 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. Thus, biotechnology, especially recombinant
DNA technology, has many useful applications in crop improvement,
medicines, and industry.
Genetic Engineering
• It is the process of using 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.
• It 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.
• It is the artificial modification of an organism’s genetic composition.
Genetic engineering typically involves transferring genes from one
organism into another organism of a different species to give the latter
specific traits of the former. The resulting organism is called a transgenic
or genetically modified organism (GMO).
Once a gene has been cloned, genetic engineers begin the third step,
designing the gene to work once inside a different organism. This is done
in a test tube by cutting the gene apart with enzymes and replacing gene
regions that have been separated.
The modified gene is now ready for the fourth
step in the process, transformation, or gene
insertion.
Since plants have millions of cells, it would be impossible to insert a copy
of the transgene into every cell. Therefore, tissue culture is used to
propagate masses of undifferentiated plant cells called callus. These are
the cells to which the new transgene will be added.
The new gene is inserted into some of the cells using various techniques.
Some of the more common methods include the gene gun,
agrobacterium, microfibers, and electroporation.
The main goal of each of these methods is to transport the new gene(s)
and deliver them into the nucleus of a cell without killing it. Transformed
plant cells are then regenerated into transgenic plants. The transgenic
plants are grown to maturity in greenhouses, and the seed they produce,
which has inherited the transgene, is collected. The genetic engineer’s job
is now complete. He/she will hand the transgenic seeds over to a plant
breeder who is responsible for the final step.
done through selective breeding. This is usually done by farmers and
breeders.
Individuals with desirable traits or characteristics are bred to increase
the chances of having offspring with the same desirable traits.
Breeders are able to produce wide range of plants and animals that
look very different from the ancestors.
Type/Example
A. Plants of the genus Brassica have been bred to produce
different foods by modifying plant sections through
artificial selection.
✓ This includes broccoli (modified flower buds),
cabbage (modified leaf buds) and kale (modified
leaves).
B. Dog breeding is another example. Humans select for a
variety of traits in dogs based on personal preference and
companionship, instead of as a way to increase human
survival.
It is the process through which species adapt to their environments. It
is the engine that drives evolution.
Furthermore, it can only take place if there is variation, or differences
among individuals in population.
Type/Example

A. Raphus cucullatus or dodo bird - they become extinct

The process
engineering
successful completion of a series
of five steps.
DNA extraction is the first step in the genetic
engineering process. In order to work with DNA,
scientists must extract it from the desired organism. A
sample of an organism containing the gene of interest
is taken through a series of steps to remove the DNA.
The second step of the genetic engineering process is
gene cloning. During DNA extraction, all of the DNA
from the organism is extracted at once. Scientists use
gene cloning to separate the single gene of
interest from the rest of the genes extracted and
make thousands of copies of it.
of genetic
Transgenic plants are crossed with elite breeding lines
requires the
using traditional plant breeding methods to combine the
desired traits of elite parents and the transgene into a
single line. The offspring are repeatedly crossed back to the
elite line to obtain a high-yielding transgenic line. The result
will be a plant with a yield potential close to current hybrids
that expresses the trait encoded by the new transgene.
Mechanisms of Evolution
There are millions of other organisms by which we directly and indirectly
interact with. The number and the kinds of organisms living on Earth at a
particular time is called biological diversity. The evolutionary theory is the
scientific explanation of the diversity of life. Evolution, or change over
time, is the process of how present- day organisms have descended from
ancient ones.
Five (5) mechanisms of evolution are said to have caused disruptions in
the equilibrium. These are: artificial selection, natural selection, genetic
drift, mutation and recombination.
The nature provides the variation among different organisms so that
humans can select the variations that are useful to them. This can be
because they were nonflying, overweight and pigeonlike
birds.
✓ Scientist allegedly unfit to the environment
because they could not fly, obese, slowness and
lack of intelligence that made them easy prey.
It is a mechanism of evolution in which allele frequencies of a
population change over generations due to chance (sampling error).
It occurs in all populations of non-infinite size, but its effects are
strongest in small populations.
There were two examples of genetic drifts that can have significant
effects in small populations, namely:
✓ Population bottleneck: it occurs when a sudden
sharp decline in the population
✓ Founder effect: it happens when there is a loss
of genetic variation because of migration of a
small subgroup in population.
Type/Example
A. Brown-Eyed Children - The father of a family has brown eyes,
which is a dominant allele. The mother of the family has blue
eyes, which is a recessive allele. The four children all have
brown eyes by chance.
B. Red Hair Example - A small village has people with blonde,
brown and red hair. There is a random succession of births of
redheads. Since red hair is an incomplete dominant gene and
blonde hair is a recessive gene, red and brown hair becomes
the dominant hair color. This leads to the extinction of people
with blonde hair in the village.
It is the change in the structure if a gene caused by alterations in the DNA
sequence of an organism.
There were different types of mutations such as;
✓ Substitution: it occurs when the genetic codon has one altered
nitrogenous base;
✓ Insertion: which characterized by the addition of an extra set
of base pairs to the genetic material, and
✓ Deletion: occurs when a set of base pair in the genetic material
is omitted.
Type/Example
A. Increased bone density - One of the genes that governs bone
density in human beings is called low-density lipoprotein
receptor-related protein 5 (LRP5).
✓ Mutations which impair the function of LRP5 are
known to cause osteoporosis.
It simply a rearrangement of genes. This process naturally occurs during
the crossing over stage in meiosis, where there is an exchange of DNA
between homologies chromosomes.
Type/Example
A. Chromosomal Crossing Over - During meiosis (specifically,
during prophase I), when homologous chromosomes line up in
pairs and swap segments of DNA. It creates gametes that
contain new combinations of genes, which helps maximize the
genetic diversity of any offspring that result from the eventual
union of two gametes during sexual reproduction.
Mechanisms: The Process of Evolution
Biological evolution, simply put, is descent with modification. This
definition encompasses small-scale evolution (changes in gene — or more
precisely and technically, allele — frequency in a population from one
generation to the next) and large-scale evolution (the descent of different
species from a common ancestor over many generations). Evolution helps
us to understand the history of life.
Biological evolution is not simply a matter of change over time. Lots of
things change over time: trees lose their leaves, and mountain ranges rise
and erode, but they aren’t examples of biological evolution because they
don’t involve descent through genetic inheritance.
