Download The Classification of Living Things

The Classification of Living Things
Taxonomy
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The science of classifying organisms
Purpose:
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To identify organisms
To represent relationships among them
Aristotle
•4th century B.C.E.
•Grouped organisms according to habitat:
land-dwellers, water-dwellers, air-dwellers
St. Augustine
•3rd century C.E.
•Classified animals us useful, harmful, or superfluous
Middle Ages
•Herbalists classified plants according to what
they produced: fruit, vegetable, or wood
Carolus Linnaeus
1707-1778
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Used simple physical characteristics to
identify different species
Classification system known as binomial
nomenclature
The first part of the name refers to the genus
name and the second part of the name refers to
the species name
This system uses Latin, the language of scholars
The generic name is always
in Europe at the time
Domestic Cat: Felis sylvestris
Genus
species
capitalized and the species name
is not. A short form for the
generic name may be used;
Escherichia coli  E. coli
Kingdoms
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There are 6 kingdoms to
which organisms can be
classified
Organization: organisms are
grouped according to
shared characteristics. In
the past the groupings were
determined by shared
physical characteristics
The advances in
biochemistry this century
has added to the
sophistication of these
groupings
What is our grouping?
1.
A.
B.
C.
D.
E.
F.
G.
The groups, in order of size: with the group
names for humans included…
KINGDOM – Animalia (The largest grouping)
PHYLUM – Chordata
CLASS – Mammalia
ORDER – Primata
FAMILY – Hominidae
GENUS – Homo
SPECIES – sapiens
(the smallest grouping)
KINGDOM ANIMALIA
Characteristics: all are multicellular, all are
heterotrophs (consumers), most
reproduced sexually, terrestrial and
aquatic habitats, invertebrates and
vertebrates
 Eukaryotes
 No cell wall
 E.g.: sponges, worms,
lobsters, starfish, humans

KINGDOM PLANTAE
Characteristics: All are multicellular, all
are autotrophs (producers), reproduce
sexually and asexually, most are
terrestrial, sessile*
 Eukaryotes
 Cell walls present (cellulose)
 E.g.: mosses, ferns, conifers,
flowering plants
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*DEFINITION: SESSILE = permanently attached or
established : not free to move about
KINGDOM FUNGI (12.4)
Characteristics: Most are multicellular, all are
heterotrophs, reproduce sexually and asexually
(spores, budding), most are terrestrial (sessile),
decomposers
 Eukaryotes
 Cell walls are present
but not made of cellulose,
But of chitin instead
 E.g.: mushrooms, yeasts,
bread moulds

The Fungi Kingdom: Common
Characteristics
Structure of Fungi
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Multicellular, bodies are
made up of hyphae (a
network of filaments)
Feed by extracellular
digestion  as hyphae
grow they release
digestive enzymes that
break down large
molecules

