Biology I-EVOLUTION

MBLA010, MBIO011,
MBLB010,MBLC010

INTRODUCTION
Where does the theory of evolution
come from?

Introduction
 Biblical / Pre-Darwinian Post-Darwinian
Charles Darwin

The earth is young (created in the

afternoon, on 23 October 4004 The earth is old (4 to 4.62 billion
BC) years)

Species are related by descent; they

Each species was created as is; are also not static over time; they
species do not change, and can change or diverge or become
species do not become extinct extinct

Species are adapted to the

Species are adapted to the environment because of natural
environment because they were selection acting on random genetic
divinely created so variation, under certain climatic
conditions
 Aristotle

Aristotle (384-322
BC) proposed:
-“ladder of nature”,
- Biological matter
can arise
spontaneously
from dead matter.

Plato
 St. Augustine (354-430 AD)
proposed:
-the Biblical account of
creation as an alternative.
- Spontaneous creation was
accepted throughout the
Middle Ages, and until the
Renaissance when
Francesco Redi and
Spalanzani managed to
St Augustine disproved it in 1688.
Antoni van Leeuwenhoek
-Designed the microscope,
-Discovered the microscopic
world, and the exceedingly
tiny and apparently primitive
organisms that inhabit it
(1683).
-The idea of “Spontaneous
Generation of living
organisms from non-living
matter” was rekindled for
many people by the
discovery of such primitive
animals
Louis Pasteur :
-The discovery that
micro-organisms is the
cause of disease.
-Demonstrated in 1861
that many of the
examples of
“Spontaneous
generation” could be
explained at the hand of
non-sterile techniques
used in medicine, food-
preparation, storage etc.
- Carolus Linnaeus:
- Fixity of species.
- Species were created ideally suited
to their habitat.
- Scale of Nature on which the most
primitive organisms are placed low
on the scale, and with increasing
complexity; animals are sequentially
assigned higher positions on this
ladder of life. Humans, of course,
were placed on top of this ladder.
- Linnaeus never believed that
animals could “spontaneously be
created’).
- Linnaeus is well known for devising
the Binomial system of
Classification by which each
species is given a scientific name
consisting of two parts (e.g. Homo
sapiens, Pan troglodytes, Panthera
leo etc.).
Cuvier :
- Challenged the view of the Fixity of Species,
Fossils proved that many animals once existed
that were no longer alive This means that they had
to have become extinct.
- Since layers in the earth even showed a
succession of life forms, the fossil record even
seemed to imply that species could change over
time.
- Many people looked at fossils of large animals,
and believed that they were animals who died in
the Great Flood of Noah. Other people looked at
fossils (of dinosaurs, for example) and believed
them to be creations of the Devil, etc.
-Cuvier explained the changing fossil succession
by the hypothesis of Catastrophism (periodic local
extinctions, followed by repopulation, by closely
related species from surrounding areas. A cycle of
periodic extinctions in an area, followed by
repopulation from surrounding areas, could give
an appearance of change occurring over time
Baptiste Lamarck :
- Inheritance of acquired characteristics.
Physical characteristics developed
during the life of an animal will be
transferred to the children. According to
Lamarck, for example, body builders
should have more muscular children
than non-body builders.
- His famous example was the origin of the
Giraffe. Giraffes have to stretch their necks
to reach the upper branches of trees, to get
to more nutritious leaves not reachable by
shorter animals. By many generations of
stretching their necks, each generation will
progressively have slightly longer necks.
- Unfortunately, absolutely no evidence
exists that Lamarck was correct
- Lamarck was the first biologist to
both believe in evolution and the
adaptation of animals to the local
environment.
Alfred Wallace
– independently
suggested the
mechanism through
which evolution could
have occurred – Natural
selection (Charles Darwin
published his famous
book, “On the Origin of
Species” in the same
year, 1859).
Three people that influenced the thinking of Charles Darwin:

(1) Erasmus Darwin,

grandfather of Charles
Darwin already discussed
the mechanism of Natural
Selection with the “lunatic
society” early in the 19th
century
(2) Charles Lyell, who proposed
the idea of Uniformitarianism:
-the same processes occurring in
the world today, also acted on the
world throughout history.
-Geological processes are
extremely slow,
-Therefore, the earth had to be
very, very old.
-This provided the huge amount of
time that Darwin’s theory required
for evolution to have taken place
(the biblical idea of the Earth being
only 6,000 years old could not have
been long enough for complex
animals to have evolved through
natural selection).
Thomas Malthus published:
-“An Essay on the Principle of Population”.
Food production by humans increased at a
linear rate, while the human population
increased at an exponential rate.
-The human population must have (and may
still) outstrip the ability of agriculture to
provide food for everybody.
-This means that many (of even most)
people must die through famine, war and
pestilence, and that these factors curb the
human population, and prevent
overpopulation.
-This lead Darwin to ponder the possibility
that some individuals may be better at
surviving than others. “Survival of the fittest”
 LECTURE 2