Evolution is the process by which modern organisms have descended from
ancient ancestors. Evolution is responsible for both the remarkable
similarities we see across all life and the amazing diversity of that life —
but exactly how does it work?
Fundamental to the process is genetic variation upon which selective
forces can act in order for evolution to occur. This section examines the
mechanisms of evolution focusing on:
• Descent and the genetic differences that are heritable and passed on
to the next generation;
• Mutation, migration (gene flow), genetic drift, and natural selection as
mechanisms of change;
• The importance of genetic variation;
• The random nature of genetic drift and the effects of a reduction in
genetic variation;
• How variation, differential reproduction, and heredity result in
evolution by natural selection; and
•How different species can affect each other’s evolution through
coevolution.
Populations evolve, but individual organisms do not. A population is an
interbreeding group of individuals of one species in a given geographic
area at the same time. A population evolves because the population
contains a collection of genes called the gene pool. As changes in the gene
pool occur, a population evolves.
Mechanisms of change
Each of these four processes is a basic mechanism of evolutionary change.
Mutation is a change in DNA, the hereditary material of life. An organism’s
DNA affects how it looks, how it behaves, and its physiology — all aspects
of its life. So, a change in an organism’s DNA can cause changes in all
aspects of its life.
A mutation could cause parents with genes for bright green coloration to
have offspring with a gene for brown coloration. That would make genes
for brown coloration more frequent in the population than they were
before the mutation.
Mutation is a change in a DNA sequence, usually occurring because of
errors in replication or repair. Mutation is the ultimate source of
genetic variation. Changes in the composition of a genome due to
recombination alone are not considered mutations since
recombination alone just changes which genes are united in the same
genome but does not alter the sequence of those genes.
SOURCES OF GENETIC VARIATION
Without genetic variation, some of the basic mechanisms of
evolutionary change cannot operate.
1. Mutations - are changes in the DNA. A single mutation can have a
large effect, but in many cases, evolutionary change is based on the
accumulation of many mutations.
2. Gene flow - is any movement of genes from one population to
another and is an important source of genetic variation.
3. Sex - can introduce new gene combinations into a population. This
genetic shuffling is another important source of genetic variation.
Mutations are random
Mutations can be beneficial,
neutral, or harmful for the
organism, but mutations do
not ”try”; to supply what the
organism “needs”; In this respect, mutations are random — whether
a particular mutation happens or not is unrelated to how useful that
mutation would be.
Not all mutations matter to evolution
Since all cells in our body contain DNA, there are lots of places for
mutations to occur; however, not all mutations matter for evolution.
Somatic mutations occur in nonreproductive cells and won’t be passed
onto offspring.
For example, the golden color on half of this Red Delicious
apple was caused by a somatic mutation. The seeds of this
apple do not carry the mutation.
The only mutations that matter to large-scale evolution are those that
can be passed on to offspring. These occur in reproductive cells like
eggs and sperm and are called germ line mutations.
A single germ line mutation can have a range of effects:
1. No change occurs in phenotype - Some mutations don’t have any
noticeable effect on the phenotype of an organism. This can happen in
many situations: perhaps the mutation occurs in a stretch of DNA with
no function, or perhaps the mutation occurs in a protein-coding
region, but ends up not affecting the amino acid sequence of the
protein.
2. Small change occurs in phenotype
3. A single mutation caused this cat’s ears to curl
backward slightly.
4. Big change occurs in phenotype - Some really important phenotypic
changes, like DDT resistance in insects, are sometimes caused by single
mutations. A single mutation can also have strong negative effects for
the organism. Mutations that cause the death of an organism are called
lethals — and it doesn’t get more negative than that.
There are some sorts of changes that a single mutation, or even a lot of
mutations, could not cause. Neither mutations nor wishful thinking will
make pigs have wings; only pop culture could have created Teenage
Mutant Ninja Turtles — mutations could not have done it.
Mutations happen for several reasons.
1. DNA fails to copy accurately-
Most of the mutations that we
think matter to evolution are
“naturally occurring”; For
example, when a cell divides, it
makes a copy
of its DNA — and sometimes the copy is not quite
perfect. That small difference from the original DNA
sequence is a mutation.
2. External influences can create mutations - Mutation can also be caused
by exposure to specific chemicals or radiation. These agents cause the
DNA to break down. This is not necessarily unnatural — even in the most
isolated and pristine environments, DNA breaks down. Nevertheless,
when the cell repairs the DNA, it might not do a perfect job of repair. So,
the cell would end up with DNA slightly different than the original DNA
and hence, a mutation.
Sex and genetic shuffling - Sex can introduce new gene
combinations into a population and is an important source of genetic
variation.
You probably know from experience that siblings
are not genetically identical to their parents or
to each other (except, of course, for identical
twins). That’s because when organisms
reproduce sexually, some genetic “shuffling”;
occurs, bringing together new combinations of
genes. For example, you might have bushy
eyebrows and a big nose since your mom had genes associated with bushy
eyebrows and your dad had genes associated with a big nose. These
combinations can be good, bad, or neutral. If your spouse is wild about
the bushy eyebrows/big nose combination, you were lucky and hit on a
winning combination! This shuffling is important for evolution because it
can introduce new combinations of genes every generation. However, it
can also break up “good” combinations of genes.
Gene flow — also called migration — is any movement of individuals,
and/or the genetic material they carry, from one population to another.
Gene flow includes lots of different kinds of events, such as pollen being
blown to a new destination or people moving to new cities or countries. If
gene versions are carried to a population where those gene versions
previously did not exist, gene flow can be a very important source of
genetic variation. In the graphic below, the gene version for brown
coloration moves from one population to another.
Gene flow is the movement of genes between populations. This may
happen through the migration of
organisms or the movement of
gametes (such as pollen blown to a
new location).
Some individuals from a population of brown beetles might have joined a
population of green beetles. That would make genes for brown coloration
more frequent in the green beetle population than they were before the
brown beetles migrated into it.
Another mechanism for evolution is genetic drift, which can occur when a
small group of individuals leaves a population and establishes a new one
in a geographically isolated region. Fitness of a population is not
considered in genetic drift, nor does genetic drift occur in a very large
population.
Imagine that in one generation, two brown beetles happened to have four
offspring survive to reproduce. Several green beetles were killed when
someone stepped on them and had no offspring. The next generation
would have a few more brown beetles than the previous generation —
but just by chance. These chance changes from generation to generation
are known as genetic drift.