Small molecules diffuse
into the fungus where they
are used to fuel growth
and repair
Ecological Importance of Fungi
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Decomposers
Symbiotic: Many fungi
live in relationships with
plants or animals that
benefit both species
Parasitic
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Puffball
Drops of rain trigger
the release of spores
Pholiota spp
Degrades wood
very quickly
On plants
On animals
Mutualistic
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Lichens
Mycorrhizae: when fungi live
close to the roots of trees
Epidermophyton
floccosum,
fungi causing
athlete’s foot
KINGDOM PROTISTA (12.3)
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Characteristics: mostly
single-celled, some are
autotrophs, some
heterotrophs, reproduce
sexually and asexually, live in
aquatic or moist habitats
Eukaryotes, producers or
consumers
No cell wall
Some move with flagella,
pseudopods or cilia
Animal-like, plant-like and
fungus-like groups
E.g.: algae, protozoa, slime
moulds & water moulds
Zoomastigina – the trypanosoma
This type of Protist can cause
diseases
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Of the approximately 23 species of
Glossina recognized, all but three will
transmit trypanosomes to mammals.
Several species are particularly
important vectors of African
trypanosomiasis (‘sleeping sickness’)
in humans. Adult tsetse flies typically
measure 7 to 14 mm long.
Life cycle of trypanosoma
Sporozoa – the plasmodium
Malaria - Life Cycle of
Plasmodium
Ecological Importance of Protists
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Important foundation in food chain
Produce vast amount of O2
Decomposition
Symbiotic relationships
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Mutualistic
Parasitic
Medicinal and Industrial Uses
Volvox
Colonial green alga
KINGDOM ARCHAEA (MONERA)
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Characteristics: simple organisms lacking nuclei,
either heterotrophs or autotrophs, reproduce
asexually, producer/consumers/decomposers
live in harsh habitats of extreme saltiness, low
O2 concentration, high temperature
or extreme acidity
Prokaryote
Cell wall often present
E.g.: halobacteria, pyrolobus
fumarii, pyrococcus furiosis
KINGDOM BACTERIA (12.2)
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Characteristics: Simple organisms lacking
nuclei, either heterotrophs or autotrophs,
reproduce asexually, live nearly everwhere
Prokaryote
Cell wall often present
E.g.: Streptococcus mutans, treponerna
pallidum, clostridium botulinum
Types of
Bacteria
Different ways to classify Bacteria
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
presence/absence of cell wall
Cell wall stain (gram positive/gram negative)
Morphology (shape/growth)
Type of colony
Size
Formation of endospore
Site/source of bacteria
Susceptibility to viruses/antibiotics
Aerobic/anaerobic
Ability to grow on different media
Presence/absence of pilli, capsules, flagella
-phile, -phobe (acidophile – love acidic conditions,
halophile – love salty conditions, thermophobic –
dislikes heat)
colour
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Autotrophic: Bacteria can make their
own food by 1) photosynthesis and 2)
chemosynthesis
1. Bacterial photosynthesis does not
produce oxygen as a byproduct. Example:
blue-green bacteria
2. Chemosynthesis does not use light
energy but gets energy from breaking
down iron, sulfur, and nitrogen. Example:
prokaryotes
Heterotrophic bacteria cannot make their own
food and depend on other living things or dead
organisms. There are two kinds of
heterotrophs: saprophytes and parasites
1.
Saprophytes are organisms that get their
food from non-living materials such as dead
plants, dead animals, waste materials. These
bacteria are often called decomposers.
2.
Parasites are organisms that obtain their food
by living attached to or inside living organisms.
These bacteria invade your living tissue. An
organism that supports a parasite is called a
host. Parasitic bacteria that cause a disease in
the host are called pathogens.
Reproduction in Bacteria
1.
2.
Asexual reproduction – binary fission
Quasi Sexual – exchange of genes
a)
b)
c)
d)
Transformation
Transduction
Conjugation
Plasmid transfer
*Quasi sexual is not really sexual reproduction because
there is no formation of gametes
Binary Fission
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Bacteria cell is haploid, i.e. they only contain
1 copy of DNA (circular chromosome)
Sporulation in Bacteria
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Bacterial cells have the ability to form an
endospore. Often the formation of an
endospore is a response to harsh
environmental conditions. (However,
spore formation can also be part of the
bacteria’s regular life cycle). While in the
endospore, bacteria do not grow or
reproduce.
Quasi-Sexual Reproduction- transfer of
DNA from one bacterium to another
1.
Transformation: The transfer of a portion of bacterial DNA from one
bacteria, living or dead, to another living bacteria (with the second
bacteria incorporating the DNA pieces)
Plasmid Cloning
2. Plasmid Transfer: This is just like transformation except the DNA which is
transferred is not chromosomal, rather it is an independent circular piece
--- plasmid.
3.
Transduction: the
process by which a
virus transfers bacterial
DNA from one bacterial
cell to another.
Viral Reproduction
4. Conjugation: The
process by which two
bacteria join together
and exchange pieces of
DNA by means of a sex
pilus.
BioInteractive's Animation
Console: Bacterial Conjugation
The Three Domains
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A level of classification above kingdom
Tutorial 27.1 The
Evolution of the
Bacteria, Archaea, and Eukarya
Three Domains
Eukarya contains the greatest biological diversity in the
kingdom Protista
Protists have lived on earth for a longer time than plants and
animals --- it has had a longer time to diversify and change
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Prokaryotic, Circular DNA,
asexual reproduction, many
are anaerobic
Three main groups of
archaea
 Methanogens: live in
O2 free environments
(swamps, marshes &
sewage disposal plants)
 Halophiles: requires a
salty environment
 Thermoacidophiles:
grow in hot sulfur
springs at low pH,
volcanoes or near deep
sea vents and grow best
at temperatures above
80° C
Archaea
Viruses, Viroids, and Prions
Are Viruses Living or Nonliving?
Viruses are both and neither
 They have some properties of life
but not others
 For example, viruses can be killed,
even crystallized like table salt
 However, they can’t maintain a
constant internal state
(homeostasis).