THE ORIGIN OF LIFE

- The “Big bang” happened 15 billion
years ago after the collision of a number
of large black holes
-Our solar system gradually formed
over the last 10 billion years
- The primitive earth was fully formed by
± 4.5 billion years ago by cold accretion
- The early earth melted, and slowly
cooled into several layers. Heavier
elements accumulated on the inside (i.e.
iron, nickel) to form a denser, molten,
liquid core. A less dense layer of silica
minerals became the semi liquid mantle
floating on top of the core. Slight cooling
of the outer layer of this mantle, combined
with ongoing volcanic eruptions produced
the thin crust, a layer about 100km thick,
on which we live and go about our lives.
-
- The gravitational attraction retained some
of the gases produced by degassing so
that an atmosphere formed. The lightest
elements escaped into space (e.g.
Hydrogen, Helium, Oxygen, Argon).
Heavier elements were retained in our
atmosphere (e.g. gases like Carbon
Dioxide, Nitrogen, Suphur Dioxide, and
other molecules like water vapour,
Ammonia and Silicon dioxide).
- As the earth slowly cooled, water vapour
condensed into dense rain which
created the oceans.
- Continued bombardment of the earth by
meteorites took place
- At first, the earth’s atmosphere
contained no free Oxygen and would as
a result not have possessed an outer
layer of Ozone. During the Archaean
Period (± 3,8 billion years ago) a slight
ozone layer formed.
- Gradually the earth cooled
2.2.1 Conditions favorable for the origin of life
1) Oxygen must have been absent, or occurred only in very minute
quantities. Oxygen breaks down simple chemicals through oxidation. This
condition was probably fulfilled with most of the oxygen having escaped
from the primitive earth, and the remainder having been tied up as Oxides.

2) An external source, or sources, of energy must have existed to

power the process. Fortunately, the primitive earth had no lack of these.
a) Solar radiation
b) Heat (volcanoes, meteorites impacting the earth)
c) Lightning
d) Radioactivity

3) Chemical molecules must have existed for the above energy sources
to act upon (see later).

4) A huge amount of time must have been available for all of these to
work together to produce the first life forms. The earth is generally believed
to be more than 4.5 billion years old. The earliest fossil evidence we have for
life is about 3.8 billion years old. This means that several hundred millions
years may have elapsed between the formation of the earth and the first
tangible signs of life.
2.2.2 Stages during the origin of life

Monomers evolved
- Oparin (1938): Suggested that simple
organic compounds (e.g. nucleic acids,
amino acids) could have spontaneously
been created by the earth's atmosphere,
under the influence of strong energy
sources
Monomers evolved
-Stanley Miller (1953) performed an
experiment in which he combined the
gases which would have existed in the
earth's atmosphere (water vapour,
Hydrogen, Methane, Ammonia), sealed
them in a chamber, and added electricity
(to simulate lightning). A collection of
organic molecules was formed.
- it was demonstrated that many the basic
building blocks important in modern, living
organisms could be created in the lab.
- Nucleotide bases of RNA and DNA
- All 20 amino acids
- Lipid molecules
- Certain sugars
- Adenosine triphosphate (the molecule
responsible for energy transfer in modern
organisms)
Polymers evolve
-Simple compounds combining into
longer chains – forming polymers.
- Sidney Fox showed experimentally
that amino acids polymerise
abiotically when exposed to dry heat
- Subsequent experiments have
confirmed that simple organic
compounds can combine into
polymers on hot rock or hot clay
surfaces.
-This could have happened on the
early earth as well. Amino acids,
plentiful in the early ocean, would have
collected in shallow puddles where
they could have been cooked on clay
surfaces by the sun to produce simple
polypeptides
Coacervates
form
- Returning these proteinoids to
water, they formed
microspheres (protein balls with
some properties of a cell).
- Some of them can divide into
two (similar to binary fission).
- Some of them have internal
environments different from that
of the surrounding environment
(a primitive type of homeostasis”
being maintained).
- Some of them can absorb
molecules from the surrounding
environment.
- If lipids were to become available
to these microspheres, they
became incorporated into it as a
simple membrane.
Oparin: Under appropriate conditions
of temperature, ionic composition and
pH, coacervate droplets, a special
type of microsphere, could have
formed.
- Coacervates can absorb and
incorporate molecules “nutrients”
from the surrounding environment.
- Have a limited catalytic ability to
break down such nutrients. (e.g.
when adding Glucose phosphate to
the environment, the coacervates
can absorb it, and convert it to
Maltose).
- Coacervates have the ability to grow.
- Eventually, a semipermeable
membrane may form around the
coacervates if lipids are absorbed from
the surrounding environment.
- They also have the ability to only
reproduce experimentally. This means
that they cannot yet be called alive.
Primitive cells develop
- RNA often has self-replicating capabilities = Ribozymes.
- If self-replicating, catalytic RNA strands were absorbed by a
coacervate with a cell membrane, the coacervate would have
turned into a primitive prokaryotic “cell” by definition.
- The coacervate, would be stimulated to reproduce, while the
RNA strand would be protected from external damage or
degradation.
- With nucleic acids having been incorporated into a “proto-cell”,
biological information about an entity could then have been
stored.
- Some of the ribozymes could replicate themselves, and transfer
their own phenotypes (physical characteristics) to their “offspring.
- Some of them would have been better at doing this than others.
They had a Selective advantage, and could out-compete others
which were not as successful-Start of Natural Selection.
The origin of complex cells
Complex cells have existed by 3.5 billion years ago.
- The first cells: prokaryotic heterotrophs (organisms
unable to synthesise their own organic compounds,
absorbing these compounds from the surrounding
environment).
- They would probably have used up the available
sources of free nutrients, leading to competition
between them.
- Later, chemosynthetic and photosynthetic
autotrophs (sulphur bacteria) would have evolved. They
obtained the ability to store energy from the sun in
hydrogen bonds by oxidising inorganic compounds like
hydrogen sulphide, and releasing sulphur into the
atmosphere
- The cyanobacteria were the
first bacteria to evolve
“modern” photosynthesis,
using not hydrogen sulphide
for photosynthesis (and
releasing sulphur into the
atmosphere), but water
instead (as modern plants do),
and releasing oxygen into the
atmosphere. Traces of
chlorophyll, found in rocks,
suggest that this could have
happened between 3 and
3.5bya (Billion years ago).
-Organisms evolve that could feed on the energy-rich
autotrophs (between 3.5 and 2.5 bya). These
Heterotrophs used primitive metabolisms:
- methanogens (reduced carbon dioxide to methane)
- sulphate reducers (reduced sulphate to hydrogen
sulphide)
- The heterotrophs didn't have a cell nucleus; possibly
only a self-replicating RNA strand. They were
therefore prokaryotes.
- By 2.5-2 bya, Cyanobacteria were producing
increasing quantities of oxygen, and it eventually
become an increasingly important component of the
atmosphere.
- Formation of a protective layer of Ozone surrounding
the atmosphere, reducing the levels of ultraviolet
radiation from the sun. This allowed organisms to live
closer to the surface of the oceans (no organisms
were living on land, by this stage).
- Secondly, the heterotrophs could use Oxygen to fuel
their metabolisms.
Eukaryotes
developed
 LECTURE 3