Genetic drift — along with natural selection, mutation, and migration —
is one of the basic mechanisms of evolution.
In each generation, some individuals may,
just by chance, leave behind a few more
descendent (and genes, of course!) than other individuals. The genes of
the next generation will be the genes of the “lucky”; individuals, not
necessarily the healthier or “better”; individuals. That, in a nutshell, is
genetic drift. It happens to ALL populations — there’s no avoiding the
vagaries of chance.
Random Drift consists of random fluctuations in the frequency of
appearance of a gene, usually, in a small population. The process may
cause gene variants to disappear completely, thereby reducing genetic
variability. In contrast to natural selection, environmental or adaptive
pressures do not drive changes due to genetic drift. The effect of genetic
drift is larger in small populations and smaller in large populations.
Genetic drift is a stochastic process, a random event that happens by
chance in nature that influences or changes allele frequency within a
population as a result of sampling error from generation to generation.
It may happen that some alleles are completely lost within a
generation due to genetic drift, even if they are beneficial traits that
conduct to evolutionary and reproductive success. Allele is defined as
any one of two or more genes that may occur alternatively at a given
site (locus) on a chromosome. Alleles are responsible for variations in
a trait.
The population bottleneck and a founder effect are two examples of
random drift that can have significant effects in small populations.
Genetic drift works on all mutations and can eventually contribute to
the creation of a new species by means of the accumulation of non-
adaptive mutations that can facilitate population subdivision.
Bottleneck effect - occurs when there is a sudden sharp decline in a
population’s size typically due to environmental factors (natural
disasters such as: earthquakes or tsunamis, epidemics that can
decimate the number of individuals in the population, predation or
habitat destruction, etc.). It is a random event, in which some genes
(there is not any distinction) are extinguished from the population.
This results in a drastic reduction of the total genetic diversity of the
original gene pool. The small surviving population is considerably
farther from the original one in its genetic makeup.
Founder effect - is the loss of genetic variation that occurs when a new
population is established by a small number of individuals that are
cleaved from a larger population. This new population does not have
the genetic diversity of the previous one. Because the community is
very small and also geographical or socially isolated, some genetic
traits are becoming more prevalent in the population. This leads to the
presence of certain genetic diseases in the next generations. In some
cases, founder effect plays a fundamental role in the emergence of
new species.
Generation 1: The frequency of alleles in
the population is the same.
Generation 2: Randomly and due to a
catastrophic natural or man-made event,
most of individuals of the population
died (there is no influence of adaptive
pressures).
Generation 3: As a result, the original
large population is reduced to a small
population composed by few individuals.
This new surviving population subset contains much less genetic
variability than the previous population.
Generation 4: Later, the drastic reduction in the population size is
followed by an expansion (population is recovered). The final
population is no longer genetically representative of the original one.
In this particular case, an allele is completely removed from the gene
pool.
A new population is established
by a small number of individuals
that are cleaved from the original
population. This leads to a loss of
genetic variability as the founders of the new colony are not genetically
representative at all of the population from which they come from. The
right figure shows an evident predominance of orange circles in the
newly founded population. These orange circles may correspond to a
given allele responsible for the variation in a trait (for example, specific
eyes color). In extreme cases, founder effect also plays a fundamental
role in the emergence of new species.
Genetic drift affects the genetic makeup of the population but, unlike
natural selection, through an entirely random process. So although
genetic drift is a mechanism of evolution, it doesn’t work to produce
adaptations.
Another mechanism for evolution is natural selection, which occurs when
populations of organisms are subjected to the environment. The fittest
creatures are more likely to survive and pass their genes to their offspring,
producing a population that is better adapted to the environment. The
genes of less-fit individuals are less likely to be passed on to the next
generation. The important selective force in natural selection is the
environment.
Imagine that green beetles are easier for
birds to spot (and hence, eat). Brown
beetles are a little more likely to survive to
produce offspring. They pass their genes for brown coloration on to their
offspring. So, in the next generation, brown beetles are more common
than in the previous generation.
All of these mechanisms can cause changes in the frequencies of genes in
populations, and so all of them are mechanisms of evolutionary change.
However, natural selection and genetic drift cannot operate unless there
is genetic variation — that is, unless some individuals are genetically
different from others. If the population of beetles were 100% green,
selection and drift would not have any effect because their genetic make-
up could not change.
Natural selection is one of the basic mechanisms of evolution, along with
mutation, migration, and genetic drift.
Darwin’s grand idea of evolution by natural selection is relatively simple
but often misunderstood. To find out how it works, imagine a population
of beetles:
1. There is variation in traits. For example, some beetles are green and
some are brown.
2. There is differential reproduction. Since the environment can’t support
unlimited population growth, not all individuals get to reproduce to their
full potential. In this example, green beetles tend to get eaten by birds and
survive to reproduce less often than brown beetles do.
3. There is heredity. The surviving brown beetles have brown baby beetles
because this trait has a genetic basis.
4. End result: The more advantageous trait, brown coloration, which
allows the beetle to have more offspring, becomes more common in the
population. If this process continues, eventually, all individuals in the
population will be brown.
If you have variation, differential reproduction, and heredity, you will have
evolution by natural selection as an outcome.
NATURAL SELECTION: HEREDITY There is heredity. The
surviving brown beetles have brown baby beetles because
this trait has a genetic basis.
NATURAL SELECTION: END RESULT The more advantageous
trait, brown coloration, which allows the beetle to have more
offspring, becomes more common in the population.
NATURAL SELECTION: DIFFERENTIAL REPRODUCTION
There is differential reproduction. Since the environment
can’t support unlimited population growth, not all
individuals get to reproduce to their full potential. In this example, green
beetles tend to get eaten by birds and survive to reproduce less often than
brown beetles do.
Natural Selection leads to an evolutionary change when some individuals
with certain traits in a population have a higher survival and reproductive
rate than others and pass on these inheritable genetic features to their
offspring. Evolution acts through natural selection whereby reproductive
and genetic qualities that prove advantageous to survival prevail into
future generations. The cumulative effects of natural selection process
have giving rise to populations that have evolved to succeed in specific
environments.
Natural selection
operates by
differential
reproductive
success (fitness)
of individuals.
