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A Level Biology Unit 5
page 1
Heckmondwike Grammar School Biology Department
Edexcel A-Level Biology B
Contents
Classification ............................................................................ p3
Phylogenetics ........................................................................... p5
Five Kingdoms ......................................................................... p8
Three Domains ....................................................................... p10
Natural Selection .................................................................... p12
Speciation.................................................................................. p17
Biodiversity............................................................................... p21
Conservation ........................................................................... p24
These notes may be used freely by biology students and teachers.
I would be interested to hear of any comments and corrections.
Neil C Millar ([email protected]) June 2016
Y12
Unit 1 Biochemistry
Unit 2 Cells
Unit 3 Reproduction
Unit 4 Transport
Unit 5 Biodiversity
Unit 6 Ecology
Y13
HGS Biology A-level notes
Unit 7 Metabolism
Unit 8 Microbes
Unit 9 Control Systems
Unit 10 Genetics
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A Level Biology Unit 5
page 2
Biology Unit 5 Biodiversity
Specification
Classification
The classification system consists of a hierarchy of
domain, kingdom, phylum, class, order, family, genus
and species.
The limitations of the definition of a species as a group
of organisms with similar characteristics that
interbreed to produce fertile offspring. Why it is
often difficult to assign organisms to any one species
or to identify new species.
Phylogenetics
DNA
sequencing,
gel
electrophoresis
and
bioinformatics can be used to distinguish between
species and determine evolutionary relationships.
Classification Models
The evidence for the three-domain model of
classification as an alternative to the five-kingdom
model and the role of the scientific community in
validating this evidence.
Natural selection
Evolution can come about through natural selection
acting on variation bringing about adaptations.
Organisms occupy niches according to physiological,
behavioural and anatomical adaptations. There is an
HGS Biology A-level notes
evolutionary race between pathogens and the
development of medicines to treat the diseases they
cause.
Speciation
Reproductive isolation can lead to allopatric and
sympatric speciation. The role of scientific journals,
the peer review process and scientific conferences in
validating new evidence supporting the accepted
scientific theory of evolution.
Biodiversity
Biodiversity can be assessed at different scales:
 within a species at the genetic level by looking at
the variety of alleles in the gene pool of a
population.
 within a habitat at the species level using a formula
to calculate an index of diversity
Conservation
The ethical and economic reasons (ecosystem
services) for the maintenance of biodiversity. The
principles of ex-situ (zoos and seed banks) and in-situ
conservation (protected habitats), and the issues
surrounding each method.
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A Level Biology Unit 5
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Classification
There are millions of different types of organisms on the planet, from large animals and plants to
microscopic fungi and bacteria, and each type is unique. We call each different type a species. Biologists
have so far found and named around 1.5 million different species, and the more we find, the more we
realise how few we know. Our knowledge is patchy: we know a lot about vertebrate animals and flowering
plants, but not much about bacteria, fungi or worms. We know a lot about species living in temperate
lands, but little about those living in the tropics, where 75% of all species probably live. The total number of
living species may well exceed 10 million, and if we include extinct species the figure is increased by a factor
of 100. A good classification system is needed to keep track of all this variety. The science of classification is
called taxonomy.
Principles of Taxonomy
Many different classification systems have been devised, but the one biologists use is based on the work of
the Swede Carolus Linnaeus in the mid-18th century. Linnaeus introduced three important innovations.
 He devised a hierarchical structure for classification. In a hierarchy organisms with similar characteristics
are grouped together, and these groups are contained within larger composite groups. There is no
overlap between groups, and a species can only appear once. These two diagrams represent hierarchical
classifications, and both forms are used in biology.
 He gave each rank in the hierarchy a standard name. There are seven ranks or levels in the biologists’
classification:
(Some modern classifications also include a higher rank called the domain, as we shall see.) So you need
to remember KPCOFGS.
 He introduced the binomial nomenclature for naming organisms unambiguously. This simply consists of
the first two ranks: the generic name (with a capital letter) and the specific name (with a small letter),
and he used Latin names rather than different local-language names. The binomial names are italicised
when printed (or underlined if hand-written) and after a first mention, the generic name can be
abbreviated to the first letter e.g. Panthera leo (lion) and P.tigris (tiger). For most purposes the binomial
name is enough to identify an organism, but a full 7-rank lineage can be given to avoid confusion.
