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How Evolution Works?
An introduction
The “dead-leaf moth” (Oxytenis modestia) has
evolved camouflage that resembles a dead leaf.
Observations on the diversity of life
• When you look around in nature you see a great diversity of life in different forms.
• We can call these forms species
• A species is a group of living organisms consisting of similar individuals capable
of interbreeding. That is to exchange genes.
• It is estimated there are 8.7 million eukaryotic species on earth.
• Why are there so many diverse species and why do many of them look the same?
Observations about the diversity of life
• An example of this diversity is the Dead leaf
moth (Oxytenis modestia). This species is one of
over 120,000 members of the Lepidoptera
(butterflies and moths).
• Found in the Peruvian rain forest it has evolved a
shape and colouring that makes it look like a
dead leaf.
• The caterpillar of this species has a head shaped
like that of a snake that it waves from side to side
to warn off predators.
• These strategies are examples of the natural
selection of traits that increase survival of the
fittest in a particular environment.
• Can you spot this camouflaged moth
Observations on the diversity of life
• The Lepidoptera (butterflies and moths) with
over 120,000 members are classified on the basis
of common characteristics.
• A juvenile stage characterised by a welldeveloped head and many chewing mouthparts.
• The adults share other features;
• three pairs of legs.
• two pairs of wings covered with small scales.
• But the lepidopterans also differ from one
• How did there come to be so many different
moths and butterflies, and what causes their
similarities and differences?
Observations on the diversity of life
The similarities between this moth and its 120,000
relatives illustrates three key observations about life.
1. The striking ways in which organisms are suited
for life in their environments (the term
environment refers not only to the physical
surroundings but to the presence of other
organisms as well).
2. The many shared characteristics (unity) of life.
3. The rich diversity of life.
This is the result of evolution.
Definitions of Evolution
•Darwin defined evolution as “descent with
•Meaning that present day species are
descendants of ancestral species that were
•It can also be defined as a change in the
genetic composition of a population from
generation to generation.
Definitions of Evolution
• Evolution can be seen in two related but different ways: (1) as
a pattern and (2) as a process.
1. The pattern of evolutionary change is revealed by data from
many scientific disciplines, including biology, geology,
physics, and chemistry. These data are facts—they are
observations about the natural world—and these
observations show that life has evolved over time.
2. The process of evolution consists of the mechanisms that
cause the observed pattern of change. These mechanisms
represent natural causes of the natural phenomena we
Definitions of Evolution
•Indeed, the power of evolution as a unifying
theory is its ability to explain and connect a
vast array of observations about the living
•As with all theories, Scientists constantly
challenge evolutionary theory to advance
our understanding of the processes involved.
Evolution of evolution theory
• Before Darwin many people had considered how life had formed.
• Empedocles (c. 494–434 B. C. E.), proposed that the origin of life had
taken place in a manner that suggested evolution.
• Aristotle (384–322 B. C. E.) viewed the universe and species as
unchanging. This view dominated for over 2000 years as it agreed with
religious teachings that species were fixed (unchanging) since the act
of creation.
• Al-Jahiz (776-868) (Basra) described three mechanisms of evolution:
Struggle for Existence, Transformation of Species into each Other, and
Environmental Factors.
• Erasmus Darwin (Darwin’s grandfather) published “Zoonomia” in 1794
proposing that species changed to adapt and survive.
• Others had similar ideas. But none had facts to support them.
Evolution of evolution theory
• Carolus Linnaeus (1707–1778) a Swedish physician and botanist developed a
system to classify life’s diversity.
• He developed the two-part, binomial, format for naming species (such as Homo
sapiens - the wise Man for humans) that is still used today.
• His system classified plants based on the number of male and female reproductive
parts of flowers (sexual system).
• He used a nested classification system, grouping similar species into increasingly
general categories.
• For example, similar species are grouped in the same genus, similar genera (plural
of genus) are grouped in the same family, and so on (more in a later lecture).
• Linnaeus considered the similarity among species was due to the pattern of their
• We now know his system had faults. But at the time this was a great advance
in scientific understanding.
• See videos below.
• His system revolutionized the classification of species.
• See how his system is still used today.
Evolution of evolution theory
The concept of geological time
• In the 1700’s the study of fossils (Paleontology) led to new
theories on the age of the earth.
1 Rivers carry sediment into
aquatic habitats such as seas and
swamps. Over time, sedimentary
rock layers (strata) form under
water. Some strata contain fossils.
• Previously scholars (e.g. Sir Isaac Newton) had estimated
the earth to have formed in approximately 4000 B. C. E.
• Many fossils are found in sedimentary rocks formed from
the sand and mud that settle to the bottom of seas, lakes,
and swamps. As new layers cover older ones they
compress them into layers of rock called strata (singular,
• The fossils in a particular stratum provide a view of some
of the organisms that populated Earth at the time that
layer formed.
• Later, erosion carves through upper (younger) strata,
revealing deeper (older) strata that had been buried.
2 As water levels change
and geological activity
pushes layers of rock
upward, the strata and
their fossils are exposed.
Younger stratum
with more recent
Older stratum
with older fossils
Evolution of evolution theory
The concept of geological time
• Georges Cuvier (1769–1832): This French scientist developed the
science of palaeontology. He noted that fossils in older strata of
rock were different from current life forms. And that in each
strata new species appeared while others disappeared.
• He proposed that catastrophic events lead to extinction of local
species followed by colonisation by new species migrating from
• He opposed the idea of evolution.
Was I an
Image: Palais_de_la_Decouverte_Tyrannosaurus_rex
Evolution of evolution theory
The concept of geological time
In contrast to Cuvier’s emphasis on sudden events, others suggested that
profound change took place through the cumulative effect of slow but
continuous processes.
James Hutton (1726–1797): This Scottish geologist proposed that Earth’s
geologic features could be explained by gradual mechanisms, such as
valleys being formed by rivers.
Charles Lyell (1797–1875), the leading geologist of Darwin’s time
incorporated Hutton’s thinking into his proposal that the same geological
processes are operating today as in the past, and at the same rate.
And that these changes take place over enormously long periods of time.
These ideas would come to strongly influence Darwin’s thinking regarding
the time required for evolution to occur.
Evolution of evolution theory
Lamarckism - The first modern theory of evolution
• Jean-Baptiste de Lamarck (1744-1829) proposed the first testable
mechanism for how life evolves over time in response to a changing
• Published in 1809, the year of Darwin’s birth, this was revolutionary
as it recognised that evolutionary changes explained patterns of
fossils and the match of organisms to their environments.
• By comparing living species with fossils he identified several lines of
descent from older to younger fossils leading to a living species.
Jean-Baptiste de Lamarck
Evolution of evolution theory
Lamarckism - The first modern theory of evolution
He based his theory on two principles.
1. Use and disuse, the idea that parts of the body that are used
extensively become larger and stronger, while those that are not
used deteriorate.
2. Inheritance of acquired characteristics, stated that an organism
could pass these modifications to its offspring.
Evolution of evolution theory
Lamarckism - The first modern theory of evolution
• An example used was that giraffes necks grew longer by stretching for
leaves in high branches. This trait was then passed on with each
Evolution of evolution theory
Lamarckism - The first modern theory of evolution
• Lamarck thought that evolution happens because organisms have an innate
drive to become more complex.
• Darwin rejected this idea but did think that variation was introduced in to the
evolutionary process by the inheritance of acquired characteristics.
• Lamarck’s theory eventually failed as it breaks the rules of genetic inheritance
proposed by Gregor Mendel.
• It is important to remember that:
• He recognized the fact that organisms are well suited for life in their
environments and this can be explained by gradual evolutionary change.
• It was only in the early 1900’s, after the deaths of Darwin and Mendel, that the
significance of Mendel’s identification of genetic inheritance was realised.
Evolution of evolution theory
Darwin’s theory of evolution; a theory that changed the course of history
The world has seen many scientific breakthroughs.
But none as revolutionary in the way that Darwin’s theory of evolution has been.
This theory was REVOLUTIONARY, overturning over 2000 years of scientific and
cultural thinking.
The impact of this theory was felt throughout society.
Scientific Darwinism has lead the advancement of science leading in to the age
of molecular genetics.
Social Darwinism used to justify imperialism, racism, eugenics and social
inequality at various times over the past century and a half.
Political Darwinism was used drive political movements such as Communism,
and Fascism resulting in World War 2.
Despite the overwhelming evidence for evolution its impact is still controversial
This is how it began.
Charles Darwin (1809 – 1884)
• Darwin studied botany at Cambridge University and had a life long
interest in nature.
• On graduating his supervisor recommended him to Captain Robert
Fitzroy the commander of the Royal Navy survey ship HMS Beagle.
• The Beagle was to survey the coast line of south America then sail
round the world.
• Darwin was to be a companion for Capt. Fitzroy and the ships unpaid
Voyage of HMS Beagle (1831 – 1836)
Voyage of HMS Beagle
• When ever the ship stopped to survey the coast Darwin was taken
ashore where he observed and collected 1000’s of plant and animal
• He described the features that allowed them to survive in such
diverse environments as the humid forests of Brazil, grasslands of
Argentina, and the Andes mountains.
• Also noting that plant and animals in temperate regions of South
America more closely resembled those in tropical regions of S.
America than those in temperate regions of Europe.