DEVELOPMENT OF COMPLEX
MULTICELLULAR LIFE
Sedimentary rocks are formed from particles of older rocks that have been
broken apart and transported by water or wind. The gravel, sand, and mud settle
to the bottom in rivers, lakes, and oceans. These sedimentary particles may bury
living or dead animals and plants on the lake or sea bottom. With time, the
sedimentary particles become cemented by lime, silica or iron and they turn into
rock again. Gravel becomes a rock called conglomerate, sand becomes
sandstone, mud becomes mudstone or shale
-Animal skeletons and plant pieces can become trap in sediment and can become
mineralized to form fossils.
In the late eighteenth and early nineteenth centuries, the English geologist
and engineer William Smith and the French paleontologists Georges
Cuvier and Alexandre Brongniart discovered that rocks of the same age
may contain the same fossils even when the rocks are separated by long
distances. By careful observation of the rocks and their fossils, these men
and other geologists were, for example, able to recognize rocks of the
same age on opposite sides of the English Channel
They published the first geologic maps that show large areas of which
rocks contain similar fossils.
-Geologists didn’t, at first, know absolute
age of the different layers (strata).
-They knew the relative order in which strata
occurred.
-They knew that the strata have had to been
formed over a huge amount to time.
-It is only with the advent of Radiometric
dating in the 1960’s, that we were able to
assign specific ages to these individual
rocks.
2.5 “OUR WANDERING CONTINENTS”
-Not only did life originate and diversified on
earth over the past 3,5 by, but the anorganic
earth itself has also gradually changed over
time.
-Symptomatic of powerful changes taking place
in the mantle and crust of the earth has been
continental drift, i.e. the movement of tectonic
plates.
-The splitting up of large continents to form the
present day ones had a big influence on the
biogeography of plants and animals
-It has always struck people how complementary in
shape the East coast of South America was to the West
Coast of Africa. The rock formations between these
coastlines were also found to closely match up. How
was this to be explained?
-It used to be believed that the earth’s crust was
immobile, and that the continents had always looked the
way they do today. However, the distribution of related
terrestrial animals species on different continents had no
explanation. How did they manage to cross oceans?
-Other anomalies also became evident as people
obtained more information. Coal seams were discovered
in the Arctic circle, and evidence of earlier plant life was
found in Antarctica. This could not be explained by the
present position of Antarctica at the cold South Pole.
- Alfred Wegener and Alex du Toit: the continents are actually
moving, relative to each other, a process that has been ongoing
since the primitive earth nearly 4 bya.
-Around the core of molten magma we find a semi-liquid layer of
cooler magma referred to as the mantle, which flows by means of
convection and gravitational effects, at extremely slow rates.
-The crust is of the earth is fragmented into a series of large
plates called tectonic plates that float on the outer layer of the
mantle and that form the six continents, some islands and the
seafloor.
As the semi-liquid mantle moves, the continental crust (and thus,
the continents), are carried along. As these plates move, some
plates are torn apart, or shoved together. You may have heard of
the San Andreas fault in California. Here, two tectonic plates form
a boundary, and these two plates grind against each other. This
sometimes leads to earthquakes. In places the molten magma
breaks through weaknesses in the overlying crust resulting in
volcanic eruptions
During the Palaeozoic and Carboniferous the landmasses drifted together to form a large landmass in the Permian called Pangaea (fig. 1).
(Pan- means “all” while Gaea means “earth”. All the continents of the world were joined together in one single super-continent.