What are Viruses?
A
virus is a noncellular particle
made up of genetic
material and protein
that can invade
living cells.
Discovery of Viruses
Beijerinck (1897)
coined the Latin
name “virus”
meaning poison
 He studied
filtered plant
juices & found
they caused
healthy plants to
become sick

Tobacco Mosaic Virus
Wendell Stanley
(1935) crystallized
sap from sick tobacco
plants
 He discovered viruses
were made of nucleic
acid and protein
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Smallpox
Edward Jenner
(1796) developed a
smallpox vaccine
using milder cowpox
viruses
 Deadly viruses are
said to be virulent
 Smallpox has been
eradicated in the
world today

Viewing Viruses
Viruses are smaller
than the smallest cell
 Measured in
nanometers
 Viruses couldn’t be
seen until the
electron microscope
was invented in the
20th century

Size of Viruses
Viral Structure:
Characteristics
Non living structures
 Noncellular
 Contain a protein coat called the
capsid
 Have a nucleic acid core containing
DNA or RNA
 Capable of reproducing only when
inside a HOST cell

Characteristics
Some viruses are
DNA
enclosed in an
protective envelope
 Some viruses may have
spikes to help attach to
the host cell
 Most viruses infect
only SPECIFIC host
ENVELOPE
cells
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CAPSID
SPIKES
Characteristics
Viral capsids
(coats) are made
of individual
protein subunits
 Individual
subunits are
called
capsomeres
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CAPSOMERES
Characteristics
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Outside of host cells,
viruses are inactive
Lack ribosomes and
enzymes needed for
metabolism
Use the raw materials
and enzymes of the
host cell to be able to
reproduce
HIV VIRUS
EBOLA VIRUS
Characteristics
Some viruses cause
disease
 Smallpox, measles,
mononucleosis, influenza,
colds, warts, AIDS,
Ebola
 Some viruses may cause
some cancers like
leukemia
 Virus-free cells are rare
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MEASLES
BioInteractive -Animations -- Viral
infection
Viral Shapes
Viruses come in a variety of
shapes
 Some may be helical shape like
the Ebola virus
 Some may be polyhedral shapes
like the influenza virus
 Others have more complex
shapes like bacteriophages
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Helical Viruses
Polyhedral Viruses
Complex Viruses
Viral Taxonomy
Family names end in -viridae
 Genus names end in -virus
 Viral species: A group of viruses
sharing the same genetic information
and ecological niche (host).
 Common names are used for species
 Subspecies are designated by a
number
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Viral Taxonomy Examples
Herpesviridae
 Herpesvirus
 Human herpes virus 1, HHV 2, HHV
3
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Retroviridae
 Lentivirus
 Human Immunodeficiency Virus 1,
HIV 2
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Herpes
Virus
Adenovirus
SIMPLEX I and II
COMMON COLD
Influenza
Virus
Chickenpox
Virus
Papillomavirus –
Warts!
Used for Virus
Identification
 RNA
or DNA Virus
 Do or do NOT have an
envelope
 Capsid shape
 HOST they infect
Bacteriophages
Viruses that attack
bacteria are called
bacteriophage or just
phage
 T-phages are a
specific class of
bacteriophages with
icosahedral heads,
double-stranded
DNA, and tails
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T-phages
The most commonly
studied T-phages are T4
and T7
 They infect E. coli , an
intestinal bacteria
 Six small spikes at the
base of a contractile tail
are used to attach to
the host cell
 Inject viral DNA into
cell
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Escherichia Coli Bacterium
T - EVEN PHAGES ATTACK THIS BACTERIUM
Diagram of T-4
Bacteriophage
Head with
20 triangular
surfaces
 Capsid
contains
DNA
 Head & tail
fibers made
of protein

Retroviruses
Contain RNA, not DNA
 Family Retroviridae
 Contain enzyme called Reverse
Transcriptase
 When a retrovirus infects a cell,
it injects its RNA and reverse
transcriptase enzyme into the
cytoplasm of that cell