Voyage of HMS Beagle
• He read Lyell’s Principles of Geology during the voyage.
• Experience geological change first hand during an earthquake in Chile.
Observing that the land had been thrust up several metres.
• And found fossils of ocean species high in the Andes mountains.
• This led him to conclude that Lyell was correct in that the physical
evidence indicating the earth was very old.
• This contradicted the view held then that the earth had been created
around 4000 B. C. E.
• This would be a critical point when he developed his theory of
evolution by natural selection.
Voyage of HMS Beagle
The Galapagos Islands
• His interest in species diversity was further stimulated in the
Galapagos islands, near the equator, 900 km west of S. America.
• He observed several types of mockingbirds. That looked similar but
seemed to be different species. Some unique to a single island some
to more than one.
• Similar observations were made for Finches and Tortoises.
Darwin’s Finches
Variation among tortoises: Hood island tortoise has a long neck and a curved shell open round the
neck and legs, allowing it to reach the sparse vegetation found on the island. The tortoise from Isabela
Island has a dome-shaped shell and a short neck. On this island vegetation is more abundant and
close to the ground. The Tortoise from Pinta Island has a shell intermediate between the two forms.
Voyage of HMS Beagle
Darwin’s finches
• There are more than a dozen species of closely related finches on the
islands. Some found on only one island.
• We now know their beaks are adapted to specific diets
Voyage of HMS Beagle
The Galapagos islands
• Darwin saw that animals on the Galapagos islands were similar to
those on the S. American mainland but not found any where else in
the world.
• His observation of the diversity of amongst species such as finches,
mocking birds and tortoises led him to a revolutionary idea.
• That the islands had been colonised by South American species
carried across the Pacific ocean. These species had then adapted so
diversifying in to different species on the various islands.
What is adaptation
• During his voyage, Darwin saw many examples of adaptations.
• These are inherited characteristics that improve an organisms chances of
survival and reproduction in a specific environment.
• Later, he realised that adaptation to the environment and the origin of new
species were closely related processes.
• He thought, and we now know, that new species could arise from an
ancestral form by the gradual accumulation of adaptations to a different
• He realized that explaining such adaptations was essential to
understanding evolution. His explanation of how adaptations arise centred
on natural selection. This is a process in which individuals that have certain
inherited traits tend to survive and reproduce at higher rates than do other
individuals because of those traits.
To publish or not?
• By the early 1840s, Darwin had worked out the major features of his
• In 1844, he wrote a long essay on descent with modification and its
underlying mechanism, natural selection.
• He was reluctant to publish his ideas, because of the controversy it
would generate.
• He continued to collect evidence.
• By the 1850’s he had described his ideas to Lyell, and few others.
• So controversial were his ideas that he only told those he trusted.
• Lyell, although not yet convinced by evolution encourage him to
publish before someone else had the same idea.
Lyell’s prophecy comes true
• In 1858, Darwin received a manuscript from Alfred Wallace a British
naturalist working in the islands of Malaysia.
• Wallace had developed a hypothesis of natural selection almost
identical to Darwin’s.
• Darwin wrote to Lyell “Your words have come true with a vengeance. .
. . I never saw a more striking coincidence . . . so all my originality,
whatever it may amount to, will be smashed.”
• In July that year Darwin and Wallace’s papers were presented at the
Linnean Society of London.
Alfred Russel Wallace (1823 – 1913)
On the Origin of Species by Means of Natural
• Darwin quickly finished his book and published it
in 1859.
• Publication caused protests from all levels of
society and the establishment.
• However, within 10 years most scientists of the
time were convinced that life’s diversity is the
result of evolution.
• Darwin succeeded by presenting a plausible
scientific mechanism argued with simple logic
and supported with overwhelming evidence.
Ideas from “The Origin of Species”
• Darwin attributed the unity of life to the descent of all
organisms from an ancestor that lived in the remote past.
• He also thought that as the descendants of that ancestral
organism lived in various habitats, they gradually
accumulated diverse modifications, or adaptations, that
fitted them to specific ways of life.
• He reasoned that over a long period of time, descent with
modification eventually led to the rich diversity of life we see
Ideas from “The Origin of Species”
• Darwin viewed the history of life as a tree.
• In this tree each fork in a branch indicated a
common ancestor of all the lines arising from that
• Those labelled A-D represented living species those
unlabelled were extinct.
• He thought this branching, along with extinction
could explain morphological gaps that sometimes
exist between related groups of organisms.
• He formulated this idea in 1837 soon after returning
from his voyage on the Beagle.
• In the corner he writes “I think”.
Artificial and natural selection, and adaptation
• Darwin used artificial selection that is used to domesticate plants
and animals to support his idea of natural selection.
• Arguing that domesticated crops and animals bear little
resemblance to their wild ancestors.
• He then argued a similar process occurred in natural selection. He
based his argument on two observations.
Artificial and natural selection, and adaptation
These two observations were as follows:
Observation #1: Members of a population often vary in their inherited traits.
Observation #2: All species can produce more offspring than their environment can
support, and many of these offspring fail to survive and reproduce.
Inference #1: Individuals whose
inherited traits give them a higher
probability of surviving and reproducing
in a given environment will leave more
offspring than do other individuals.
Inference #2: This unequal ability of
individuals to survive and reproduce will
lead to the accumulation of favourable
traits in the population over generations.
Artificial and natural selection, and adaptation
Evolutionary pressure
Darwin had read a famous essay by the economist Thomas Malthus,
who stated that much of human suffering—disease, famine, and
war—resulted from the human population’s potential to increase
faster than food supplies and other resources.
This led to competition for resources (energy, food, land, water).
Similarly, Darwin realized that the capacity to over reproduce was a
characteristic of all species.
This introduces competition for resources – evolutionary pressure.
In an environment with such pressure adaptation can happen.
Artificial and natural selection, and adaptation
Key Features of Natural Selection
• Natural selection is a process in which individuals that have certain
heritable traits survive and reproduce at a higher rate than do other
individuals because of those traits.
• Over time, natural selection can increase the frequency of
adaptations that are favourable in a given environment.
• If an environment changes, or if individuals move to a new
environment, natural selection may result in adaptation to these
new conditions, sometimes giving rise to new species.
• Heritable traits that give an advantage in one environment may not
do in another.
Artificial and natural selection, and adaptation
Remember the following
• Only populations evolve not individuals.
• Natural selection only amplifies or reduces heritable traits that
differ within the population. If a population is genetically identical
for a heritable trait, evolution by natural selection cannot happen.
• Environmental factors vary from place to place and over time. A
trait that is favourable in one place or time may be useless—or
even detrimental—in other places or times.
• Natural selection is always operating, but which traits are favoured
depends on the environment in which a species lives and mates.
The power of adaptation
• Through natural selection adaptation can be both subtle or extreme.
• This depends on the selection pressure and how favourable is the outcome.
• Examples below are for camouflage.
• Different environments shaped the adaptation of form and colour in these
species of Preying Mantis.
South African flower-eyed mantis
Common form of Mantis
Malaysian orchid mantis
The power of adaptation
Natural selection for antibiotic resistance
Penicillin, the first antibiotic was a major break through in the treatment of
bacterial diseases. Large numbers of antibiotics are now in use.
1943, Penicillin was first widely used. By 1945, 20% of Staphylococcus aureus
bacterial strains in hospitals were resistant. They had an enzyme penicillinase
that destroyed penicillin.
Other S. aureus strains quickly developed resistance to other antibiotics.
Finally in 1959, Methicillin was used. Methicillin deactivates an enzyme the
bacteria uses to synthesize its cell walls. However some used a different enzyme
so resistance soon developed. Leading to the designation MRSA (Methicillin
resistant S. aureus)
Now some S. aureus strains are resistant to multiple antibiotics.
Many other bacteria have also developed multi-drug resistance e. g. gonorrhoea
and tuberculosis.
Natural selection in action
• The following video shows E.coli bacteria developing antibiotic
resistance in real time.
• This is an example of Darwin's evolution by natural selection and his
“tree of life”.
The Evolution of Bacteria on a “Mega-Plate” Petri Dish (Kishony Lab)
• The generation time of E.coli is 20 minutes.
• This experiment took 11 days that is 792 E. coli generations.
• If the generation time for humans is 20 years it is the equivalent of
15,840 years.
• This is longer than recorded human history.
Investigating the tree of life
Phylogenetics is defined as the study of evolutionary history that
reveals relationships among biological entities - often species,
individuals or genes (which may be referred to as taxa).
Nature can be deceptive.
• This looks like a snake but it is a legless lizard, the
European glass lizard (Ophisaurus apodus).
• What tells us it is not a snake?
• It does not have the classic traits of a snake such as;
• a highly mobile jaw.
• a large number of vertebrae
• a short tail located behind the anus
• These three traits are shared by all snakes.
Phylogenetic tree
• Snakes and lizards are part of the
continuum of life extending from
their common ancestor to the
most recent species.
• We will now look at hypotheses
regarding how diversity evolved
from the point of the view of the
pattern of evolution –
observations of evolutions
products over time. Rather than
the evolutionary process
Phylogenies show evolutionary
How are organisms named?
• Common names - such as monkey and finch are useful but confusing
as there are many species of monkeys and finches.