-At the start of the Jurassic, about 200 million years ago, Pangaea began to break up to form two landmasses, Laurasia to the North
(today North America, Greenland, Europe, most of Asia) and Gondwanaland to the South
(today Antarctica, South America, Africa, Arabia, Madagascar, India, Australia and New Zealand).
-As the Jurassic wore on, India broke free from present day Antarctica and drifted northwards (fig. 2).
-Towards the end of the Cretaceous the continents composing Gondwanaland gradually broke free from one another,
-while India steadily moved north as an island finally making contact with Asia about 35 million years ago. India crashed into Asia, and as
it pushed into Asia, it created the mountains known today as the Himalayas. This process is still continuing today.
 -Laurasia finally broke up about 20 million years ago during the Miocene, and North America, Greenland and Eurasia
become separated,
- Australia broke free from Antarctica (fig. 3 & 4).

Fig. 3) -North America and Greenland separating from Eurasia, Australia free from Antarctica.

Fig. 4 Continents are they are positioned today. North & South America are connected, India is a part of Asia, and Arabia
has split off from Africa to form part of Asia. The continents are, of course continuing to move, and with sophisticated technology
it is actually possible to measure the rate at which continents do so
 SKIP THIS PART

It is predicted that Africa will eventually split into two along the fault line that is known as the Rift valley in East Africa, and most of
Africa will crash into Europe; the Mediterranean sea will disappear and a mountain range will form across Europe towards India.
Australia will crash into Asia or perhaps slide along the eastern edge of Asia, pushing the islands of Japan ahead of it until it
eventually crashes into Siberia. The Atlantic ocean will increase in size as North America drifts West until the Atlantic is bigger than
the Pacific Ocean. Antarctica will move North into the Indian Ocean. All of this will, of course, take many millions of years. America is
drifting West, while Australia is drifting North, at a rate of no more than 4 cm per year. In one person’s lifetime, therefore, the
continents will move no more than one or two metres.
The influence of continental drift on the distribution of animal and plant species was moderated by the oceans rising
and dropping during the ages. During cyclical (in other words, they occur at regular intervals) cold periods known as ice ages, much
of the earth’s water is caught up as ice, spread across the globe in the form of glaciers. With so much water in ice-form, the ocean
levels are much lower than they are during non-Ice ages, as we are living in today. The last Ice-age ended about 10,000 years ago.
When the last ice-age was still present, much of Northern Europe and North America was covered with ice. Because the sea level
was much lower than today, people could walk between France and England on dry land, or from Alaska to Russia. North- and South
America, now connected through Panama, were previously separate. Africa has been in contact with Europe in the past across the
Strait of Gibraltar a number of times.
The changes in sea level made it possible for organisms to move from one continent to another at different time during
the ages. In other cases organisms were isolated for long periods of time, e.g. the marsupials of Australia.
The moving continents also resulted in climatic changes associated with latitudinal changes. Continents, once tropical
became deserts. Other continents, once close to the Arctic Circle moved across the equator, with resulting temperature changes. As
the climate changed, organisms could not adapt, and many become extinct, leaving space in which other organisms could develop
and radiate
 LECTURE 4

EVOLUTION AND GENETICS

3.1.1 Introduction
-When evolution happen, it is the population that
change and not only a single individual.
-Evolution affects both the phenotype (what the
organisms of the population look like) and the genes that
control the phenotype (the genotype) of the members of
the population.
-All the genes of a population together is called the gene
pool.
-The relative abundance of different genes in the gene
pool will not change during reproduction but only
because of evolution.
-In this section we will see that normally, the genes of a
population remain the same generation after generation
unless evolution takes place.
3.1.2 Mendelian Inheritance
Gregor Mendel was an Austrian monk who revolutionized the
study of Genetics in the early 1860s (although nobody realized
this until the beginning of the 1900s) when he discovered genes.

Prior to Mendel, most breeders of plants and animals only knew

that both parents contribute equally to the appearance of
offspring, and that offspring fall someplace in between either
parent in appearance. They mistakenly believed that this worked
in a way similar to the mixing of paint. This is referred to as a
Blending Theory of Inheritance (i.e. parental characters are
blended together in producing offspring).

The contribution that Gregor Mendel made was to show that the
original characters controlling the phenotype are not destroyed
during breeding. This is referred to as the Particulate Theory of
Inheritance (i.e. the “Units of Inheritance” which determine
offspring appearance, Genes, remain distinct units.
You have two Homologous Chromosomes of each type of chromosome in each cell in
the body: it means that you also have two genes occurring on these two chromosomes
at corresponding positions (loci) that control the same characteristic in the phenotype.

Originally, when you were a zygote, one chromosome/gene came from your Father, and
one from your Mother.