Retrovirus
ENZYME
Retroviruses
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The enzyme reverse
transcriptase (or
RTase), which causes
synthesis of a
complementary DNA
molecule (cDNA)
using virus RNA as a
template
RTase
Retroviruses
 HIV,
the AIDS
virus, is a
retrovirus
 Feline
Leukemia Virus
is also a
retrovirus
Life Cycle of HIV, a
Retrovirus
HIV
Replication
Viroids & Prions
Viroids
Small, circular
RNA molecules
without a protein
coat
 Infect plants
 Potato famine in
Ireland
 Resemble introns
cut out of
eukaryotic
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Prions
Prions are “infectious
proteins”
They are normal body
proteins that get
converted into an
alternate configuration
by contact with other
prion proteins
They have no DNA or
RNA
The main protein involved
in human and mammalian
prion diseases is called
“PrP”
Prion Diseases
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Prions form insoluble
deposits in the brain
Causes neurons to
rapidly degeneration.
Mad cow disease
(bovine spongiform
encephalitis: BSE) is an
example
People in New Guinea
used to suffer from
kuru, which they got
from eating the brains
of their enemies
How Prions Arise
Viral Replication
Viral Attack
Viruses are very specific as to
which species they attack
 HOST specific
 Humans rarely share viral diseases
with other animals
 Eukaryotic viruses usually have
protective envelopes made from
the host cell membrane

5 Steps of Lytic Cycle
1. Attachment to the cell
2. Penetration (injection) of viral DNA
or RNA
3. Replication (Biosynthesis) of new viral
proteins and nucleic acids
4. Assembly (Maturation) of the new
viruses
5. Release of the new viruses into the
environment (cell lyses)
Bacteriophage
Replication
Bacteriophage inject
their nucleic acid
 They lyse (break
open) the bacterial
cell when replication
is finished

Lytic Cycle Review
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Attachment

Penetration
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Biosynthesis
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Maturation
Release
Phage attaches by tail fibers to
host cell
Phage lysozyme opens cell wall,
tail sheath contracts to
force tail core and DNA into
cell
Production of phage DNA
and proteins
Assembly of phage particles
Phage lysozyme breaks cell wall
Bacterial
cell wall
Bacterial
chromosome
Capsid
DNA
Capsid
Sheath
1 Attachment:
Phage
attaches to
host cell.
Tail fiber
Base plate
Pin
Cell wall
Tail
Plasma membrane
2 Penetration:
Phage pnetrates
host cell and
injects its DNA.
Sheath contracted
Tail core
3 Merozoites
released into
bloodsteam from
liver may infect
new red blood cells
Tail
DNA
4 Maturation:
Viral components
are assembled into
virions.
Capsid
5 Release:
Host cell lyses
and new virions
are released.
Tail fibers
Viral Latency
Some viruses have the ability to
become dormant inside the cell
 Called latent viruses
 They may remain inactive for long
periods of time (years)
 Later, they activate to produce
new viruses in response to some
external signal
 HIV and Herpes viruses are
examples

Lysogenic Cycle
Phage DNA injected
into host cell
 Viral DNA joins host
DNA forming a
prophage
 When an activation
signal occurs, the
phage DNA starts
replicating

Lysogenic Cycle
Viral DNA (part of
prophage) may stay
inactive in host cell for
long periods of time
 Replicated during each
binary fission
 Over time, many cells
form containing the
prophages