Linnaeus’s universal standard system replaced non-standard common and local names, and is still universally
used today.
HGS Biology A-level notes
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A Level Biology Unit 5
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What is a Species?
For such a fundamental and apparently simple concept, the species is surprisingly hard to define. Here are
four different definitions, each focussing on a different aspect of the “species”:
1. Morphology definition: members of the same species have similar characteristics. These
characteristics could include their appearance or morphology (e.g. body shape, number of legs, leaf
shape, etc.); the structure of their cells (e.g. composition of organelles, ribosomes, cell walls); their
biochemistry (e.g. particular metabolic pathways or storage molecules). This is the most obvious
definition, and is still useful, but it can be misleading for determining a phylogeny. It can be difficult to
distinguish between homologous structures (which look similar because they arose from a common
ancestor, e.g. the pentadactyl limb); and analogous structures (which look similar because they arose
independently to do a similar job, e.g. a wing).
2. Ecological definition: members of the same species have the same ecological niche. An organism’s
niche is its role in the ecosystem: where it lives, how it feeds, what conditions it needs to survive, who
it competes with, how it reproduces and so on. Members of the same species must have the same
niche, since that is what they are adapted to.
3. Reproduction definition: members of the same species can breed together in their natural
environment to produce fertile offspring but cannot breed with members of other species. This is the
most useful definition, as it can be tested fairly easily, and applies directly to the process of speciation
itself (p17), but it too has its limitations. For one thing, this definition doesn’t apply to the millions of
asexually-reproducing organisms, nor to extinct species. And even for sexually-reproducing species,
two organisms that would not normally breed in the wild (perhaps because they live in different parts
of the world) may be able to interbreed in the artificial environment of a zoo, a garden or a lab. This is
particularly true of plants, which can quite easily be hybridised. Even in the wild, some closely-related
species can interbreed, such as a horse and donkey to produce a mule, but the offspring is usually
sterile, so is not a fertile organism.
4. Evolutionary definition: members of the same species share a unique common ancestor with each
other but not with members of any other species. This is the most modern definition of a species and
is the basis of phylogenetics – placing species in their correct evolutionary family tree. This can only be
done by analysing the DNA sequences of different species to see how closely related they really are
(see below). It can still be difficult to deduce relationships accurate since some genes can be
transferred from one species to another by horizontal gene transfer.
Biologists will no doubt continue to debate this species problem, but that doesn’t stop us using the species
as a useful basic unit of classification.
HGS Biology A-level notes
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A Level Biology Unit 5
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Phylogenetics
We now know that all life on Earth is related, and all species have arisen through evolution. So the aim of
taxonomists today is to develop phylogenies; family trees representing true evolutionary relationships,
rather than just convenient groupings. Phylogenies are represented by
phylogenetic trees, just like family trees. Branching points on phylogenetic
trees can be interpreted in two ways:

Going forward in time from the past, they represent speciation events,
when one species splits in two (see p17).

Going backward in time from the present, they represent the most
recent common ancestor (MRCA) of all the species after the branch.
In the tree shown here, species A and B are closely related because they have
a recent common ancestor (at point Y), while they are more distantly related
to species C because their common ancestor with C lived further in the past
(at point X).
This diagram (from the Ancestor’s Tale) shows the phylogeny of some mammals. The numbers are the
times in millions of years (My) between branches:
HGS Biology A-level notes
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A Level Biology Unit 5
page 6
Sequencing DNA
Phylogenies and true ancestry can only be determined by comparing the DNA sequence of different
species, since it is only DNA that is actually passed down from generation to generation. DNA can be
extracted from the cells of living organisms and the sequence of bases read using sequencing machines.
These sequencing machines use a kind of chromatography called gel electrophoresis that separates DNA
fragments by length so that their base sequence can be read off the gel (more in unit 10).
The entire genomes of thousands of species have now been
sequenced, allowing more detailed phylogenies to be deduced.