Because the genes have different origins, they may or may not be identical.
- A character like “eye colour” for example, has a large number of possible “gene states”
in which it can be found in people; e.g. blue, brown, green. These different forms of the
same gene are called Alleles “Blue eyes”, “Green eyes”, “Brown eyes” are thus Alleles
for eye-colour.

Those are the possible genes floating around in the gene pool of the population. You can
only have two of them at any one time, however, because you only have 2 copies of
each chromosome.

Like you will hear in the section on genetics, if you have two genes that are the same,
you are called Homozygous for that Character. If they are not the same, you are
Heterozygous for that character.

What happens during Meiosis? Homologous Chromosomes separate!

It means that one copy of each gene goes towards one sperm cell / egg cell, while
another copy goes to another sperm cell / egg cell
Example 1
A male has the gene for “Blue eyes” on one copy of Chromosome 1, while he has the
gene for “Brown eyes” on its’ Homologous Chromosome (thus being Heterozygotic for
eye colour).
Meiosis occurs. After Meiosis 1, he will have two sex cells, one of which will contain the
gene for “Blue eyes” while the other contains the gene for “Brown eyes”.
After Meiosis 2, in the male, you will have two sperm cells with the gene for “Blue eyes”
and two sperm cells that contain the gene for “Brown eyes”.
The individual will therefore produce sperms with a 50:50 ratio for Blue-eyes : Brown-
eyes.
In other words – after fertilization, he will have a 50:50 chance of producing offspring
containing either gene.
During fertilization, and the creation of a zygote, it is completely random whether the
sperm that is involved in fertilization is one containing the “Blue-eyes” gene, or one
containing the “Brown-eyes” gene.
Fertilization, of course, requires an egg as well.
Imagine the female in our example is Homozygous for this attribute. She received a
“Brown-eye” gene from each of her parents, meaning that each of her Chromosome 1’s
has a “Brown-eye” gene.
Following Meiosis 2, all her egg cells will therefore carry the “Brown-eye” gene, since
there is no way for any of her egg cells to carry anything else.
100% of all of her offspring will therefore receive a “Brown-eye” gene from her.
While the father therefore has a 50:50 possible ratio for Blue eyed vs. Brown eyed
offspring, the mother has a 100% chance of producing Brown-eyed offspring.
What will the offspring look like?
- Naturally, there is no way in the world that you can predict which gametes, out of all
the millions produced by you, will be the exact one involved in producing a zygote. You
can only determine the likelihood / probability of a certain outcome.
In this case, (because each parent contributes an equal amount to the next generation),
the offspring will have the following possible appearances.
50 % will be Heterozygous, with one copy each of “Brown-eyes” and “Blue-eyes”
respectively, on the two homologous chromosomes.
50% will be Homozygous, with both chromosomes in the Homologous pair carrying the
gene for “Brown-eyes”.
- As you know from the section on genetics, it is custom not to write out lengthy names
for Alleles. One usually refers to them with letters; the dominant one is referred to with a
capital and the recessive with lower case letters.
- “Brown-eyes” Allele can therefore be written as B and the “Blue-eyes” Allele as b.

- In the above example, all the Offspring will have Brown eyes because of complete
dominance of the B allele over the b allele. The chances of the Phenotype is therefore
“100% Brown eyes”. The genotype, however, can be determined using a Punnet
diagram and in this example would be is written as - 50 BB : 50 Bb. This is usually
simplified to 1 BB : 1 Bb.
- In simple terms this means that, while we have no way of knowing for certain which
genes will be transferred to the offspring, we know that
1) all of them will have brown eyes
2) on average, we would expect half of any children to be Heterozygous and half to be
Homozygous.
 A population in Hardy-Weinberg equilibrium

Imagine a population has 100 diploid individuals. Each of these therefore has two
copies of each gene – Let us consider only one gene at a time; fur colour
That means that there are 200 alleles in the population which control fur colour
Let’s imagine further that there are only two alleles for fur colour: black and grey

This means that the 200 genes in the population that control fur colour, all control
only for two colours…either black fur or grey fur.
Imagine further that in this entire population, ¼ of the individuals are Homozygotic
for Black; the dominant allele (i.e. BB)
½ are heterozygotic (i.e. Bb) while ¼ are homozygotic for the recessive allele (i.e.
grey, bb).
of B alleles in the population:
We can see that there are indeed 200 alleles.
What is the frequency of the B aIleles? In other words, in the population of 100
individuals, 25 are BB, 50 are Bb and 25 are bb. (A real population will obviously
not be as simple, but this simplified example is adequate to demonstrate the
principle).
 We now determine allele frequencies as follows:
We know that there are indeed 200 alleles.