• Others do not accurately describe the organism they refer to. An
example are the three “fishes”: jellyfish (a cnidarian), crayfish (a
small, lobster like crustacean), and silverfish (an insect).
• And organisms have different names in different languages: Frog in
English becomes kurbağa in Turkish.
Phylogenies show evolutionary
How are organisms named?
Binomial nomenclature
The two-part format of the scientific name, commonly called a binomial,
was developed in the 18th century by the botanist Carolus Linnaeus.
The first part is the genus (plural, genera) to which the species belongs.
The second part is unique for each species within a genus.
Example Panthera pardus, the scientific named for a Leopard.
The first letter is always capitalised and the whole binomial is italicized.
Phylogenies show evolutionary
Hierarchical classification of organisms
This taxonomic system was developed by Linnaeus and is
called the Linnaean system.
Closely related species are grouped into the same genus.
Example: The leopard (Panthera pardus), is in the genus
containing the African lion (Panthera leo), the tiger
(Panthera tigris), and the jaguar (Panthera onca).
In addition taxonomists use progressively more
comprehensive categories for classification.
This system places related genera in the same family,
families into orders, orders into classes, classes into phyla
(singular, phylum), phyla into kingdoms, and, more
recently, kingdoms into domains.
Each level is a taxon. Panthera is a taxon at the genus
level and Mamalia is a taxon at the class level.
Taxon above the genus level are not italicized.
Phylogenies show evolutionary
Hierarchical classification of organisms
• This hierarchical system allows us to group similar species together and group them into
increasingly broader categories.
• This allows us to catalogue/classify the world of diversity.
• Example: Pine and Fir trees look similar (remember the legless lizard and the snake) but different
enough to be different species (genera). But are similar enough to be in the same family, the
• As categories become broader the characters used to classify one group of organisms will be of no
use in another.
• For example the level of morphological and genetic diversity between an Order of snails and an
Order of mammals is not the same.
• The placement of species within this hierarchy does not always fit evolutionary history.
• Watch these videos they explain phylogenetic trees.
• Example of how to make a tree https://www.youtube.com/watch?v=6_XMKmFQ_w8
• Phylogenetics https://www.youtube.com/watch?v=fQwI90bkJl4
Phylogenies show evolutionary
Linking Classification and Phylogeny
Evolutionary history can be shown as
phylogenetic tree like Darwin’s original tree of
This was originally based on species having key
morphological features in common (taxonomy).
The Linnaean system distinguishes groups
(amphibians, mammals, reptiles etc.). But it tells
us nothing about their evolutionary relationship.
An alternative system is cladistics where
organisms are classified based on evolutionary
relationships. With species assigned to groups
including a common ancestor. In this system
taxon's are called clades.
This tree shows the evolutionary relationships
within the Carnivora.
Evolutionary relationship between members of the Carnivora
Phylogenies show evolutionary
Phylogenetic trees
Phylogenetic trees represent hypothetical evolutionary
On the left is the root, the common ancestor.
The relationships are represented by two-way branch
Each branch point represents a common ancestor of
the two evolutionary lineages diverging (arising) from
The order that Taxa appear on the tree does not
indicate the sequence of evolution.
They show patterns of descent not phenotypic
Phylogenies show evolutionary
Phylogenies show evolutionary
Practical applications of phylogenetic trees
• Maize originated in the Americas, and is now a global crop.
• A tree based on DNA sequence data identified two wild grass species
that may be maize’s closest living relatives.
• These may be useful “reservoirs” of beneficial genes that can be
introduced to cultivated maize by cross breeding.
Wild Maize
Darraq et al 2010 DOI: 10.1186/1471-2164-11-233
Phylogenies are inferred from
morphological and molecular data
• Phenotypic and genetic similarities due to shared ancestry are called
• Morphological homology: The similarity in the number and
arrangement of bones in the forelimbs of mammals is due to descent
from a common ancestor.
• Genetic homology: The similarity of genes or other DNA sequences if
descent is from sequences carried by a common ancestor.
• Generally organisms with similar morphologies or DNA sequences are
likely to be closely related.
Phylogenies are inferred from
morphological and molecular data
• However, morphological divergence between related species
can be greater than the genetic diversity. The opposite is also
• Example: Hawaiian silversword plants, some species are tall
trees. Others are dense ground-hugging shrubs. Despite the
morphological differences the genetic differences are very
• The molecular divergence indicates the group began diverging
5 million years ago. This is called a molecular clock.
Dubautia scabra
Dubautia linearis
Phylogenies are inferred from
morphological and molecular data
Convergent evolution
• This is when similar environmental pressures and natural selection
produce similar adaptations in organism from different lineages.
• Example: the two mole-like animals shown.
• They look similar. But their internal anatomy, physiology and
reproductive systems are different. Differences in the genetic and
fossil evidence indicates their common ancestor lived 140 million
years ago.
• Phylogenetically, they are far apart.
An organism’s evolutionary history
is documented in its genome
• Comparison of nucleic acid and other molecules can be used to
deduce relationships.
• Molecular data can uncover evolutionary relationships between
groups that have little common ground for morphological
comparison, such fungi which are more closely related to animals
than plants.
• Molecular methods allow reconstruction of phylogenies among
groups of living organisms for which there is little or no fossil record.
An organism’s evolutionary history
is documented in its genome
Evolution leaves a footprint in nucleic acids
Different genes evolve at different rates even in the same evolutionary lineage.
Molecular trees can represent short or long periods of time depending on which genes
are used.
Slow change: DNA coding for ribosomal RNA (rRNA) changes slowly. Comparing DNA
sequences in these genes is used to investigate relationships between taxa that diverged
100’s millions of year ago.
Example: Such studies show that fungi are more closely related to animals than to
Rapid change: Mitochondrial DNA (mtDNA) evolves rapidly and is used to investigate
recent evolutionary events.
Example: This method was used to trace relationships among Native American groups. It
confirmed other evidence that the Pico (Arizona), May (Mexico) and Yanomami
(Venezuela) are closely related. And probably descended from the first of three waves
migrants that crossed the Bering land bridge form Asia to the Americas 15,000 years ago.
Image source: https://dna-explained.com/2013/09/18/nativeamerican-mitochondrial-haplogroups/
An organism’s evolutionary history
is documented in its genome
Gene duplication and gene families
• Gene duplication plays an important part in evolution as it increases
the number of genes in the genome. This increases the opportunity
for further evolutionary changes.
• These molecular phylogenies must account for repeated duplications
that result in gene families. These are groups of related genes within
an organisms genome.
• By accounting for duplication we can distinguish two types of
homologous genes. Orthologous and paralogous genes.
An organism’s evolutionary history
is documented in its genome
Gene duplication and gene families
A) Orthologous genes (from the Greek orthos, exact):
Homology results from speciation (one species becoming two
or more species) and occurs in genes found in different
Example: Genes coding for cytochrome c in humans and dogs
are orthologous.
B) Paralogous genes (from the Greek para, in parallel):
Homology results from gene duplication; multiple copies have
diverged from one another within a species.
Example: Olfactory receptor genes have under gone many
duplications in vertebrates. Humans have 380 and mice have
1200 functional copies of these paralogous genes.
An organism’s evolutionary history
is documented in its genome
Gene duplication and gene families
Orthologous genes diverge only after speciation; that is after the genes are
found in different species.
Example: Although cytochrome c serves the same function in humans and
dogs, the gene sequence in humans has diverged from that of dogs since
they last shared a common ancestor.
Paralogous genes can diverge within a species as there is more than one
copy in the genome.
Example: Human olfactory receptor gene family members have diverged
from each other during our long evolutionary history. They now specify
proteins conferring sensitivity to varied molecules, ranging from food
odours to sex pheromones.
An organism’s evolutionary history
is documented in its genome
Genome evolution
We can now compare the entire genomes of different organisms and two
patterns have emerged.
Pattern 1: Lineages that diverged long ago often share many orthologous
Example: Although the human and mouse lineages diverged about 65
million years ago, 99% of human and mice genes are orthologous. As are
50% of human and yeast genes despite one BILLION years of divergent
This explains why many divergent organisms have the same biochemical
and developmental pathways.
Because of these shared pathways, the function of genes linked to human
diseases can be studied in yeast and other distantly related organisms.
An organism’s evolutionary history
is documented in its genome
Genome evolution
Pattern 2: The number of genes a species has does not seem to increase
through duplication at the same rate as phenotypic complexity.
Humans have about four times as many genes as yeast, a single-celled
eukaryote, even though—unlike yeast—we have a large, complex brain and
a body with more than 200 different types of tissues.
There is evidence that humans genes are more versatile than those in
A single human gene can encode multiple proteins that perform different
tasks in different tissues.
The mechanism underlying this genomic versatility and phenotypic
variation are an ongoing challenge.
Molecular clocks help track
evolutionary time
• Evolutionary biology aims to understand the relationships between
organisms. To do this it is important to know when lineages diverged
from each other.
• Earlier we saw that the ancestral Hawaiian silversword diverged 5
million years ago. This estimate relied on the concept of a molecular
Molecular clocks help track
evolutionary time
How molecular clocks work
• Molecular clocks are based on the observation that some genes and
other regions of the genome appear to evolve at constant rates.
• An assumption underlying the molecular clock is that the number of
nucleotide substitutions in orthologous genes is proportional to the
time that has elapsed since the genes branched from their common
• In the case of paralogous genes, the number of substitutions is
proportional to the time since the ancestral gene was duplicated.