THE DARWIN’S
FINCHES
DIAGRAM
illustrates the
way the finch has
adapted to take
advantage of
feeding in
different
ecological niches:
Natural selection at work
Scientists have worked out many examples of natural selection, one of
the basic mechanisms of evolution. Any coffee table book about
natural history will overwhelm you with full-page glossies depicting
amazing adaptations produced by natural selection, such as the
examples below.
a. Orchids fool wasps into ‘mating’; with them.
b. Katydids have camouflage to look like leaves.
c. Non-poisonous king snakes mimic poisonous coral snakes.
Behavior can also be shaped by natural selection. Behaviors such as
birds’ mating rituals, bees’ wiggle dance, and humans’ capacity to
learn language also have genetic components and are subject to
natural selection.
In some cases, we can directly observe natural selection.
Very convincing data show that the shape of finches’ beaks on the
Galapagos Islands has tracked weather patterns: after droughts, the
finch population has deeper, stronger beaks that let them eat tougher
seeds.
In other cases, human activity has led to environmental
changes that have caused populations to evolve through natural
selection. A striking example is that of the population of dark moths in
the 19th century in England, which rose and fell in parallel to industrial
pollution. These changes can often be observed and documented.
Descent with Modification
Descent with modification refers to the passing on of traits from
parent organisms to their offspring. This passing on of traits is known
as heredity, and the basic unit of heredity is the gene. Genes are the
blueprints for making an organism and, as such, hold information
about its every conceivable aspect: its growth, development, behavior,
appearance, physiology, and reproduction
Descent with modification by natural selection explains the
adaptations of organisms and the unity and diversity of life.
“DESCENT WITH MODIFICATION” -CHARLES
DARWIN
Evolution described as “descent with modification” by Charles
Darwin refers to the species that changed over time, giving rise to the
new species and share a common ancestor. Although Charles Darwin’s
name is virtually synonymous with the word evolution, he was not the
first person to recognize the phenomenon of species change nor did
he even use the word “evolution”; in the original theory he set forth in
On the Origin of Species.

Charles Darwin (1809–1882) was born in western England. As a boy,
he had a consuming interest in nature. When Darwin was 16, his father
sent him to the University of Edinburgh to study medicine, but he
dropped out without a degree and enrolled at Cambridge University
with the intent of becoming a clergyman. At that time, most naturalists
and scientists belonged to the clergy. After graduation, Darwin joined
the crew of the survey ship HMS Beagle as ship naturalist and
conversation companion to Captain Robert FitzRoy. FitzRoy chose
Darwin because of his education and because his age and social class
were like those of the captain.
According to
Charles Darwin, all
species descended from only a few life forms that had been modified
over time. This “descent with modification” as he called it, forms the
backbone of his Theory of Evolution, which posits that the
development of new types of organisms from pre-existing types of
organisms over time is how certain species evolve.
How It Works
The passing on of genes is not always exact. Parts of the blueprints may
be copied incorrectly, or in the case of organisms that undergo sexual
reproduction, genes of one parent are combined with the genes of
another parent organism. That is why children are not exact carbon
copies of either of their parents.
There are three basic concepts that are helpful in clarifying how
descent with modification works:
✓ Genetic mutation
✓ Individual (or natural) selection
✓ Evolution of the population (or species as a whole)
It is important to understand that genes and individuals do not evolve;
only populations evolve. The process looks like this: Genes mutate,
and those mutations have consequences for the individuals within a
species. Those individuals either thrive or die out due to their genetics.
As a result, populations change (evolve) over time.
Natural selection comes into play, according to Darwin, when a species
adapts to its environment, thanks to its specific genetic makeup. Say
at some point in time two species of wolves lived in the Arctic: those
with short, thin fur and those with long, thick fur. Those wolves with
long, thick fur was genetically capable of living in the cold. Those with
short, thin fur were not. Therefore, those wolves whose genetics
allowed them to live successfully in their environment lived longer,
bred more frequently, and passed
on their genetics. They were
“naturally selected” to thrive.
Those wolves that were not
genetically adapted to the cold eventually died out.
Darwin never used the word evolution in the first edition of The Origin
of Species, although the final word of the book is evolved. Instead,
Darwin used the phrase descent with modification.
• All living organisms are related to each other due to their descent
from a common ancestor that lived in the distant past.
• Over evolutionary time, the descendants of that common ancestor
have accumulated diverse modifications, or adaptations, that allow
them to survive and reproduce in specific habitats.
• Over long periods of time, descent with modification has led to the
rich diversity of life we see today. If we try to visualize descent with
modification, the history of life resembles a tree, with multiple
branches from a common trunk.
• Closely related species, the twigs on a common branch of the tree,
shared the same line of descent until their recent divergence from a
common ancestor.
Three important points need to be emphasized about evolution
through natural selection.
1. Although natural selection occurs through interactions between
individual organisms and their environment, individuals do not
evolve. A population is the smallest group that can evolve over time.
2. Natural selection can act only on heritable traits, traits that are
passed from organisms to their offspring. Characteristics acquired by
an organism during its lifetime may enhance its survival and
reproductive success, but there is no evidence that such
characteristics can be inherited by offspring.
3. Environmental factors vary from place to place and from time to
time. A trait that is favorable in one environment may be useless or
even harmful in another environment.
Development of Evolutionary
Thought
Many people assume that the theory put forth by Darwin in Origin of
Species is the final say on evolutionary theory. Biologists, however,
know that the theory of evolution has evolved over time. For example,
evolutionary theory dramatically changed when Darwin’s original
ideas were merged with ideas from genetics to become the Modern
Synthesis. People will see that evolution makes sense when they
realize that the theory of evolution has been updated. The updated
and revised theory becomes easier to understand, appreciate, and
embrace. This more integrated theory of evolution has even greater
power to explain the origins of the great diversity of life on Earth.
Three theories of evolution have different facts to support Variation,
Inheritance, Selection and Time. Darwin’s theory is represented by the
color green. Updated information supporting the “Modern Synthesis”
is highlighted in blue. Updated information supporting the “Integral
Model” is highlighted in purple.
Although Charles Darwin’s name is virtually synonymous with the
word evolution, he was not the first person to recognize the
phenomenon of species change nor did he even use the word
“evolution” in the original theory he set forth in On the Origin of
Species (1859).
Antiquity
The history of evolution long predates Darwin and his theory. The
belief in a changing or dynamic universe can be first seen in ancient
Greek philosophy. Heraclitus (c. 500 B.C.E.), also known as the
“philosopher,” believed that change was a fundamental property of
the universe. His successor, Empedocles (c. 392–432 B.C.E.), first
articulated a crude but dynamic theory that postulated that the origin
of life had taken place in a manner that suggested evolution.