Number of B alleles Number of b alleles

BB 2B x 25 = 50 BB 0b x 25 0

Bb 1B x 50 = 50 Bb 1b x 50 50

bb 0B x 25 =0 bb 2b x 25 50

Total B 100 Total b 100

Number of B alleles/ Number of b alleles/

Frequency = Total # of alleles = Total # of alleles

= 100 / = 100/
200 200

= 0.5 = 0.5
So, 0.5 of all the alleles in the population available for fur colour are B and 0.5 are b

Let’s assume for the moment that there is no selection, and that all of them have
an equal chance of being transferred to the next generation. What will the next
generation
. look like
Draw up a Punnett diagram:
(This Punnett Diagram differs from the previous Punnett Squares in that in this case we do not calculate the
expected Phenotypic/genotypic ratio for the next generation for an individual crossing, but for the entire
population).
O.5 B 0.5 b
.
0.5 B 0.25 BB 0.25 Bb

0.5 b 0.25 Bb 0.25 bb

This means that the next generation of the population is expected to look like this:
25 % of all individuals will be BB,
50% (25%+25%) will be Bb,
25% will be bb.

What can we see from this?

- Sexual Reproduction alone cannot change allele frequencies in a population
- Dominance does not change allele frequencies
This states that the Allele frequencies in a population
will not change, from one generation to the next,
unless evolution has occurred.
Allele frequencies will occur in equilibrium from one generation to
the next, according to the following formula

p² + 2pq + q² = 1 (and simple probability theory states

that (p + q = 1)

p² is the frequency of homozygous, dominant individuals

p is the frequency of the dominant allele
q² is the frequency of the homozygous, recessive individuals
q is the frequency of the recessive allele
2 pq is the frequency of the heterozygous individuals
A population will remain in Hardy-Weinberg Equilibrium
as long as the following conditions are met:
1) No mutations occur in the population
2) No gene flow occurs (there is no migration into the population, of
out of the population)
3) Random mating occurs – all individuals have an equal chance of
reproducing, and mate choice is not influenced by genotypes or
phenotypes
4) No genetic drift occurs. The population is very large, and no
changes in allelic frequencies occur due to chance
5) No selection occurs. All genotypes have an equal chance of
surviving
 Lecture 5

MICROEVOLUTION
The factors that can cause microevolution are therefore:

1) Mutation
2) Gene Flow
3) Non-random mating
4) Genetic Drift
5) Natural Selection
3.2.1 Mutation:
- Mutations create new alleles, and therefore constitute the
source of new variation in a population.
- Most mutated alleles tend to be harmful to a greater or lesser
extent. Some are, however, beneficial. Some mutations are
neutral (i.e. they have no apparent effect).
- Furthermore, it may be that a mutation is harmful in one
environment, but beneficial under eg. another set of climatic
conditions.
- Once alleles have mutated, Genetic Recombination
(independent assortment, crossing over and sexual reproduction)
is important in spreading the mutation through the population.
This will happen if the new mutated gene has a selective
advantage.
3.2.2) Gene flow:
- Species are divided into populations. These
populations are sometimes in contact with each other
when migrating individuals move from one population to
another. When such individuals reproduce, genes from
one population can be spread to another population (e.g.
a mutation created a new allele in one population, and
this allele is taken to another population by a migrating
animal).
3.2.3) Non-random mating:
- Random mating occurs when individuals mate purely by chance, and their phenotypes
do not play a role. This usually does not happen, and phenotype does influence mate
choice. Three examples of non-random mating:
- Inbreeding (between humans, animals or plants). Individuals mating with closely related
individuals. This does not alter Allele Frequencies in the population, but does increase the
incidence of homozygous individuals and reduces the incidence of heterozygosity at all
loci.
Many genetic disorders in humans are recessive, and if heterozygosity is reduced,
dormant (hidden) recessive alleles will be expressed with greater frequency.
-Assortive mating occurs when individuals tend to mate with individuals with a similar
phenotype (e.g. in humans, tall people tend to mate with individuals who are also tall).
This causes the population to subdivide into two phenotypic classes, between which gene
exchange will be reduced
-Sexual selection occurs when males compete for the right to reproduce, and females
choose to favour males with a certain phenotype.
The elaborate tail of a peacock is where female choice leads to selection
The size difference in elephant seals between males and females is an example where
female choice does not play a role
 Genetic drift

a) Bottleneck Effect:
If a population suddenly undergoes a very severe population reduction (overhunting,
sudden climate change, fire etc.), and then increases afterwards, the alleles that are
available are probably very unrepresentative of the original alleles.

Cheetahs for example have reasonably high population numbers, but they have very
low genetic diversity. It is postulated that they have, at some point in the past, suffered a
very severe reduction in numbers. The current population is the result of those few
individuals who survived having reproduced.
b) Founder Effect:
When a few individuals from a large
population colonize a new habitat, they
very possibly may not have the same allele
frequencies as the original population.
e.g. In the human population, there is a
recessive allele which creates a form of
dwarfism (involving only the arms and legs)
as well as polydactilism (more than 5 fingers
on a hand). In the general population, this
occurs in about 1/1000 individuals. In the
Amish in Pennsylvania, however, this can
occur in as many as 1/14 individuals because
the original Amish (by chance) had this
recessive allele in a large frequency, and
since they tend not to marry outside their own
small community, this allele has remained
common in the population.
Natural Selection
1) Organisms have heritable variations:
- Members of a population differ from each other in many physical attributes. Often,
these attributes are heritable
2) Organisms struggle to exist
- In a population, many more individuals are born than can be supported by the
environment.
Which ones survive?
3) Organisms differ in Fitness
- Some of the individuals in a population have – by virtue of their heritable attributes – a
greater ability to survive and reproduce than others.
-Fitness is the Reproductive success of an individual relative to other individuals in a
population
4) Inheritance of fitness
- These attributes favourable for survival are inherited, which means the offspring will
also carry the genes for speed, or water conservation, etc.
5) Adaptation
- The environment is changing all the time, which means that Natural Selection occurs
continuously,
- At the same time, mutations continue to create new diversity, so that there is always a
pool of new genetic diversity available: the population increasingly adapts to the local
environment.
HUMAN SELECTION
OVER THE PAST
10000 YEARS
4.1 Types of natural Selection
- Most physical (phenotypic) characteristics upon which
Natural Selection operates results from large numbers of
genes, each possessing several different alleles.
- Genes interact to produce a certain phenotype, since
many physical characteristics are too complex to be
controlled by only one or two genes.
- In a large population, if one measures a physical
attribute (for example size), and plots it on a graph, the
frequency distribution will have the appearance of a bell-
shaped curve.