Molecular clocks help track
evolutionary time
How molecular clocks work
• We can calibrate the molecular clock of a gene that has a reliable
average rate of evolution by graphing the number of genetic
differences—for example, nucleotide, codon, or amino acid
differences—against the dates of evolutionary branch points that are
known from the fossil record.
• The average rates of genetic change inferred from such graphs can
then be used to estimate the dates of events that cannot be
discerned from the fossil record, such as the origin of the silverswords
discussed earlier.
Molecular clocks help track
evolutionary time
The mammalian molecular clock
The number of accumulated
mutations in seven proteins has
increased over time in a consistent
manner for most mammal species.
The three green data points
represent primate species, whose
proteins appear to have evolved
more slowly than those of other
mammals. The divergence time for
each data point was based on fossil
By averaging the number of mutations in more than one
gene or protein variation in the mutation rate is smoothed
Molecular clocks help track
evolutionary time
Differences in clock speed
• Some mutations are selectively neutral –they are not beneficial or
• Others are harmful, and are quickly removed from the gene pool by
natural selection.
• In genes were mutations are neutral or have little or no effect of
fitness, then the rate of mutation will be regular like a clock.
• The less important the gene is for fitness the faster its clock.
• The more important the gene is for fitness the slower its clock will
Molecular clocks help track
evolutionary time
Applying a molecular clock: Dating the origin of HIV
Phylogenetic analysis shows that HIV, the virus that causes AIDS, is
descended from viruses that infect chimpanzees and other primates.
When did it jump the species barrier in to humans?
HIV’s genetic material is RNA, and like other RNA viruses, it evolves quickly.
Using HIV-1M, the most common HIV strain in humans, samples were
compared that had been collected at different times. The earliest sample
was from 1959.
Sequence comparison showed the virus had evolved in a clock like fashion.
It indicated the jump to humans of HIV-1M happened around 1930. Later
work using a more advanced molecular clock indicated a date of 1910.
Molecular clocks help track
evolutionary time
Applying a molecular clock:
Dating the origin of HIV
• Sequence comparison showed
the virus had evolved in a clock
like fashion.
• It indicated the jump to
humans of HIV-1M happened
around 1930. Later work using
a more advanced molecular
clock indicated a date of 1910.
• Black dots based DNA
sequences of an HIV gene in
patients blood.
The tree of life continues to
change based on new data
• As phylogenetic data has accumulated we have gone from two
Kingdoms (plants and animals) to five Kingdoms (Monera
(prokaryotes), Protista (a diverse kingdom consisting mostly of
unicellular organisms), Plantae, Fungi, and Animalia).
• This system highlighted the two fundamentally different types of cells,
prokaryotic and eukaryotic. Prokaryotes were separated from all
eukaryotes by placing them in their own kingdom, Monera.
• But genetic phylogenies showed that some Prokaryotes were more
different from each other than they were from Eukaryotes.
• This resulted in the domain system (Bacteria, Archaea, and Eukarya) a
taxonomic level higher than Kingdoms.
The tree of life continues to
change based on new data
• In the new Domain system.
• The domain Bacteria contains most of the prokaryotes.
• The domain Archaea are diverse prokaryotes inhabiting a wide variety
of environments.
• The domain Eukarya contains all organisms containing true nuclei.
This includes single celled organisms and multicellular plants, fungi,
and animals.
• This system reflect the fact that most of evolutionary history has been
about single celled organisms.
180 years of progress in phylogenetics
First tree of life. Darwin 1838
A speculatively rooted tree for rRNA genes, showing the three life
domains: bacteria, archaea, and eukaryota. The black trunk at the bottom
of the tree links the three branches of living organisms to the last universal
common ancestor. (https://en.wikipedia.org/wiki/Phylogenetic_tree)
HOW EVOLUTION WORKS -microevolution
How Evolution Works?
Terminology review
• Population – group of individuals belonging to
same species in a defined area.
• Allele – alternate form of a given gene sequence.
• Genotype – allele combination of a
specific set of genes.
• Phenotype – physical apperance of an
• Gene pool – all allele forms of a given population.
• How does it work?
• Microevolution is driven by changes in the
genetic make up of individuals and
ultimately populations.
Exactly how do
populations evolve?
• There are many
different alleles in a
population but a
frog can only have
• These two frogs
have different
alleles for
All possible allele
combinations present in a population of a
• States that allele frequencies (genetic variation) in a
population will remain constant from generation to
generation if there are no factors causing those
frequencies to change.
• This situation in which allele frequencies remain
constant is called genetic equilibrium.
• Populations that are not evolving are said to be in
Hardy-Weinberg equilibrium.
• At Hardy-Weinberg equilibrium, allele frequencies don’t
change. The sum of allele frequencies is equal to 1
• Genotypes frequencies:
• Genotype AA Aa aa
• Frequency p2 2pq q2
Conditions required for HardyWeinberg equilibrium to hold true:
– Very large population
– No gene flow into or out of the population
– No mutations
– Random mating
– No natural selection
• Departure from these conditions results in a
change in allele frequencies in the population.
– Evolution has occurred!
In reality
Populations in nature never meet the
conditions of Hardy–Weinberg equilibrium—
All biological populations evolve.
The model is useful for predicting approximate
genotype frequencies of a population.
Specific patterns of deviation from Hardy–
Weinberg equilibrium help identify mechanisms
of microevolutionary change.
How does it work?
Microevolution is driven by five processes.
Small sample size.
Non random mating.
Gene flow.
Natural selection.
Short time scale events (generation-togeneration) that change the genotypes
and phenotypes of populations
Allelic frequency will remain constant generation to generation unless disturbed by
mutation, migration, nonrandom mating, natural selection, or genetic drift.
These are sources of microevolutionary change.
Sources of genetic variability
1. Mutations
• Changes in:
– Nucleotide base pairs
– Arrangement of genes on a chromosome
– Chromosome structure
• Only mutations in gametes are inherited
• Most mutations are silent:
– Only a small % of the DNA is expressed
– Mutations that are expressed are usually harmful
– Mutations do NOT cause evolution, but natural selection
needs the variations which mutations create
Sources of genetic variability
2. Gene Flow
 Genetic exchange due to the migration of fertile individuals
or gametes between populations.
 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.
Sources of genetic variability
3. Sexual Reproduction
• Mating in which a given member of a population is not
equally likely to mate with any other given member.
• Sexual selection is a form of nonrandom mating. This
is mating based on phenotype, based on the choices
made by the female of the species.
• The male will increase the proportion of his alleles in
the next generation.
The most common cases of nonrandom mating involve
inbreeding – mating between individuals of similar
genotypes, either by choice or due to environmental factors
such as location.
Sexual reproduction con’t
Inbreeding does not change genetic variation, but increases the
allele frequency of homozygous genotypes.
Inbreeding depression is seen in some cases, where inbred
individuals have lower fitness than non-inbred individuals.
fitness – relative ability of a genotype to contribute to future
fertility declines and high juvenile mortality associated with
“unmasking” harmful recessive alleles can reduce fitness for
inbred individuals.
hybrid vigor leads to higher relative fitness for hybrids by
increasing heterozygous allele frequency.
Self-fertilization is the most extreme case of inbreeding.
Sexual Reproduction con’t
Assortive mating – a type of nonrandom mating
where mates are (sexually) selected based on
phenotypes – really is an aspect of natural
positive assortive mating – selection for the same
phenotype; works like inbreeding for the genes governing
that phenotype, and for loci closely linked to those genes.
negative assortive mating – selection for the opposite
less common than positive assortive mating.
leads to a decrease in homozygous genotypes for the genes
governing the selected phenotype, and for loci closely linked to
those genes.
Population-environment interactions
1. Small sample size: Genetic drift
Consequences of small population
size: genetic drift
Genetic drift tends to
decrease genetic variation
within a population.
Consider taking a small sample of
individuals from a larger
Genetic drift tends to increase
genetic variation between
If only two individuals were picked
they almost certainly won’t reflect
the allele frequency in the larger
NOTE: Genetic drift is a major factor
population (in many cases, they
in evolution, especially when
can’t even possibly do so).
populations are split, but does
The same holds true for 3, 4, or 5
NOT involve natural selection.
As the selected sample gets larger
it becomes more likely that the
sample reflects the allele frequency
in the larger population.
Genetic Drift con’t
• Two reasons of genetic drift
– Bottleneck effect
– Founder’s effect
• A small sample of alleles is likely to yield a gene pool that
is different from the distribution found in the larger
Genetic Drift con’t
• Bottleneck effect – The change in allele
frequency in a population due to change
following a sharp reduction in the
population size.
• Founder effect – When a small portion of
a population migrates/separated to
another area, starting a new population.
Genetic Drift con’t
If there is a drastic change (disease, migration or natural
catastrophe) in the survival of a large population, there is little
change in the frequency of that population's alleles. In a smaller
population, drastic change can result in loss of an entire allele.
Bottleneck effect
Bottleneck effect
Cheetahs survived a drastic bottleneck
after the last ice age, 10,000 years ago.
Bottleneck effect
• Consequences: low genetic diversity and
depressed reproduction.
• Examples;
– Golden hamster; most captive hamsters
descended from one wild litter found in Syria
in the 1930’s.