From Aristotle to Linnaeus
However, beginning with the philosophical worldview established by
Aristotle (384– 322 B.C.E.), the belief in a changing universe fell into
disfavor. Aristotle and his numerous medieval and Renaissance
translators, commentators, and supporters instead believed in a static
universe which held that living organisms were created initially and
then remained essentially unchanged. These ideal types or species
were arranged hierarchically in what came to be known as the ”scala
naturae” or the ladder of creation.
Buffon, Lamarck, and Transmutationism
Belief in species change, or transmutationism, slowly began to emerge
during the Enlightenment. This period saw the emergence of the belief
in a progressive world, both scientific and social. It also saw the
beginnings of the new science of geology. Geological theories
suggested that fossils were of organic (once-living) origin and that
uniform or constant processes rather than catastrophic or one-time
events had shaped Earth’s history.
The French naturalist Comte de Buffon (Count Buffon, 1707–1788)
was one of the first to question the fixity of species and to suggest a
transmutationist theory with a startling resemblance to Darwinian
evolution. Although he was a respected naturalist, his theoretical
explanations for the origin of life and of species change were not
accepted during his time. Buffon’s transmutationist ideas were also
not accepted because they opposed the philosophical teachings of his
French colleague Georges Cuvier, the great comparative anatomist
and the father of modern paleontology.
The first to suggest a viable theory of species change was Frenchman
Jean-Baptiste Lamarck. Lamarck was interested in adaptation or the
manner and process by which organisms are able to adapt
physiologically and morphologically to their environment. He was
especially interested in how well-adapted organs like the neck of the
giraffe had originated. According to Lamarck, the use or, in many
cases, disuse of such a vital organ could lead to the development of
novel but well-adapted traits. The cumulative effect of these
adaptations could eventually lead to a new species.
Transmutationism itself became increasingly acceptable by the early
nineteenth century. It captured the interest of Darwin’s own
grandfather, Erasmus Darwin (1731–1802), who suggested that life
had originated from “one living filament” Other transmutationists
included French anatomist Isidore Geoffroy Sainte Hilaire (1805–
1861), who studied birth defects. He suggested that through such
“monstrous births”; new species might suddenly arise.
Darwin and On the Origin of Species
Charles Darwin was the leading transmutationist of the nineteenth
century. Darwin had developed the major features of his theory as
early as 1837 after returning from his five-year voyage of the HMS
Beagle and after reading the famous Essay on the Principle of
Population by Thomas Malthus (1766–1834). However, Darwin did
not make his work public until much later. He felt that he needed to
collect solid evidence to his support what he knew would be a
contentious theory. He was finally forced into joint publication of an
abbreviated version of his theory in 1858, shortly after English
naturalist Alfred Russel Wallace (1823–1913) independently
formulated his own nearly identical theory.
It took Darwin less than a year to outline in book form his theory of
species change which he called “descent with modification” by means
of the mechanism of natural selection. The full title of his famous book
was On the Origin of Species or the Preservation of Favored Races in
the Struggle for Life. The book appeared in bookstores on November
24, 1859 and sold out on the first day. It went through six editions as
Darwin modified his theory in response to his many critics. It is
generally thought that the first edition is a more accurate account of
the workings of evolution because subsequent editions included a
watered-down version of his original theory.
Darwin thought “descent with modification” took place primarily Relative time ("chronostratic") -- subdivisions of the Earth's geology
through the mechanism he termed natural selection. Natural selection in a specific order based upon relative age relationships (most
occurs when an organism with a favorable variation in some trait commonly, vertical/stratigraphic position). These subdivisions are
reproduces more as a result, thereby increasing the frequency of the given names, most of which can be recognized globally, usually on the
variation in the next generation. In addition to this mechanism for basis of fossils.
driving species change, Darwin included some four of five other
mechanisms that he thought could account for species change Absolute time ("chronometric") -- numerical ages in "millions of
including the inheritance of acquired characters. years" or some other measurement. These are most commonly
obtained via radiometric dating methods performed on appropriate
rock types.
EVIDENCE OF EVOLUTION
According to Dubeck et al., 2004 all living organisms share
TWO TYPES OF EVIDENCE
characteristics which biologically distinguish them from non - living
things. The following are the characteristics: • DIRECT EVIDENCE -can be directly observed or seen
• INDIRECT EVIDENCE- does not involve actual observation
A. Cellular complexity- all living things are composed of either of evolution but from which evolution may be inferred.
one or more cells
B. Growth and Development – organisms undergo different EVIDENCE OF EVOLUTION
stages, which follow a systematic process from birth to Biogeography is the study of the distribution of species on Earth
maturity in the past and present, and how the distribution is affected by abiotic
C. Reproduction- to ensure continuity of life, organisms factors such as habitat, climate and terrain. The field is divided into
undergo reproduction that pass traits from one generation three disciplines of biogeography: historical, ecological and
to next. conservation.
D. Irritability/ Ability to response to stimuli- all organisms are Historical biogeography is also called paleobiogeography and
very sensitive to different stimuli. This response refers to studies species distribution now as it relates to distribution in the past.
any movement to stimuli in the organisms’ own volition. Ecological biogeography examines the distribution of species in
E. Homeostasis- The ability of the organism to maintain relation to biotic and abiotic factors in the environment. Finally,
balance in different environmental condition. conservation biogeography is a relatively new field of biogeography
which combines the study of conservation with biogeography to try
EVIDENCE OF EVOLUTION and anticipate future conditions so that planning can be done to
Geologists have protect the biodiversity on Earth.
divided Earth's The great diversification of the marsupials in Australia and the
history into a series absence of other mammals reflects that island continent’s long
of time intervals. isolation. Australia has an abundance of endemic species—species
These time intervals found nowhere else—which is typical of islands whose isolation by
are not equal in expanses of water prevents migration of species to other regions. Over
length like the hours time, these species diverge evolutionarily into new species that look
in a day. Instead, the very different from their ancestors that may exist on the mainland. The
time intervals are marsupials of Australia, the finches on the Galápagos, and many
variable in length. species on the Hawaiian Islands are all found nowhere else but, on
This is because their island, yet display distant relationships to ancestral species on
geologic time is mainland.
divided using
significant events in Alfred Russel Wallace: The Father of
the history of the Biogeography.