Three types of Natural Selection occur:

LECTURE 6

SPECIATION
 Speciation is the splitting of one
species into two or more, or the
transformation of one species
into a different species over time.

We generally use the Biological Species Concept to define a

species:
A species comprises all the members of a population, or a
group of populations who:
- share a common gene pool
- who can interbreed with each other
- produce viable, fertile offspring
- and are reproductively isolated from all other species.
 Application of the biological
concept.
Homo sapiens: although populations are very widely
distributed and show great differences in physical
attributes, they share a common gene pool – gene flow
between them does occur (...or can potentially
occur...) and they can reproduce to produce viable
offspring. The human species is therefore a good
biological species.

- A male Donkey and female Horse can interbreed to

produce the Mule, but the mule is infertile. They
therefore belong to different species.
In nature, gene flow is prevented by Reproductive Isolating
Mechanisms.
- A reproductive isolating mechanism is any Structural, Functional
or Behavioural attribute that prevents successful mating between
individuals.
- We can divide these into Prezygotic and Postzygotic Isolating
mechanisms.
- Prezygotic mechanisms – prevent mating from occurring, or
prevent successful fertilisation even if mating is attempted.
- Postzygotic mechanisms – prevent the offspring of individuals
from different species (we call such offspring hybrids) from
surviving, or reproducing even if they survive.
 Prezygotic Mechanisms
- Geographical isolation: Populations are separated from each other by means of
impassable barriers (e.g. finches in the Galapagos islands;).
- Habitat/Ecological isolation: Species occur in different areas, and therefore do not
come into contact with each other to mate (even if they occur in the same area, they
may inhabit different areas inside that area, e.g. different layers in the forest canopy.
- Temporal/Seasonal isolation: Species may occur in the same area, but may be active
at different times of day, and not come into contact with each other to be able to breed.
Many species also have very specific mating periods/seasons, and if two species have
different breeding seasons / times, they cannot reproduce, even if they occur in the
same area.
- Behavioural isolation: Many animals have complex mating calls (birds or crickets) or
mating dances, or they release chemical attractants into the air (called pheromones)
which are recognised only by other members belonging to the same species.
- Mechanical isolation: This can occur when animal or plant genitalia are incompatible,
or do not match, e.g. male dragonflies have to grasp females before they can mate, but
their grasping "arms" (claspers) can only hold females of their own species.
- Gamete isolation: Even if two individuals of different species mate, it is still possible to
prevent fertilisation since sperm cells often cannot survive in the reproductive tract of
another species, or the sperm cell does not recognise the egg cell, or cannot fuse to it
because the egg cell has an incompatible cell membrane (remember that the sperm cell
head is covered by an acrosome that carries enzymes needed by the sperm cell to
penetrate the egg).
 Postzygotic Mechanisms

- Zygote mortality: The sperm and egg cells fuse to form a zygote,
but the zygote fails to develop further (i.e. dies without developing
into a foetus).

- Hybrid sterility: The hybrids survive, but are infertile and cannot
reproduce, e.g. crossing a female horse and a male donkey
produces the mule. Even though a mule may be healthy
otherwise, it cannot produce functioning sex cells.

- F2 fitness: The Hybrids survive, and are even fertile, but their
own offspring in turn (i.e. the F2 generation) are weak / have
reduced fitness, and may not be able to compete successfully with
other animals for food, shelter or breeding mates.
 Types of Speciation
- Allopatric speciation – occurs when a population is
geographically isolated from other populations and gene flow
stops.
- Sympatric Speciation – Occurs when a population develops
into two or more reproductively isolated groups without prior
geographic isolation. e.g. through Disruptive selection, competitive
speciation, polyploidy.
- Parapatric Speciation – One species has a wide geographic
distribution, and because of this, not all the populations making up
this species live under the same environmental conditions (e.g.
some populations live in drier conditions, some populations have
to adapt hunting strategies to feed on different prey, etc.).
Because of this, selection for different phenotypes occurs in
different populations, and populations will slowly diverge from
each other, even though they are still in contact with each other,
and gene flow still occurs between them.
 LECTURE 7