By 2016, the genomes of some 1,000 eukaryotic species and
10,000 prokaryotic species had been published. There are a
number of projects to organise the sequencing of different
groups of life on Earth. For example the Global Genome
Initiative aims to sequence at least one species from every one
of the 9,500 known animal and plant families.
Using DNA Sequences for Classification
By comparing the DNA sequences from two different living species we can determine their relatedness.
The more similar the two sequences the more closely related the species are. This is because over long
periods of evolutionary time DNA slowly accumulates random mutations.
 Closely-related living species have similar DNA sequences because they have a recent common ancestor
so their DNA has only had a short time to accumulate different mutations.
 More distantly related species have more different sequences because their common ancestor lived
longer ago so their DNA has had more time to accumulate different mutations.
Because the DNA mutations happen at a steady and predictable rate, the number of differences in DNA
sequences can be used as a molecular clock to estimate the
time since the last common ancestor. For example, the gene
for the protein cytochrome C mutates at an average rate of
1 base every 4 million years, so if two living species have 3
bases differences in their genes for cytochrome C, they must
have diverged about 12 million years ago.
Various genes are commonly used to compare species:
 The gene for the blood protein haemoglobin is found in all animals.
 The gene for the respiratory enzyme cytochrome C is found in all eukaryotes.
 The gene for the small subunit ribosomal RNA molecule (16S rRNA) is found in all known organisms.
HGS Biology A-level notes
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A Level Biology Unit 5
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This 16S rRNA molecule is ideal for classification studies because it and accumulates mutations only very
slowly (since its role is so fundamental), so its sequence can be compared over long periods of time. The
16S rRNA gene is only about 1500 bases long, small enough to be sequenced easily using early, crude
sequencing techniques but also large enough to retain organism-specific information.
Bioinformatics
These genome sequences represent vast amounts of data. Bioinformatics is a new branch of biology
concerned with storing, analysing, using and making sense of all that biological data. The sheer quantity of
data is so large that the field has required the development of powerful new computers; novel mathematical
algorithms for searching and analysing the databases; and statistical analysis techniques. All
new DNA sequences are deposited in the international database GenBank, which is
maintained by the US National Centre for Biotechnology Information (NCBI). Anyone can
access and search GenBank, and NCBI provides numerous tools for searching and analysing
sequence data.
Some of the goals of bioinformatics are:
 to assemble large complete genome sequences from the sequences of the short fragments used in
sequencing machines.
 to compare the DNA sequences of different species, in order to draw phylogenetic trees and deduce
evolutionary history.
 to find genes within a sequence of DNA, by comparison with known genes.
 to predict the amino acid sequence of proteins from their gene sequence and so predict the protein’s
structure and even function.
 to develop interesting and informative new ways of visualising all this complex data.
 to design new drugs and enzyme inhibitors
DNA and human classification
Comparison of DNA sequences have led to a new phylogeny for humans. It used to be thought that
humans were separate from all other apes, but we now know that humans are closely related to
chimpanzees, and indeed some taxonomists think that humans should be reclassified as the "third
chimpanzee":
HGS Biology A-level notes
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A Level Biology Unit 5
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Classifying Life on Earth
Many different systems have been tried to classify life on Earth as this chart shows:
1735
Linnaeus
1866
Haeckel
1938
Copeland
1969
Whittaker
1990
Woese
2 kingdoms
3 kingdoms
4 kingdoms
5 kingdoms
3 domains
Monera
Prokaryota
Protoctista
Protoctista
Protista
Fungi
Fungi
Plantae
Plantae
Animalia
Animalia
Protista
Vegetabile
Plantae
Plantae
Animale
Animalia
Animalia
Bacteria
Bacteria
Archaebacteria
Archaea
Eucarya
From Greek times until the 19th century, living things have been divided into just two groups: animals (if
they moved) and vegetables (if they didn’t). The great German biologist Haeckel first introduced a kingdom
of microbes (called Protista), and in the 20th century the division between prokaryotes and eukaryotes was
finally recognised. In the 1960s the American biologist Whittaker introduced a 5 kingdom system, which
has proved to be influential and is still the system most used in biology education.