Earth. He was born January 8, 1823 in Usk, Monmouthshire, Wales.
Two ways to Wallace started an expedition of his own in 1848 through the
relate time in Amazon and South Asian region. Wallace spent eight years in
geology:
the Malay Archipelago, from 1854 to 1862, traveling among
✓ Relative time
("chronostratic")
the islands, collecting biological specimens for his own
research and writing scores of scientific articles on mostly
✓ Absolute time
("chronometric") zoological subjects. He devised what became known as the
Wallace Line, the boundary separating Australian fauna from
Asian fauna.
FOSSIL RECORD
The fossil record helps paleontologists, archaeologists, and
geologists place important events and species in the
appropriate geologic era. It is based on the Law of
Superposition which states that in undisturbed rock
sequences, the bottom layers are older than the top layers.
Therefore, some discovered fossils can be dated according to
the strata, a distinct layer of rock, that they are found
in. Another common way that fossils are dated, is through
radiocarbon dating. The development of this type of dating, in
the 1950s, transformed paleontology and enhanced the
accuracy of the fossil record. With every new fossil discovery,
our understanding of the environment in a particular time
becomes richer.
Fossils provide solid evidence that organisms from the past are
not the same as those found today; fossils show a progression
of evolution. Scientists determine the age of fossils and
categorize them all over the world to determine when the
organisms lived relative to each other. The resulting fossil
record tells the story of the past, and shows the evolution of
form over millions of years.
However, the information obtained from fossil is relatively
incomplete for several reasons.
1. Only a small number of fossils are found;
2. Soft tissues are rarely preserved;
3. Most fossils have been destroyed by erosion, and or/
movement of the earth’s crust may have caused
some fossils to be buries deeply; and
4. Fossilization takes place only in places where
conditions are favorable.
DNA AND PROTEIN STRUCTURE
DNA and protein structure. All living cells have the same basic
DNA structure and use the same genetic code. Proteins
produced from genes all come from the same set of amino
acids. Comparing sections of DNA in difference species has
shown that even organisms that seem to be different, actually
have large sections of identical DNA.
Organisms that seem fairly similar on the basis of comparative
anatomy, show more genes in common than organisms that
aren’t much alike. For example, 96% of the genes in humans
and chimpanzees are identical. That two species and their
common ancestor have similar DNA is strong evidence
supporting evolution. Protein amino acid sequences can also
be used to compare similarities between species. Proteins are
made from amino acids and the sequence of these amino acids
is controlled by genes. Comparing how many of the amino
acids are in the same positions on the protein chain can
provide some idea of how closely related two species are. For
example, humans and chimpanzees only have one position
where they are different on the amino chain, while humans
and moths have 31 different positions.
HOMOLOGY
Homology.
Homology
defined as similar
biological
structures
sequences
different taxa, thus implies divergent evolution. Homologous
structures evolved from a common ancestor. Examples of
homologous structures include the forelimbs of a variety of
mammals. For example, human, cat, whale, and bat. These
species show the same skeletal elements in the humerus,
radius and ulna as share a common origin. Similarly, the
forelimbs of ancestral vertebrates have evolved into the front
flippers of whales, the wings of birds, the running forelegs of
dogs, deer, and horses, the short forelegs of frogs and lizards,
and the grasping hands of primates including humans. The
same major forearm bones (humerus, radius, and ulna) are
found in fossils of lobe-finned fish such as Eusthenopteron.
However, these skeletal elements have been modified over
time to suit the different functions suitable for the type of
mammal. Homologous structures result from divergent
evolution.
EMBRYOLOGY
Embryology. Embryology is the study of the development,
structure, and function of embryos. When comparing
vertebrate embryos in the early stages of development, you
will see striking similarities. Even species that bear little
resemblance in their adult form may have strikingly similar
embryonic stages. For example, when looking at humans we
see that the embryo passes through a stage in which it has gill
structures like those of the fish from which all terrestrial
animals evolved. For a large portion of its development the
human embryo also has a tail, much like those of our close
primate relatives. This tail
is usually reabsorbed
before birth. Gills could be
considered homologous
traits between humans
and fish: in humans the
parathyroid glands
(endocrine glands in your
neck) develop from the
branchial arches. In fish, a
gene called Gcm-2 controls
the development of branchial arches into gills. If the gene
mutates (or if scientists prevent it from working) then the gills
fail to develop. The development of mammals, fish, reptiles,
is
and birds are linked to the branchial arteries. Biologists long
ago proposed that fish evolved into amphibians, which evolved
into reptiles, which evolved into birds. More recent studies of
or
embryonic development support this idea.
in
KEYPOINTS!
• Comparing sections of DNA in difference species has
shown that even organisms that seem to be different
actually have large sections of identical DNA
• The layers of fossils in sedimentary rock shows the
progression of organisms through time.
• Distribution - isolation islands have unusually high
proportions of unusual species.
CONTRIVANCES. Some characters that are passed on through
generation will not be “perfectly” adapted based on
evolutionary theory. Since natural selection occurs on the
genetic variation that is presently available in a population, the
“best” alternatives cannot constantly be found. Most of the
time, existing traits are modified (contrived) to serve a new
function.
EVIDENCE FROM PHYSIOLOGY AND
BIOCHEMISTRY
All living things evolved from a single common ancestor. There
are certain key molecules and biochemical mechanisms shared
by incredibly different organisms. For example, all organisms
use DNA and/or RNA for their genetic code.
Photosynthesis, cellular respiration, transcription, and
translation are all identical or very similar in various types of
organisms. When we look closer, we can see that there are
many biochemical molecules which are identical in nearly all
life forms.
A classic example is cytochrome c, which is found in all life
forms. Although the genetic coding of this molecule differs
among species, it performs all the same functions everywhere.
This highly conserved protein is a key component of the
electron transport chain, which is a part of cellular respiration.
Cytochrome c also has a function in many other reactions,
including initiating programmed cell death.
Two somewhat related molecules are hemoglobin and
myoglobin. Hemoglobin is a molecule used to transport
oxygen, and myoglobin is used to store oxygen. Another very
common molecule is trypsin, a protease involved in the
absorption of protein during digestion.
All these molecules perform essential functions in cells, which
is why it would make sense that most organisms have them.