EVIDENCE FOR EVOLUTION

- Very much in evidence is the succession of life forms
from simple forms (deep geological layers) to the very
complex (closer to the surface).
- Fossils provide evidence of animals changing over
time,
- We find transitional fossils – fossils which combine the
appearance of different animals; reptile-like birds,
amphibious fish, amphibians looking like reptiles, and
mammal-like reptiles (therapsids).
- These intermediate fossils, for example suggests that
Amphibians evolved from fish, Reptiles evolved from
Amphibians and Mammals and Birds evolved from
Reptiles.
Archaeopteryx
Transitional fossil
Between reptiles
And living birds
- The fossil record is sometimes very complete, and
allows us to trace the evolution of specific animals very
precisely. The evolution of the horse (Equus) evolving
from Hyracotherium, a small forest dwelling animal the
size of a large dog (roughly 35kg) is such an example.
- The evolution of the whale has also, for example, been
traced with some evidence to 4-legged land-living
animals, mesonychians, who gradually started adapting
to swimming in shallow seas 50-60 million years ago.
- Many extinct branches of modern groups of plants and
animals are evident. An example is Glossopteris,
Complete series: Horse evolution
Palaeontological evidence:
complete series of Human anatomical evolution
Cetacean evolution: complete series mesonychians to whales
Anatomical Evidence

- Homologous structures (homologous = corresponding) are structures

whose basic anatomical structure developed once in history,
-e.g. the forelimb of vertebrates, which is used for flying (birds and bats),
swimming (whales and seals), running (horses, cats, dogs), climbing (arboreal
(tree living) lizards), swinging (monkeys), digging (moles) etc. Despite dissimilar
functions, the forelimbs all have the same bones, arranged in a similar way, as
well as the same muscles.
- The most plausible explanation for this is that the basic forelimb plan belonged
to a common ancestor; the structure was then gradually modified by selective
pressures to adapt to a specific habitats/behaviour.
 ANALOGOUS STRUCTURES

-Analogous structures (analogous= similarly

shaped non- corresponding structures), are
structures serving the same function, but without
a common ancestral structure. E.g. wings of birds
and insects, or flippers of seals and fins of fish.
Analogous structures provide evidence that
evolution adapts various organisms to available
habitats
- Vestigeal Structures – Reduced anatomical structures that
serve no purpose, and are not functional.
- They occur, however, in functional form in related species, and
they presumably also served a function in the own body at
some point in the distant past.
- The best explanation for them is that the structures have been
selected against until they no longer can function, but they are
still useful in related species.
- Vestiges therefore show that the forms in which they occur are
modified by evolution from forms where these organs were
functional.
Embryonic evidence: recapitulation of ancestors
- Embryonic development – During embryonic
development, stages resemble the adult condition of
more primitive life forms. All vertebrates including H.
sapiens show a post-anal tail and pharyngeal pouches in
early stages of development. We as humans usually
lose our tails before we are born.
- Pharyngeal gill pouches homologous with gill slits of
fish become modified into tonsils and the thymus and
parathyroid glands in humans. The middle ear ossicles
in mammals developed from elements of the lower jaw
and jaw articulation- a development process seen in the
embryology and the therapsid fossil record.
- The most likely explanation for the presence of these
structures in the embryonic development of humans is
that fishes and therapsids are our ancestors
Fossil evidence shows a supercontinent existed 250-200 mya
6.3 Biogeographical Evidence
Patterns of distribution
- Similarities in widely separated (even on on different continents) species of the same
genus suggest a common ancestry, while differences between obviously related species
in close proximity suggests isolation and independent evolution.
- eg. Large catlike species occur all over the world, but they are separated by
impenetrable barriers like oceans. e.g. the Jaguar in South America, and the Leopard in
Africa and Asia and the Tiger in India. Their similarities suggest a common ancestry, but
differences suggest that they started diverging genetically when the African and South
America continents drifted apart.
Parallel adaptation
- Marsupial animals in Australia and placental animals in the rest of the world, which
have been geographically isolated for millions of years, have both developed similar
ecotypes in similar niches.
- Similarly, islands tend to have few, but unique resident species. These species are
often similar, yet obviously different from species in other, neighbouring islands (e.g.
finches in the Galapagos Island where many species on islands close together appear
very similar, but with slight differences as they adapted to specific habitats).
6.4 Biochemical Evidence / Molecular record
- Almost all living organisms use the same basic biochemical pathways such
as respiration
- Their DNA works on the same principles, and their proteins consist of the
same 20 different amino acids which are arranged in sequence.
- Our DNA controls the arrangement of amino acids in proteins, and genetic
mutations change the sequence of amino acids, and hence, the structure of
the protein
- a great many genes are shared by all animals – humans share many genes
with very primitive animals, especially developmental genes (i.e. genes
responsible for body form before birth, during gestation).
- It is possible to compare the degree to which important genes, or gene
products (proteins) differ. As would be expected from evolutionary theory,
the more closely related animals are, the more similar their genes. The
genes of humans and the genus Pan (chimpanzees and gorillas)
corresponds nearly 98%, indicating a common ancestry
- Human and chimpanzee chromosome are also closely similar.