– European Bison descended from 12 animals.
– Video of founder and bottle neck effect.
Founder effect
• When small groups of individuals in secluded areas (eg
islands) found larger populations.
• In humans this often leads to genetic diseases due to
• Example Cohn’s syndrome a fatal genetic disease
common in the Amish community in the USA.
• The Amish are a reclusive religious select descended
from a few 100 migrants from Europe in the 18C.
• Such diseases are common in historically isolated
• Another example are Darwin’s Finches. Here the result
over a longer time period was new species.
Population-environment interactions
2. Natural Selection
• Traits of those who are more successful in
reproducing (survival of fittest) will become
more widespread in a population, the alleles that
bring about these traits will increase in
frequency from one generation to the next.
• Natural selection is environment oriented and
thus selected adaptive traits change according
to changes in the environment.
• Natural selection can only ‘work’ if there is preexisting variation within the population.
Artificial selection
• Artificial selection:
Humans choose
traits they prefer in
animals or plants
and breed to achieve
those “desirable”
Natural Selection con’t
• Natural selection is the only one of the
five agents of microevolution that
consistently works to adapt organisms to
their environment.
– Genetic drift is random.
– Mutation has a negative effect, or no effect.
– Gene flow doesn’t necessarily bring in genes
that are better suited to the environment.
– Non random mating doesn’t have anything to
do with matching individuals to environment.
Three modes of
Natural Selection
• When natural selection operates on
characters that are polygenic and
continuously variable, it can proceed in
one of three ways.
stabilizing selection
disruptive selection
directional selection
Stabilizing Selection
• Intermediate forms are favored over extreme forms.
Example: Human baby birth weight.
• Infant deaths are higher at the extremes of birth weight,
children most likely to survive have an average birth
Directional Selection
• When natural selection moves
a character towards one of its
• Example
Video - Mutation behind the colour change
Disruptive Selection
• When natural selection moves a
character to both its extremes.
• Occurs much less frequently in nature.
• Examples in nature are Darwin’s
finches and the Peppered moth
• The following video
give examples of the
five processes that
contribute to
1. Small sample size.
2. Non random mating.
3. Mutation.
4. Gene flow.
5. Natural selection.
• Video of
Microevolution in
• Wisdom teeth: When we had to
• Lactose tolerance: The ability to
chew roots, nuts and eat raw meat
digest lactose in our mothers milk
we wore out our molars so we had
was lost when we were weaned.
an extra set –Wisdom teeth that
Cattle, goats and sheep were
erupted after puberty. Now our
domesticated 10,000 years ago
food is easier to chew and our
providing milk. 8,000 years ago a
jaws and mouths are smaller with
mutation occurred in Europe that
no room for the extra teeth.
allowed people to digest lactose
as adults. This gave them a
• Now 35% of people are born with
nutritional advantage. This
no wisdom teeth.
mutation spread as far a India.
Today 95% of people of north
European descent have this
mutation. Similar mutations also
arose in Arabia and sub-Sharan
Microevolution in
• The human genome is still
• Extra Artery in the arm: The
changing as we adapting to our
median artery forms in the
post hunter-gatherer
foetus and supplies blood the
environment: Over 40,000 years
fore arm and hand. It vanishes
approximately 1800 genes have
once the radial and ulnal
become more common, many
arteries form. But now 1 in 3
are involved in fighting diseases
people keep this artery for life.
such as malaria and
We do not know yet if this
tuberculosis. When we adopted
gives us any advantage.
our agrarian life style 10,000
years ago the population
• The links below are to popular
increased as did the incidence
articles in the press on
of disease. This increased the
selection pressure for increased
disease resistance.
How Evolution Works?
• Macroevolution is essentially the formation of new species (speciation) and
accompanying events.
What are species?
relatively easy to define for sexual organisms, hard for asexual organisms
biological species concept (for sexual organisms) – one or more
populations whose members are:
capable of interbreeding
able to produce fertile offspring
reproductively isolated from other such groups
What is species con’t
Asexual species – definition based on biochemical differences
(think DNA sequence) and morphological differences; no solid
Also includes use of “race,” “subspecies,” and “strain”
In asexual species, microevolution over time directly leads to
macroevolution (speciation).
Macroevolution– causes of speciation
There are two basic mechanisms via which speciation can occur:
• Allopatric speciation (geographical isolation)
• Sympatric speciation (reproductive isolation)
Polyploidy (extra sets of chromosomes) is a major
factor in sympatric speciation in plants
Polyploidy (extra sets of chromosomes) is a major
factor in sympatric speciation in plants.
There are different mechanisms for producing
Autopolypoidy – multiple sets from one
parent species.
The resulting tetraploid plant can produce fertile
These are reproductively isolated from the 2n
plants of the original population.
This is because triploid (3n) offspring from a 4n x
2n cross have reduced fertility.
Naturally occurring polyploidy has occurs in Soybean and
This is called the triploid block.
So in one generation we have reproductive
Bananas are a famous example of a sterile triploid crop. Fruit
are produced without fertilisation and are seedless.
Polyploidy is a major factor in sympatric speciation
in plants – cont.
2. hybridization + allopolyploidy – closely related
species produce a hybrid that must double its
chromosome number to reproduce successfully; a
new, viable hybrid species is thus formed.
1. Species A undergoes a doubling in the
chromosome number during gamete formation.
2. Gametes from both species then hybridize during
3. The resulting hybrid has the full complement of
chromosomes from the one parent (Species A)
but not the other.
4. In the next generation the hybrid gamete is not
reduced. And the plant can not self pollinate.
5. On hybridization with a gamete from species B a
fertile hybrid id produced.
This form of polyploidy greatly increases genetic
diversity in the new hybrid.
It is a major force in plant diversification eg wheat.
Example of Allopatric speciation
Video of Darwin’s Finches
Food choice in finches
Macroevolution con’t
Sympatric Speciation
• The basis of macroevolution in sexual species is microevolution coupled
with reproductive isolation (ways of preventing gene flow between
---Reproductive isolation can occur in a variety of ways
Reproductive isolating mechanisms can be classified as either
prezygotic or postzygotic.
Prezygotic barriers – prevent fertilization (zygote formation) between gametes
from two species.
Postzygotic barriers – reproductive isolation after fertilization has occurred.
Pre-zygotic barriers – prevent
Habitat isolation (or ecological isolation) – isolation by
differences in habitat occupied at the time of mating.
Temporal isolation – isolation by differences in timing
of mating;
Ex: different mating season in some skunks, diffent flowering time in some
plants, different mating dates in some frogs
Behavioral isolation – differences in behavior that
cause reproductive isolation
Ex: mating calls, courtship patterns, and other mating rituals.
Ex: Tigers vs Lions
Pre-zygotic barriers – prevent
fertilization con’t
• Mechanical isolation – differences in physical structure
make mating impossible. Ex: two species of dragonfly flower differ in
flower color and shape which attract different pollinator animals (hummingbird
vs bumbble bee) so they can not cross pollinate
Gametic isolation – mating occurs, but the sperm and
egg can not fuse; Ex: two species of sea urchins
Post-zygotic isolation : after fertilization has
Hybrid inviability: The most common type of
postzygotic barrier
• Zygote formed from the mating of two species does
not develop normally, the embryo is aborted.
Hybrid sterility – a zygote of a hybrid proceeds
through normal development, but is reproductively
• mostly due to problems in meiosis
Hybrid breakdown – a zygote of a hybrid proceeds
through normal development, but F2 generation is
Ex: some hybrids of cotton, rice
and sunflower species
The slow process of evolutionary change
Darwin realised two things:
• producing of different breeds of farm animals, dogs, and pigeons etc.
was an accelerated version of natural selection.
• for natural selection to result in speciation in nature requires many
thousands of years.
In this he was influenced by the work of the geologists Hutton and Lyell (see
first lecture).
Fossil evidence from the geological record supported this.
This is the result of the slow speed of micro and macro evolution.
Ultimately, over 1000’s years, small differences between populations
(microevolution) diverge and are amplified when migration between them is
reduced or stopped by allopatric or sympatric isolation. This allows
macroevolution to occur.
This is where geologic time scales become important in explaining
evolutionary change.
 Darwin realized these changes required long
periods of time.
 The geological timescale is a 'calendar' of
events in the Earth's history.
 It shows major geological and climactic events,
and how these events affected the emergence
and disappearance of species over time.
These timelines are products of several
scientific fields such as paleontology,
biogeography, plate tectonics geology, and
•The study of glaciers left over from the ice ages has
provided an important line of evidence for
continental drift.
• Glacial sediments from South America, Africa,
India, Madagascar, Arabia, India, Antarctica and
Australia showed evidence of having once been
joined together, suggesting the existence of the
supercontinent Gondwana.
Continental Drift
English naturalist Charles Darwin (1809–1882)
Almost 30 years of detailed observations and
evidence collected by Darwin led to the
publication of the book ‘ The Origin of Species’.
This is the base used to explain the mechanisms
in nature which leads to EVOLUTION.
The theory of evolution by natural selection, first formulated in
Darwin's book "On the Origin of Species" in 1859, is the process
by which organisms change over time as a result of changes in
heritable physical or behavioral traits. Changes that allow an
allow an organism to better adapt to its environment will help it
will help it survive and have more offspring.