However, it would not make sense if each of these molecules
appeared independently in each species. That would be
impossible. These shared biochemical molecules and
pathways provide strong evidence for common descent and
evolution.
Species distribution
All the places where species live is known as species
distribution. When looking closely at distributions, it is clear
that many unique species occur in isolated pockets or islands.
When looking at these unique species through the lens of
evolution, we would expect unusual species in isolated areas
because isolation is necessary before speciation can occur. The
theory of the movement of the Earth’s tectonic plates was
supported by the distribution of the fossils of a particular
species. Moving continents also explains why Australia has
most of the world’s marsupials and the only two monotremes;
the platypus and the echidna.
FOUR IMPORTANT MECHANISMS OF
HOW SPECIES EVOLVED
✓ Mutation
✓ Gene Flow
✓ Natural Selection
✓ Genetic Drift
• Mutation - Mutation is a source of new alleles in a
population. Mutation is a change in the DNA
sequence of the gene. A mutation can change one
allele into another, but the net effect is a change in
frequency. 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 selection. A mutation may produce an allele that
is selected against, selected for, or selectively
neutral. Harmful mutations are removed from the
population by selection and will generally only be
found in very low frequencies equal to the mutation
rate. Beneficial mutations will spread through the
population through selection, although that initial
spread is slow. Whether or not a mutation is
beneficial or harmful is determined by whether it
helps an organism survive to sexual maturity and
reproduce. It should be noted that mutation is the
ultimate source of genetic variation in all
populations—new alleles, and, therefore, new
genetic variations arise through mutation.
• Gene Flow- Another important evolutionary force is
gene flow, or the flow of alleles in and out of a
population resulting from the migration of
individuals or gametes. While some populations are
fairly stable, others experience more flux. Many
plants, for example, send their seeds far and wide,
by wind or in the guts of animals; these seeds may
introduce alleles common in the source population
to a new population in which they are rare.
• Natural Selection - Alleles are expressed in a
phenotype. Depending on the environmental
conditions, the phenotype confers an advantage or
disadvantage to the individual with the phenotype
relative to the other phenotypes in the population.
If it is an advantage, then that individual will likely
have more offspring than individuals with the other
phenotypes, and this will mean that the allele behind
the phenotype will have greater representation in
the next generation. If conditions remain the same,
those offspring, which are carrying the same allele,
will also benefit. Over time, the allele will increase in
frequency in the population.
• Genetic Drift - Another way a population’s allele
frequencies can change is genetic drift, which is
simply the effect of chance. Genetic drift is most
important in small populations. Drift would be
completely absent in a population with infinite
individuals, but, of course, no population is this
large. Genetic drift occurs because the alleles in an
offspring generation are a random sample of the
alleles in the parent generation. Alleles may or may
not make it into 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 fertilizations. If
one individual in a population of ten individuals
happens to die before it leaves any offspring to the
next generation, all of its genes—a tenth of the
population’s gene pool— will be suddenly lost. In a
population of 100, that 1 individual represents only
1 percent of the overall gene pool; therefore, it has
much less impact on the population’s genetic
structure and is unlikely to remove all copies of even
a relatively rare allele.
Bases on the Theories of Evolution
In scientific terms, the evolutionary history and relationship of
an organism or group of organisms is called phylogeny.
Phylogeny describes the relationships of an organism, such as
which organism it is thought to have evolved from, and which
species it is most closely related to, and so forth. Phylogenetic
relationships provide information on shared ancestry but
necessarily on how organisms are similar or different.
Evidence of evolution
Scientists who study evolution may want to know whether two
present-day species are closely related. Evidence for evolution
can be structural, genetic, or biogeographical.
Observing anatomical features shared between organisms
(including ones that are visible only during development) can
indicate that they share a common ancestor.
Structural evidence
can be compared
between extant
(currently living)
organisms and the
fossils of extinct
organisms.
Homologous structures similar because they have both
If two or more species share a unique physical trait they may experienced similar selection
all have inherited this trait from a common ancestor. Traits pressures that optimized them for
that are shared due to common ancestry are homologous walking. However, the actual
structures. structures that make up the leg are quite different, suggesting
For example, the forelimbs that the limbs are not due to a common ancestor.
of whales, humans, and
birds look different on the
outside because they're At the most basic level, all living organisms share the same
adapted to function in genetic material (DNA), similar genetic codes, and the same
different environments. basic process of gene expression (transcription and
However, if you look at the bone structure of the forelimbs, translation).
the organization of the bones is similar across species.
In order to determine which organisms in a group are most
closely related, we need to use different types of molecular
Embryology is
features, such as the nucleotide sequences of genes.
important to
Biologists often compare the sequences of related (or
understanding
homologous) genes. If two species have the "same" gene, it is
a species'
because they inherited it from a common ancestor.
evolution,
since some homologous structures can be seen only in embryo In general, the more DNA differences in homologous genes
development. For example, all vertebrate embryos, from between two species, the more distantly the species are
humans to chickens to fish, have a tail during early related.
development, even if that tail does not appear in the fully
developed organism. Segments of DNA can be analyzed using
gel electrophoresis, in which fragments of
Vestigial structures DNA are separated by size. Fragments are
Vestigial structures represented by horizontal bands. Bands
serve little or no present that are similar in size between samples
purpose for an will be on the same horizontal line and
organism. The human indicate that DNA sequence is shared. The
tail, which is reduced to more fragments two samples share, the more related they are
the tailbone during to one another.
development, is one example. Vestigial structures can provide DNA gel comparing four species: A, B, C, and D. Species A
insights an organism's ancestry. For instance, the tiny vestigial and C are most related, as they share 3 bands with one
leg bones found in some snakes reflect that snakes had a four- another.
legged ancestor.
Analogous structures The notion of biogeography is what first indicated to Charles
While similar structure can indicate relatedness, not all Darwin that species evolve from common ancestors. Patterns
structures that look alike are due to common of distribution of fossils and living species may tell us how
ancestry. Analogous structures evolved independently in modern organisms evolved.
different organisms because the organisms lived in similar
environments or experienced similar selective pressure. For example, broad groupings of organisms that had already
evolved before the breakup of the supercontinent Pangaea
For example, the leg of a cat and the leg of a praying mantis (about 200 million years ago) tend to be distributed
are analogous. Both legs are used for walking, but they have worldwide. In contrast, broad groupings that evolved after the
separate evolutionary origins. On the outside, they appear breakup tend to appear uniquely in smaller regions of Earth.