Five Kingdoms
The five kingdoms are: prokaryotae (or monera), protoctista (or protista), fungi, plantae and animalia. This
table summarises the main features of each kingdom, and the diagram on the next page shows a few of the
main phyla. The three “higher” kingdoms are defined mainly by their niches: absorption for fungi,
production for plants and consumption for animals. The protoctista kingdom is not well defined, and simply
contains all the eukaryotes that aren’t animals, plants or fungi.
Kingdom
Prokaryotae
Kingdom
Protoctista
Kingdom
Fungi
Kingdom
Plantae
Kingdom
Animalia
prokaryotic
eukaryotic
eukaryotic
eukaryotic
eukaryotic
Complexity
unicellular or
colonial
unicellular or
multicellular
mostly
multicellular
multicellular
with
differentiation
multicellular
with extensive
differentiation
Cell wall
peptidoglycan
varied
chitin
cellulose
none
Nutrition
very varied
varied
absorption
photosynthesis
ingestion
Life Cycle
asexual
varied
haploid
dominant
alternating
diploid-haploid
diploid dominant
Characteristic
Cell type
HGS Biology A-level notes
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A Level Biology Unit 5
HGS Biology A-level notes
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Three Domains
In the 1970s the American microbiologist Carl Woese realised that there was enormous diversity within
the prokaryote kingdom and proposed that it be split in two. Furthermore the differences between the two
groups of prokaryotes were even bigger than the differences between the prokaryotes and the eukaryotes.
Woese therefore proposed that all life should be divided into three domains: The Archaea (or ancient life);
the Bacteria (or true bacteria) and the Eukarya (or eukaryotes).
In the simplest version of the three domain classification (shown above), the domains Archaea and Bacteria
contain one kingdom each, while the domain Eukarya contains the four eukaryotic kingdoms. However,
DNA studies are showing that few of the traditional kingdoms are phylogenetically correct, so biologists
are moving to a more accurate phylogenetic tree like this:
The principle differences between the three domains are summarised in this table:
Bacteria
Archaea
Eukarya
nucleus and organelles
none
none
present
Ribosomes
70S
70S
80S
introns
no
sometimes
frequent
formyl-methionine
methionine
methionine
yes
no
no
10 polypeptides
5 polypeptides
12 polypeptides
circular without histones
circular with histones
linear with histones
peptidoglycan
proteinaceous S-layer
cellulose/chitin
D-glycerol, ester link
L-glycerol, ether link
D-glycerol, ester link
initiator amino acid
sensitive to antibiotics
RNA polymerase
DNA
cell wall
membrane phospholipids
HGS Biology A-level notes
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A Level Biology Unit 5
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The Archaea
The initial classification of the Archea as a separate domain was based on the sequences of the 16S rRNA
gene, which was very different from both eukaryotes and bacteria. Further study has shown that the
Archaea share some features with bacteria (they’re both prokaryotes and have 70S ribosomes) and some
features with the Eukarya (they use the same enzymes for transcription and translation). But some features
are unique to the Archaea domain. For example the Archaea have a unique phospholipid in their cell
membranes:
Many of the Archaea are extremophiles i.e. they live in extreme environments. They include:
Thermophiles
Cells that live in environments hotter than 60°C, such as hot springs and deep-sea
thermal vents. The current record for the hottest growth temperature is 122°C, for
Methanopyrus kandleri.
Psychrophiles
Cells that live in environments colder than -15°C, such as permafrost and polar ice.
Halophiles
Cells that live in environments with a salt concentration higher than 15% (compared
to 3% in seawater), such as the Dead Sea in Israel and the Great Salt Lake in Utah.
Acidophiles and
Alkaliphiles
Cells that live in environments with pH<3 or pH>9 respectively.
Barophiles
Cells that live in environments under high pressure, such as deep oceans with
pressures exceeding 300 atmospheres.
Xerophiles
Cells that live in very dry environments, such as arid desert soils and rocks.
The Archea play an important role in both the carbon and nitrogen cycles. The nitrogen fixing bacteria and
the nitrifying bacteria are Archeans. The methanogens use a unique respiration that reduces carbon dioxide
to methane using hydrogen gas.