Viral Latency
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Once a prophage cell is activated, host cell
enters the lytic cell
New viruses form a & the cell lyses (bursts)
Virus said to be virulent (deadly)
ACTIVE
STAGE
INACTIVE STAGE
Virulent Viruses
HOST
CELL
LYSES &
DIES
The Lysogenic Cycle
Latency in Eukaryotes
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Herpes viruses also
become latent in the
nervous system
SKIN TO SKIN CONTACT
A herpes infection
lasts for a person’s
lifetime
Genital herpes (Herpes
Simplex 2)
Cold sores or fever
blisters (Herpes
Simplex1)
PASSED AT BIRTH TO
BABY
Latency in Eukaryotes
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Some eukaryotic
viruses remain dormant
for many years in the
nervous system tissues
Chickenpox (caused
by the virus Varicella
zoster) is a childhood
infection
It can reappear later
in life as shingles, a
painful itching rash
limited to small areas
of the body
SHINGLES
Virulence
VIRUS DESTROYING HOST
CELL
Lytic and Lysogenic Cycles
Treatment for Viral Disease:
Vaccines
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An attenuated virus is a weakened, less
vigorous virus
“Attenuate" refers to procedures that
weaken an agent of disease (heating)
A vaccine against a viral disease can be
made from an attenuated, less virulent
strain of the virus
Attenuated virus is capable of
stimulating an immune response and
creating immunity, but not causing illness
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Other Viral Treatments
Interferon are
naturally occurring
proteins made by cells
to fight viruses
Genetic altering of
viruses (attenuated
viruses)
Antiviral drugs (AZT)
Protease inhibitors –
prevent capsid
formation
Treating Diseases
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Until the discovery of antibiotics by Alexander
Fleming, the only hope for treating disease was
to promote antibody production. With the
discovery of penicillin, it became possible to
introduce outside drugs into the body to help
fight infections.
What are antibiotics?
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They are natural waste products made during the life
cycle of many fungi and bacteria. These waste
products inhibit the growth of many other organisms.
Examples: penicillin inhibits the growth of boils,
carbuncles, tetanus, pneumonia, diphtheria and
gonorrhea.
How do Antibiotics Work?
1.
2.
The penicillin group prevents synthesis
of the bacterial cell wall. The bacteria
without a cell wall are easy prey to the
environment and quickly die. Human
cells do not have a cell wall so the
penicillin does not harm them.
Antibiotics may also interfere with some
aspect of bacterial protein synthesis.
These antibiotics may cause side effects
because they cannot distinguish between
human and bacterial metabolism.
Antiviral Agents
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Unlike bacteria, viruses are not directly
susceptible to antibiotics or chemotherapy.
Since they replicate inside a cell, any antiviral
agent must get into the cell and either kill that
cell or interfere with virus growth. There are
very few chemicals, which can do this and not
harm the entire body of the infected person.
The body responds to viral infection by the
production of a group of proteins called
interferons.
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Alpha and beta interferons – prevent virus replication
Gamma interferons – a regulator of the body’s
immune system
Vaccines – most successful strategy of preventing
viral infection
11.4: Origins of Diversity
Genetic Diversity refers to the
number of genetic
characteristics that are
expressed in any one
particular species. The
genetic diversity within a
species can leads to the
formation of a new species
through natural selection.
One gene combination may
survive certain environmental
stresses better than another.
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Species Diversity refers to the number
of different species living in a particular
Slide Show: Top 10 New Species Discovered
environment
in 2008: Scientific American Slideshows
Ecosystem diversity details the different
habitats and communities within a given
area. The biodiversity on Earth today is
the result of about 3.5 billion years of
evolutionary history.
Models for predatorprey interactions
Genetic Variation
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The range of a particular environmental
condition within which an organism can survive
is called the RANGE OF TOLERANCE
In a community, you get variation among
different species. This is a good thing because if
two species responded exactly the same way to
an environmental condition, they would both be
wiped out
There can also be variation within a species. On
hot days in the summer, you are constantly
warned to stay inside where it is cool. Some
people unfortunately die on severely hot days,
but we all don’t. Personal differences provide
the range of tolerance, which is important for
adaptation.
Phylogeny
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Phylogeny is a history that
indicates hypothesized
evolutionary paths.
Phylogenic trees show the
relationships between
different organisms that are
thought to have a common
ancestry. The common
ancestor at the base of the
tree has general
characteristics that are shared
by all the species that evolved
from it. These features are
called primitive characteristics.
New species that evolve from
the common ancestor have a
new feature called derived
characteristics.
Claudistics

This is a system based on the idea that
each new group of related species has one
common ancestor, and organisms retain
some ancestral characteristics
In 1838, Darwin had the
idea that organisms
with favourable
variations would be
better able to survive
and reproduce
passing on their
favourable traits. He
called this Natural
Selection. Darwin
published this ideas in
this book “On the
Origin of Species by
Means of Natural
Selection” in 1859.
Darwin
The
Galapago
s islands
Darwin’s Main Points
Overproduction: most species
produce far more offspring than
are needed to maintain the population
 Struggle for Existence: Food and space are limited
therefore competition takes place. Only a small fraction
survive long enough to reproduce
 Variation: In any species, the characteristics of the
individuals are not exactly alike. They may differ in shape,
or size, speed, strength, and
resistance to disease. Some
variations affect the individual’s
chances to getting food, escaping
enemies and finding mates
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Darwin’s
Main
Points
Survival of the Fittest:
Because of variation, some
individuals will be better
equipped to survive or
reproduce
Natural Selection: Since
individuals with desirable
traits survive, these
characteristics are passed on
Evolution of New Species:
Over many generations
favourable variations
gradually accumulate in the
species and the net result is
a new species
Evidence for Evolution
Comparison of
vertebrate embryos
Galapagos
finches
Origins of Modern Humans