Environment cannot always account for either similarity or
dissimilarity. Closely related species can evolve different traits
under different environmental pressures. Likewise, very
distantly related species can evolve similar traits if they have
similar environmental pressures.
Both of these phylogenetic trees shows the relationship of the
three domains of life—Bacteria, Archaea, and Eukarya—but
the (a) rooted tree attempts to identify when various species
diverged from a common ancestor while the (b) unrooted tree
does not. (credit a: modification of work by Eric Gaba)The star
represents where we are at this phylogenetic tree.
A phylogenetic tree can be read like a map of evolutionary
history. Many phylogenetic trees have a single lineage at the
base representing a common ancestor. Scientists call such
trees rooted, which means there is a single ancestral lineage
(typically drawn from the bottom or left) to which all
organisms represented in the diagram relate. Notice in the
rooted phylogenetic tree that the three domains—Bacteria,
Archaea, and Eukarya—diverge from a single point and branch
off. The small branch that plants and animals (including
humans) occupy in this diagram shows how recent and
miniscule these groups are compared with other organisms.
Unrooted trees don’t show a common ancestor but do show
relationships among species.
In a rooted tree, the branching indicates evolutionary
relationships (Figure 2). The point where a split occurs, called
a branch point, represents where a single lineage evolved into
a distinct new one. A lineage that evolved early from the root
and remains unbranched is called basal taxon. When two
lineages stem from the same branch point, they are called
sister taxa. A branch with more than two lineages is called a
polytomy and serves to illustrate where scientists have not
definitively determined all of the relationships. It is important
to note that although sister taxa and polytomy do share an
ancestor, it does not mean that the groups of organisms split
or evolved from each other. Organisms in two taxa may have
split apart at a specific branch point, but neither taxa gave rise
to the other.
The root of a phylogenetic tree indicates that an ancestral
lineage gave rise to all organisms on the tree. A branch point
indicates where two lineages diverged. A lineage that evolved
early and remains unbranched is a basal taxon. When two
lineages stem from the same branch point, they are sister
taxa. A branch with more than two lineages is a polytomy.
Many disciplines within the study of biology contribute to
understanding how past and present life evolved over time;
these disciplines together contribute to building, updating,
and maintaining the “tree of life.” Information is used to
organize and classify organisms based on evolutionary
relationships in a scientific field called systematics. Data may
be collected from fossils, from studying the structure of body
parts or molecules used by an organism, and by DNA analysis.
By combining data from many sources, scientists can put
together the phylogeny of an organism; since phylogenetic
trees are hypotheses, they will continue to change as new
types of life are discovered and new information is learned.
Scientists must collect accurate information that allows them
to make evolutionary connections among organisms. Similar to
detective work, scientists must use evidence to uncover the
facts. In case of phylogeny, evolutionary investigations focus
on two types of evidence: morphologic (form and function)
and genetic.
The study of anatomy and genetic make-up of organisms helps
us determine that evolution exists. In the same manner,
integrating anatomy and genetics also aids us in determining
the evolutionary relationship between different organisms,
helping us make scientifically sound phylogenetic trees.
Building Phylogenetic Tree
How do scientists construct phylogenetic trees and know the
degree of relatedness between living organisms by DNA? Do they
just look for similarities between the whole genomes? Or just
specific genes? Or RNA? Or what exactly?
As long as you have something
you can compare across different
species, you can make a
phylogenetic tree.
A phylogenetic tree can be built
using physical information like
body shape, bone structure, or
behavior. Or it can be built from
molecular information, like genetic sequences.
In general, the more information you’re able to compare, the When a scientist makes a phylogenetic tree based on a gene that
more accurate the tree will be. So you’d get a more accurate tree provides antibiotic resistance, the tree will reflect how that gene
by comparing entire skeletons, instead of just a single bone. Or by evolved, not necessarily how the organisms hosting the gene
comparing entire genomes, instead of just a single gene. evolved. As another example, some genes are almost never
shared among organisms, such as the genes encoding the
Any DNA, RNA, or protein sequence can be used to generate a machinery to convert DNA into RNA. These genes are critical for
phylogenetic tree. the organism to live, and they evolve very slowly. One of these
But DNA sequences are most commonly used in generating trees genes, 16S rRNA, is commonly used to build phylogenetic trees
today. showing the evolutionary relationships within Bacteria. These
trees are often very reliable in terms of the branching order, but
it turns out that there are large numbers of organisms that do not
Organisms evolve from common ancestors and then diversify. show up in the 16S rRNA data obtained using standard lab
Scientists use the phrase “descent with modification” because techniques. Other techniques have led to the identification of a
even though related organisms have many of the same huge diversity of bacteria (see Hug et al., 2016). As new
characteristics and genetic codes, changes occur. This pattern techniques become available and more data are collected, the
repeats as one goes through the phylogenetic tree of life: complexity of genes as a reflection of evolution is becoming more
apparent. And all of the complexities provide information
1. A change in the genetic makeup of an organism leads to scientists can use to understand the processes and history of
a new trait which becomes prevalent in the group. evolution.
2. Many organisms descend from this point and have this
trait.
3. New variations continue to arise: some are adaptive and
persist, leading to new traits.
4. With new traits, a new branch point is determined (go
back to step 1 and repeat).
Distantly related organisms can also share morphological features.
For example, many Bacteria are spherical in shape, as are many
Archaea. All bacteria are more distantly related to all Archaea than
lizards are to rabbits even though lizards and rabbits look much
more different from each other. Thus, morphology is not
particularly useful for determining evolutionary relationships
among some groups of organisms. In fact, genetic data have
shown that very closely related Cyanobacteria (a specific lineage
of bacteria that perform oxygenic photosynthesis) can have very
different cell shapes, and Cyanobacteria with similar shapes may
be only distantly related to each other. Thus, understanding how
morphology does or does not relate to evolutionary history is
critically important when using morphological data as the basis for
phylogenetic trees.
Many phylogenetic trees are built using genetic data. Genes are
the units of organisms that encode the results of evolution,
making them particularly useful for building phylogenetic trees.
However, different genes evolve in different ways, genes can be
swapped among organisms, and genes can be lost by organisms.
Thus, the choice of genes to use for a phylogenetic tree needs to
reflect the scientific questions being asked. As an example, genes
that encode for antibiotic resistance in bacteria can be shared
among bacteria, even between relatively distantly related species.