CO2 + 4H2 → CH4 + 2H2O
These methanogens are obligate anaerobes, poisoned by traces of oxygen. They are found in swamps,
marshes, and the intestines of mammals, and are responsible for creating natural gas and the methane gas
that is currently contributing to the greenhouse effect.
HGS Biology A-level notes
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A Level Biology Unit 5
page 12
Evolution and Natural Selection
We have seen that there are millions of different species currently living on our planet. Each species is
different and has found a unique way of living; of solving the problems of surviving and reproducing
successfully. Where did all this diversity come from?
17th Century
Most people believed in Creationism, which considered that all life was created just as it
is now. This was not based on any evidence, but was instead a belief.
18th Century
Naturalists began systematic classification systems and noticed that groups of living
things had similar characteristics and appeared to be related. So their classifications
looked a bit like family trees.
European naturalists travelled more widely and discovered more fossils, which clearly
showed that living things had changed over time, so were not always the same.
Extinctions were also observed (e.g. dodo), so species were not fixed.
Selective
breeding was widely practised and it was realised that species (like crops, working dogs,
racing pigeons) could be changed dramatically by selection.
19th Century
Lamark (1809) proposed a hypothesis that living things changed by inheriting acquired
characteristics. e.g. giraffes stretched their necks to reach food, and their offspring
inherited stretched necks. This is now known to be wrong, since many experiments (and
experience) have shown that acquired characteristics are not inherited. Nevertheless
Lamark's theory was one of the first to admit that species changed, and to try to explain
the change.
Charles Darwin (1859) published "On the origin of
species by means of natural selection, or the preservation of
favoured races in the struggle for life", which proposed
the idea of natural selection, a far better explanation
for the changes in species. “Origin” has since been
recognised as one of the most important books ever
written. A very similar theory was also proposed by
Alfred Wallace, and Darwin and Wallace agreed to
publish at the same time.
20th Century
Mendel’s work on genetics was rediscovered and combined with Darwin’s theory to
form modern Darwinism. Many new techniques, like fossil dating, DNA sequencing,
molecular biology, microbiology and mathematical modelling, gradually formed an
extensive and overwhelming body of experimental evidence for Darwinism.
HGS Biology A-level notes
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A Level Biology Unit 5
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Darwin's Theory of Evolution by Natural Selection
Darwin observed that most organisms have far more offspring than survive to maturity – most organisms
die young from predation, disease and competition, so that populations are usually fairly constant in size.
Darwin realised that the organisms that die young were not random, but were selected by their
characteristics. He concluded that individuals that were better adapted to their environment compete
better than the others, survive longer and reproduce more, so passing on more of their successful genes to
the next generation.
Darwin explained the giraffe's long neck as follows:
1. In a population of horse-like animals there would be random genetic variation in neck length.
2. Animals with long necks were slightly better adapted as they could reach more leaves, and so were
better-nourished. These longer-necked animals lived longer, through more breeding seasons, and so had
more offspring.
3. The shorter-necked animals would be more likely to lose the competition for food, so would be poorly
nourished and would probably die young from predation or disease. They would have few, if any,
offspring.
4. So in the next generation there were more long-neck alleles than short-neck alleles in the population. If
this continued over very many generations, then in time the frequency of long-neck alleles would
increase and so the average neck length would increase.
[Today it is thought more likely that the selection was for long legs to run away from predators faster, and
if you have long legs you need a long neck to be able to drink. But the process of selection is just the same.]
Darwin wasn't the first to suggest evolution of species, but he was the first to suggest a plausible
mechanism for the evolution - natural selection, and to provide a wealth of evidence for it. Darwin used
the analogy of selective breeding (or artificial selection) to explain natural selection. In selective breeding,
desirable characteristics are chosen by humans, and only those individuals with the best characteristics are
used for breeding. In this way species can be changed over a period of time. All domesticated species of
animal and plant have been selectively bred like this, often for thousands of years, so that most of the
animals and plants we are most familiar with are not really natural and are nothing like their wild relatives
(if any exist). The analogy between artificial and natural selection is a very good one, but there is one
important difference - Humans have a goal in mind; nature does not.