EVOLUTION accounts for both the unity
and diversity of life.
In many cases, features shared by two species
are due to their descent from a common ancestor.
Differences are end product of natural selection
modifying the ancestral origin in different
It is this combination of unity and diversity in life
that we will consider in future lectures.
Evidences of Unity & Diversity of Life
Evidences come from;
 Fossil record
 Homologous structures
 Vestigial structures
 Biochemical evidence
 Embryological development
 Genetics
Fossil Records
What does the Fossil Record tell us about organisms?
 Looks (size, shape, etc.).
 Where or how they lived.
 What other organisms they lived with.
 What time period they lived in (based on location in rock
 What order living things came in (based on location in rock
 Transitional forms.
 Organisms that were intermediate (between) two other
major organisms.
Example: Evolution of Horse
Homologous Structures
Homologous structures: Homologous
structures develop from the same
tissues, but have different forms with
different functions.
Same origin -- different form/function
The similarity is due to having derived
from the same common ancestor.
Example: Bone structure of arms and
legs in all vertebrates
Vestigial Structures
Todays animals may have structures that serve little or no function
 remnants of structures that were functional in ancestral species
 evidence of change over time
some snakes & whales show remains of the pelvis & leg bones of walking ancestors
EXAMPLES: Wings that do not fly
In Human: Wisdom teeth,
tailbone (coccyx), muscles
around the ear, appendix,
Vestigial Structures
Human hand
During embryo development we
have extra lizard-like muscles in our
hands. They disappear before birth.
They are a relic from when reptiles
transitioned to mammals 250
million years ago.
Biochemical Evidence
DNA is present as the heritable genetic material in all living forms.
All proteins in all living organisms contain the combinations of same 20 amino acids.
Cytochrome C (respiration) protein structure.
Hemoglobin (gas exchange) protein structure.
Evolutionary relationships among species are
documented in their DNA & proteins.
Closely related species have sequences that are more
similar than distantly related species.
Embryologic development
• Similar embryological development in closely related species
• all vertebrate embryos have a gill pouch at one stage of development
• fish, frog, snake, birds, human, etc.
They all have gills because
our common ancestor lived
in the ocean.
What else tells us we originated in the ocean?
We all have a salt water space suit.
Evolution is based on survival of the fittest.
Why does one species not dominate all others?
What evolutionary mechanism stops one species
from dominating all others?
How is evolutionary balance maintained?
It could all depend on a children’s game.
How a children's game explains
evolutionary balance
This game played between two players originated in China
over 2000 years ago and has evolved in to the game
“Rock, paper, scissors” now widely played.
Hand signals represent rock, paper or scissors.
Rock breaks scissors: Rock wins
Scissors cut paper: Scissors wins
Paper wraps rock: Paper wins
In this game, no single strategy can dominate as the
opponent can also change their strategy to counter it. In
game theory this means we have an equilibrium or
balance. This came to interest biologists who were
interested in explaining evolutionary balance.
Rock, Paper, Scissors
If evolution favours survival of the fittest.
Why is there no permanent winner?
• Populations of species continually change.
• This is because species interact with each other through competition
for resources, or predation of one by another.
• Within species, competition is usually for access to mates.
• This process results in evolutionary balance between and within
Competition between bacteria
• Eschericia coli bacteria found in the digestive tracts of
animals are an example.
• Strain C produces the antibiotic Colchicine to which it is
also resistant. Both production and resistance have an
energetic cost so its growth is slow.
• The susceptible strain, Strain S, grows quickly but is killed
by strain C
• STRAIN C WINS! But no. A resistant strain, Strain R,
develops. It is not killed by Strain C and only has the
energetic cost of resistance so grows more quickly than
strain C and out competes it and dominates.
• But, then Strain S which grows more quickly than strain R
makes comeback as there is less Colchicine in the
environment and starts to take over by out competing
strain R.
Within species
competition for mates
• The male side blotch lizard found in California plays the
same game but this time the prize is access to females.
• There are three “strains” of this small lizard.
• Orange throated: Aggressive males keep large numbers
of females and attack and drive off male rivals.
• Blue throated: Solitary males are monogamous. Males
warn each other of approaching rivals and group
together to defend their females.
• Yellow throated. Males look like females and enter rival
territory as orange throated males can not watch all
their females
• https://aeon.co/videos/how-multicoloured-sideblotched-lizards-put-game-theory-into-evolutionaryaction
Implications of this evolutionary balance
• When two species compete one will drive the other to extinction.
• Introduce a third species and you start to see a game of rock, paper,
• The more species the more complex the game. Computer simulations of
bacteria have used over 70 species.
• One species cannot be good at everything. So there is always competition.
• This competition also changes local environments. This dynamic situation
maintains and increases biodiversity.
• When an external force or barrier is introduced (e.g. pollution,
deforestation) that reduces competition between some species, one
species may be driven to extinction.
• This may produce a cascade effect with some species now able to drive
others to extinction.
• To prevent extinction we may have to protect whole ecosystems.
How might this game effect us?
• In 1900 there were 1.6 billion people on earth.
• Now there are 7.8 billion.
• Advances in medicine, public health (water and sewage
treatment, vaccination) and agriculture protect us from
diseases and famine that so often devastated populations.
• By this we reduced the restraint on population growth.
• Our rock broke natures scissors.
• Will nature change its strategy?
• Are virus’s like COVID-19, the paper that beats our rock?
 Virus (Latin for poison)
 They are infectious particles
 obligate intracellular parasites
 Can be crystallized
 Size range of 20-250 nm
(1 nanometer (nm) = 0.000000001
 Their genetic material codes for
from 3 genes to as many as 2000
Virus Structure
Nucleic acid enclosed in a capsid (protein
coat) and, sometimes, a lipid –rich envelope
(derived from host cell membrane).
 Genetic material can be DNA or RNA, linear
or circular, single- or double-stranded.
1. Nature of the nucleic acid: RNA or DNA
2. Symmetry of the capsid
3. Presence or absence of an envelope
4. Dimensions of the virion
5. Type of host organism
6. Replication type
RdRp = RNA dependent RNA polymerase
 Their genomes may consist of double-stranded DNA, single-stranded
DNA, double-stranded RNA, or single-stranded RNA, depending on the
specific type of virus. A virus is called a DNA virus or an RNA virus,
according to the kind of nucleic acid that makes up its genome.
Replication in RNA viruses
ONLY RNA viruses carry the RNA
dependent RNA polymerase
Virus classification based on how mRNA is produced during virus replication
The Baltimore system: This is the most commonly used classification system.
Devised by Nobel Laureate Peter Baltimore
The protein coat that
encloses the viral genome
is called a capsid.
Depending on the type of
virus, the capsid may be
rod-shaped (more
precisely, helical),
polyhedral, or more
complex in shape.
Capsids are built from a
large number of protein
subunits called capsomeres,
but the number of different
kinds of proteins is usually
small. Some viruses carry a
few viral enzyme molecules
within their capsids.
Classification by morphology
• Naked – ecosahedral & helical
• Enveloped ecosahedral and
• Complex –many proteins with
mixed ecosahedral and helical
 Some viruses have accessory structures that help them infect their hosts.
many viruses found in animals, have viral envelopes.
 These envelopes are derived from membrane of the host cell, but in
addition to host cell phospholipids and proteins, they also contain proteins and
glycoproteins of viral origin.
Some envelopes drive from nuclear cell membrane like in herpesvirus
(dsDNA, found latent in cell nucleus like prohage, stress activates it and cause
blisters after viral production).
 Viruses are obligate intracellular parasites; that is, they can
reproduce only within a host cell. An isolated virus is unable to
reproduce. Viruses lack the enzymes for metabolism and have no
ribosomes or other equipment for making their own proteins.
 Each type of virus can infect only a limited range of host cells, called
its host range. This host specificity depends on the evolution of
recognition systems by the virus. Viruses identify their host cells by a
"lock-and-key" fit between proteins on the outside of the virus and
specific receptor molecules on the surface of the host cell. Some
viruses have host ranges as broad as several species or as small as
single species.
 Viruses of eukaryotes are usually tissue specific.
 Viruses of prokaryotes are referred to as bacteriophages (phages).
 Viral replication shown variation with respect to host type and viral
genome type.
naked nucleic acid
 fusion of envelop with host membrane
 phagocytosis of the capsid
 release of capsid
 release of envelop and capsid.
 RNA genome –viral RNA dependent RNA polymerase
 RNA genome---viral reverse transcriptase
 DNA genome----Host DNA polymerase
 in nucleus
 in cytoplasm
 lysis of host cell membrane
 Exocytosis
Bacteriophage Reproductive
Recognition of viral coat/envelope by host
cell membrane/cell wall receptor proteins
Entery of whole virus or just virus
genome into host cell
Removal of protein coat and envelope
Copy of viral genome and synthesis of
viral proteins
Assembly of viral particals
Removal of viruses from the host cell
T4 bacteriophage attacking E. Coli
Reproduction of Bacteriophages
Lytic Cycle – culminates in the death of the host
 similar to general reproductive cycle of viruses
 phages that reproduce only by the lytic cycle are called
virulent phages
Lysogenic Cycle – does not destroy the host cell
 viral DNA (prophage) is incorporated into host cell’s
chromosome & replicated when the bacterium
 occasionally a prophage will exit the host chromosome
and initiate the lytic cycle to produce new viruses
 phages that reproduce using both types of cycles are
called temperate phages
Video – lytic and lysogenic cycles
 The prophage represses phage replication making the host immune
to further bacteriophage attack as the lytic cycle is blocked.
 Viral genome multiplies with the host genome.
 Prophage genes may code for proteins which provide new traits to
the host (ex: the botulism toxin (botulinum) is the gene product of
prophage in Clostridium botulinum bacteria) (SEE NEXT FIGURE).
 Virus may gain new trait from bacteria when prophage exits the
host genome when it starts the lytic cycle.(SEE NEXT FIG).
 Prophage promoter may activate certain genes of the host (ex:
activation of proto-oncogenes), leading to cancer. This occurs only in
animal cells.
Viral entry in to a host cell
Video examples
 Penetration
 uncoating
 sythesis
 assembly
 release
Some viruses are released by lysing host
cells (non-enveloped or naked)
Some viruses do not kill host cells, but bud
out of membrane
Budding viruses contain host covering
Video Influenza virus
Viruses infecting cells from the three domains of life,
Archaea, Bacteria and Eukarya, :, suggesting that viruses
originated very early in the evolution of life.
The origin and evolution of viruses is mostly unknown.
Viruses have never been detected as fossil particles,
probably because they are too small and too fragile to
succumb to fossilization processes. Even in fossilized
biological materials such as plant leaves or insects in
amber, preserved nucleic acid sequences of viruses have
never been detected.
Hypothesis for their origin are generally speculation.
The origin and evolution of viruses.
There is little scientific evidence to support any unifying theory.
The main hypothesis is the theory of ‘‘cell origin’’, (escape
hypothesis) which assumes that viruses reflect their origin from
cell DNA and/or RNA, which acquired the ability to auto-replicate,
create extracellular virions, exist and function independently
(example of origin from plasmid and or transposons).
Viruses may cause cancer
Often undetected
 Most particles of viruses do not induce cancer
 Cancer might develop long after viral infection
 Cancers do not seem contagious like viruses
 Cancer causing alteration to cellular proto-oncogenes
 Proto-Oncogene activated by various agents
○ Mutagenic chemicals
○ High energy radiation
○ Viruses
 Oncoviruses – viruses that can cause cancer by activating
proto-oncogenes during lysogenic state .
Viruses may cause cancer
Often undetected
 Most particles of viruses do not induce cancer
 Cancer might develop long after viral infection
 Cancers do not seem contagious like viruses
 Cancer causing alteration to cellular proto-oncogenes
 Proto-Oncogene activated by various agents
○ Mutagenic chemicals
○ High energy radiation
○ Viruses
 Oncoviruses – viruses that can cause cancer by activating
proto-oncogenes during lysogenic state .
Human papillomavirus (HPV) is a group
of viruses that are extremely common
 They are transmitted during sex.
 70% of all cervical cancer is caused by
 Vaccines that protect against HPV 16
and 18 are recommended by WHO.
•Immune respose via B- lymphocyte and T- lymphocyte cells
•Vaccines are harmless variants or derivatives of pathogens that
stimulate the immune system to mount defenses against the actual
pathogen. The antibiotics that help us recover from bacterial
infections are powerless against viruses.
Dead vaccine: viruses are treated with physical (heat, UV or Xray radiation) or chemical agents (hydrolytic enzymes, formaldehyde,
lipid solvent) to damage the genome. Capsid stays intact and trigger
immune response
Live vaccines: continuous cultivation of virus for long times may
spontaneously create mutant with slow replication rate.
•Drugs: most antiviral drugs interfere with viral nucleic acid
DNA or RNA polymerases
reverse transcriptases
Emerging Viruses
Appear suddenly
 (ex) HIV, Ebola virus, West Nile virus, coranovirus
(cause of SARS, severe acute respiratory syndrome)
Processes that contribute to the sudden
emergence of viral diseases:
 Mutation of existing viruses (ex: flu epidemics).
 Spread of existing viruses from one host species to
 Spread of a viral disease from a small, isolated
population to large populations causing epidemics.
Stanley Prusiner (1942)
• Discovered Prions
• 1997 Nobel prize for
Physiology or Medicine.
• Awarded for his discovery of
prions “a new biological
principle of infection.
What are prions?
Prions are normal constituents of cells.
 The prion protein PrPc can under go a
conformational change to PrP-sc (PrPscrapie).
 This is named after the degenerative
disease found in sheep.
Prion diseases usually transmitted via contact
with nerve tissues (brain or spinal cord)
 Examples of diseases causes by PrPSc
 Scrapie in sheep
○ Exact mechanism of transmission among sheep is unknown
 Bovine spongiform encephalitis in cows (BSE)
○ Possibly transmitted to cows from feed that was fortified
with bone marrow from sheep
 Diseases in Humans
○ Kuru in old New Guinea tribes
 Cannibalistic rituals—contact with brain matter
○ Creutzfeldt-Jakob disease (CJD)
 Known cases include
- Contamination during corneal transplants (CJD)
- Contamination from eating beef from cows with BSE (vCJD)
Video Prion diseases
How did BSE jump from
cattle to humans
After butchering the carcase remaining meat,
connective tissue, cartilage and nerve tissue was
mechanically removed from bones.
This resulting “meat” was used in low cost meat
products such as burgers and sausages.
By 2001 in the UK, the use of bones was banned in
mechanically recovered meat as was its use in the
human food chain.
Postulated Mechanism
Host cells have a neuron glycoprotein PrPC . This is nearly
identical to the prion protein.
The incoming prion protein PrPsc can modify PrPC converting it
to PrPsc.
 This gives abnormal folding patterns
 This abnormal protein loses function and protease
 Neurological symptoms begin.
Mad Cow Disease
PrPSC Structure
 High in beta-sheet content (>40%)
 Partial resistance to proteinase K digestion
 Can form aggregated fibrous or amyloid
 Involves refolding two helices into beta-sheets
Classifying Prokaryotes
• All prokaryotes were once in the
Kingdom Monera.
• Recently biologists divided them into
two different Kingdoms; the Eubacteria
and the Archeabacteria.
• Prokaryote comes from the Greek
"before" and "nut" or "kernel“.
• Prokaryotes appeared over a billion
years before the Eukaryotes.
 Prokaryotes
 lack of true nuclei
 lack the extensive compartmentalization by internal membranes
 small circular DNA
 extrachromosomal DNA= plasmids
 Contain cell wall
• Most consisting of only a few genes.
• In most environments, prokaryotes can survive
without their plasmids because all essential functions
are programmed by the chromosome.
• Endow the cell with genes for resistance to
antibiotics, for the metabolism of unusual nutrients
not present in the normal environment.
• Plasmids replicate independently of the main
• Can be readily transferred between partners when
prokaryotes conjugate
Types of Bacterial Plasmids
Based on their function, there are five main classes:
1. Fertility-(F)plasmids: Conjugation.
2. Resistance-(R) plasmids: Containing antibiotic or drug resistant
3. Col-plasmids: Contain genes that code for colicines proteins that
can kill other bacteria.
4. Degradative plasmids: Enable digestion of unusual substances,
e.g., toluene or salicylic acid.
5. Virulence plasmids: Turn the bacterium into a pathogen.
Origin of replication
Actin fibres move the two origins of replication to opposite ends of the cell.
While the chromosome is replicating the cell elongates.
Bacterial growth
• A single prokaryotic cell in a favorable environment will give rise
by repeated divisions to a colony of offspring via binary fission.
Lag phase: adaptation of bacteria to medium, start of synthesis to
prepare to division
Exponential phase: Fastest growth by continous divisions
Stationary phase: Amount of survivors and amount of death are
equal. Accumulation of waste.
Death phase: Amount of dead cells exceeds the survivor.
• GROWTH as applied to prokaryotes refers more to the
multiplication of cells and an increase in population size
than to the enlargement of individual cells. The
conditions for optimal growth--temperature, pH, salt
concentrations, nutrient sources, and so on--vary
according to species.
• In an environment with unlimited resources, the growth
of prokaryotes is effectively exponential: One cell
divides to form 2, which divide again to produce a total
of 4 cells, then 8, 16, and so on, the number of cells in a
colony doubling with each generation.
Many prokaryotes have generation times in the
range of 1-3 hours.
Some species can double every 20 minutes (ex: E.
coli) in an optimal environment. Potentially from 1 cell to
over 1 million cells in 20 generations.
• Most prokaryotes have diameters in the range of 1-5 µm,
compared to 10-100 µm for the majority of eukaryotic
Different arrangements of coccus and bacillus type of bacteria in
All bacteria secrete some sort of glycocalyx , an outer viscous covering
of fibers extending from the bacterium. The glycocalyx is usually a
viscous polysaccharide and/or polypeptide
If it appears as an extensive, tightly bound accumulation of gelatinous
material adhering to the cell wall, it is called a capsule
If the glycocalyx appears unorganized and more loosely attached, it is
referred to as a slime layer
The functions of glycocalyx: Antiphagocytic
 Aid Attachment of bacteria to
different surfaces
 Protect against drying when
exposed to dry conditions
 Trap nutrients
 Help colonization with each
• Outside cell wall
• Made of filaments of
flagellin protein
• Attached to a protein
• Anchored to the wall
and membrane by the
basal body
Rotate flagella to run or
 Move toward or away
from stimuli (taxis)
Figure 4.8
• Outside cell wall
• Made of filaments of
flagellin protein
• Attached to a protein
• Anchored to the wall
and membrane by the
basal body
Rotate flagella to run or
 Move toward or away
from stimuli (taxis)
The motor is drive by a proton
gradient making it a nanotech
hydrogen engine.
Flagella Arrangement
Figure 4.7
& Pili
Figure 4.9
Enviromental conditions determine the direction
of the movement
• In a relatively uniform environment, prokaryotes
may wander randomly
• In a heterogeneous environment, prokaryotes are
capable of movement toward or away from a
stimulus= Chemotaxis
A positive chemotaxis= moving toward food or
oxygen or light
A negative chemotaxis= moving away from some
toxic substance
Pili & Fimbriae
• Thin proteins extended from plasma
_ pilin protein
• Short protein appendages
– smaller than flagella
 The key difference between pili and fimbriae
is that pili are found in gram-negative
bacteria, whereas fimbriae are found in both
Gram-negative and gram-positive bacteria.
• Adhere bacteria to surfaces
- Attachment to surface and each other
(mostly fimbriae)
• F-pilus (Sex pilus); used in conjugation
– Exchange of genetic information
• Flotation; increase buoyancy
– swipping env. around
• Maintains the shape of the cell.
• Provides physical protection, prevents the cell
from bursting in a hypotonic environment. Like
other walled cells, however, prokaryotes
plasmolyze (shrink away from their wall) and
may die in a hypertonic medium,
• Contain a unique material called peptidoglycan,
CELL WALL- Peptidoglycan
• Polymer of disaccharide
N-acetylglucosamine (NAG) & N-acetylmuramic acid (NAM)
• Linked by polypeptides
Figure 4.13a
Β 1-4
Figure 4.13b, c
Gram positive cell wall
Gram negative cell wall
• One of the most valuable tools for identifying specific
bacteria is the Gram stain, which can be used to
separate many species into two groups based on
differences in peptidoglycan content of the cell walls.
• Gram-positive bacteria have simpler walls, with a
relatively large amount of peptidoglycan.
• Gram-negative bacteria have less peptidoglycan and are
structurally more complex. An outer membrane on the
gram-negative cell wall contains lipopolysaccharides,
carbohydrates bonded to lipids. Gr (-) bacteria are
mostly pathogenic because of the lipopolysaccharide
The gram stain indicates a high
peptidoglycan content of the cell
wall. As indicated by the blue stain
of the positive cells.
Gram-Positive cell walls
• Teichoic acids:
– Lipoteichoic acid links to plasma membrane
– Wall teichoic acid links to peptidoglycan
• Provide antigenic variation to avoid host defences.
Gram positive bacteria only
Glycerol, Phosphates, & Ribitol
containing types
Attachment surface for viruses
Gram-Negative Outer Membrane
• Lipopolysaccharides, lipoproteins, phospholipids.
 toxic,
 helps protect the pathogens against the defenses of their
 more resistant to antibiotics because the outer
membrane impedes entry of the drugs.
 O -polysaccharide antigenic site (recognised by
host immune system).
 Lipid A is an endotoxin.
• Forms the periplasm between the outer membrane and
the plasma membrane.
• Protection from phagocytes, antibiotics.
• Porins (proteins) form channels through membrane.
Gram-positive cell walls
Gram-negative cell walls
• Thick peptidoglycan
• Thin peptidoglycan
• Teichoic acids
• No teichoic acids
• Outer membrane
• (lipopolysaccharide)
Damage to Cell Walls
• Lysozyme (enzyme) digests disaccharide in
• Penicillin (antibiotic) inhibits peptide bridges in
Protoplast is a wall-less cell of plant, bacteria, fungi.
• The ability of some prokaryotes to withstand harsh conditions is
impressive. Some bacteria form resistant cells called
• Boiling water is not hot enough to kill most endospores in a
relatively short length of time.
• To sterilize media, glassware, and utensils in the laboratory,
microbiologists use an appliance called an autoclave, a pressure
cooker that kills even endospores by heating to a temperature
of 120°C.
In less hostile environments, endospores may remain dormant
for centuries or more. If placed in a hospitable environment,
they will hydrate and revive to the vegetative (colony-producing)
state. For example, in 2000, researchers revived a bacterial
spore that had apparently been encased for 250 million years in
a salt formation within caverns in New Mexico.
Bacterial ‘striptease’ evades antibiotics
• Antibiotics attack the bacterial cell wall.
• This weakens it resulting in the enclosed cell bursting.
• Scientists have observed some bacteria, found in urinary tract
infections common in old people, releasing themselves from
their cell wall when they come into contact with antibiotics.
• This is very risky as they may burst if in a low osmotic
potential environment.
• These ‘naked’ bacteria may be attacked by the immune
system but some may survive to regrow their cell wall and reinfect once the antibiotic has gone.
• In the video you can see the moment bacteria strip off their
cell wall as they lose their clear (in this case rod-like) structure
and become bigger and more flimsy.
Video: Bacterial striptease
Source: https://www.bbc.com/news/health-49826085
The developmental cycle of the Endospore.
Bacterial endospores.
Phase microscopy of sporulating bacteria
demonstrates the refractility of endospores, as well
as characteristic spore shapes and locations within
the mother cell.
Figure. An anthrax endospore. This
prokaryote is Bacillus anthracis , the
notorious bacterium that produces the
deadly disease called anthrax in cattle,
sheep, and humans.
4 Kg of powdered toxin is enough to kill
whole human population.
Bacterial Toxins
Endotoxin (Ex: Salmonella)
 components of Gr (-) bacterial cell wall
effect the host when bacteria die and components
are disintegrated
 cause muscle pain and fever
Exotoxin (Ex. Cholera, botulism)
 it is secreted out by bacteria
 cause disease even in the absence of bacteria
 inactivated upon sterilization
 very small amounts can be a potent toxin
Definition of autotrophs and heterotrophs
• Autotrophs: Organisms that can produce their own
food, using materials from inorganic sources. The
word “autotroph” comes from the root words “auto”
for “self” and “troph” for “food.” An autotroph is an
organism that feeds itself, without the assistance of
any other organisms.
• Heterotrophs: Organisms that cannot manufacture
their own food by carbon fixation and therefore
derives their intake of nutrition from other sources of
organic carbon, mainly plant or animal matter. In the
food chain, heterotrophs are secondary and tertiary
Prokaryotes can be grouped into four categories
according to how they obtain energy and carbon
Nutrition refers here to how an organism obtains two
resources from the environment: energy and a carbon
source to build the organic molecules of cells.
•Photoautotrophs are photosynthetic organisms =light energy to drive the
synthesis of organic compounds from carbon dioxide. (ex: cyanobacteria)
•Chemoautotrophs need only CO2 as a carbon source, but instead of using
light for energy, these prokaryotes obtain energy by oxidizing inorganic
substances (hydrogen sulfide (H2S), ammonia (NH3), ferrous ions (FeS)),
mode of nutrition is unique to certain prokaryotes.
•Photoheterotrophs can use light to generate ATP but must obtain their
carbon in organic form.
•Chemoheterotrophs must consume organic molecules for both energy and
carbon. This nutritional mode is found widely among prokaryotes, protists,
fungi, animals.
Mode of
Energy Source
Carbon Source
Source Types of
Photo-autotroph Light
organisms, including
cyanobacteria; plants;
certain protists (algae)
Inorganic chemicals CO2
H2S, FeS, NH3
Certain prokaryotes (for
example, Sulfolobus )
Certain prokaryotes
Organic compounds Organic compounds
Organic compounds
Saprobes (dead
organism eaters),
parasites (live within or
on live host),
m and some plastics),
nitrogen fixers
Bacterial Symbiosis
Symbiosis means living together, thus require a symbiont
and a host.
 Mutualistic; both side equally benefit.
(Ex: nitrogen fixing bacteria)
 Commensalistic; one symbiont benefits and the other
neither benefit nor damaged.
(Ex: bacteria living in intestine, mouth or genitals)
 Parasitic; one symbiont benefits extensively while the
other may even get harmed.
(Ex: disease causing bacteria = pathogens)
Clostridium difficile obtained from a human gut.
Source: Wiggs, 2007.
Gene Transfer in Bacteria
• transformation – alteration of a bacterial cell’s
genotype by the uptake of naked, foreign DNA from
the surrounding environment
• transduction – virus carry bacterial genes from one
host cell to another as a result of aberrations in the
viral reproductive cycle
• conjugation – direct transfer of genetic material from
one bacterial cell to another
Heat shock treatment
 ability to conjugate (form sex pili & donate DNA) is controlled
by the presence of an F plasmid that contains a special piece of
DNA called an F factor
 DNA donors (F+ cells) contain the F plasmid; DNA recipients
(F− cells) lack the F plasmid
 only the F plasmid DNA is transferred
 the F+ cell can convert the F− cell to an F+ cell
Video – Bacterial Conjugation
• chromosomal genes can also be transferred when the F factor is
integrated into the bacterium’s chromosome
– cells with F factor built into the chromosome are called Hfr
Video - Bacterial Conjugation
Video – General Transduction
Video – Specialized Transduction