Summary of Natural Selection
1. There is genetic variation in characteristics within a population
2. Individuals with characteristics that make them less well adapted to their environment will die young
from predation, disease or competition, so they will not pass on their alleles.
3. Individuals with characteristics that make them well adapted to their environment will live longer and
reproduce, passing on their alleles to their offspring.
4. The allele frequency will change in each generation.
HGS Biology A-level notes
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A Level Biology Unit 5
page 14
Natural Selection and Adaptation
The result of Natural Selection is that organisms who survive are well-adapted to their ecological niche. A
species’ niche means its role in its particular habitat. This role might include its position in the food chain
(producer, herbivore, predator, parasite); its use of resources (e.g. to build nests); its method of
reproduction (e.g. coloured flowers to attract insects); its contribution to matter cycles (e.g. nitrogen
fixing, decomposer); etc.
Successful organisms have features (called adaptations or adaptive traits) that make them good at surviving
in their niche, because natural selection has selected for these traits, so these traits help the organism to
survive and reproduce. These adaptive traits can take different forms:
 Anatomical adaptations. For example a cactus plant has tiny spine-shaped leaves, large roots and a
swollen stem to allow it to survive in a dry habitat.
 Physiological adaptations. For example the thermophilic archaea have special proteins and
membrane lipids that are stable at high temperatures and do not denature like normal proteins.
 Behavioural adaptations. For example the mating behaviour of many birds (including singing, dancing
and nest-building) help them to find a mate and so reproduce successfully.
All these adaptations arose by means of natural selection. Note that you can’t say that an individual
organism adapts to its surroundings in the way that a human might adapt to a new job. The process of
biological adaptation (developing adaptive traits like wings) applies to whole populations and takes place
gradually over long, evolutionary timescales of hundreds of thousands of years. An organism can be adapted
to its niche, or have an adaptation, but it can’t become adapted, and certainly not in its lifetime.
Adaptive traits give the appearance of design, but this is misleading and in fact close examination often
reveal design flaws. For example the vertebrate eye is an anatomical adaptation that has the appearance of
being designed, but the retina is actually rather poor, with an unnecessary blind spot. The explanation for
this poor design is that the eye was created by evolution from simpler structures, not designed from
scratch.
HGS Biology A-level notes
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A Level Biology Unit 5
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Examples of Natural Selection
We’ll look at some examples of natural selection in action. In fact most things you’ll study in the biology
course (like protein structure, lung anatomy, the nitrogen cycle, disease, anything) are examples of natural
selection. It has been said that nothing in biology makes sense, except in the light of evolution.
Bacterial resistance to antibiotics.
We learnt in Unit 2 how antibiotics kill bacteria, but now some antibiotics no longer work because the
bacteria are resistant to them. This resistance is a good example of natural selection. Sometimes, at
random, mutations occur when bacterial DNA is replicated. These mutations may have any effect (and
most will be fatal), but just occasionally a mutation occurs that makes that bacterium resistant to an
antibiotic. For example the mutation might modify an enzyme so that it can bind and hydrolyse penicillin – it
is a penicillinase enzyme. So this cell is now resistant to penicillin. What happens next?
Imagine the mutation happened in a bacterial cell living in
your gut. The mutated cell will reproduce by binary fission
and pass on its resistance gene to its offspring, forming a new
strain of bacteria in your gut. If there is no antibiotic present
in your gut (most likely) this mutated strain may well die out
due to competition with all the other bacteria, and the
mutation will be lost again. However, if you are taking
penicillin, then penicillin will be present in the bacteria's
environment, and these mutated cells are now at a selective
advantage: the antibiotic kills all the normal bacterial cells,
leaving only the mutant cells alive. These cells can then
reproduce rapidly without competition and will colonise the
whole environment. The mutant cells have been selected by the environment and so the frequency of the
resistance allele in the population will increase. Remember that the original mutation is a random event, not
caused by the presence of the antibiotic, but the spread of the allele is due to selection by an antibiotic-rich
environment.
There are now so many strains of antibiotic-resistant bacteria that it is getting more difficult to treat
disease. One of the most famous is MRSA (methicillin-resistant Staphylococcus aureus), a bacterium
responsible for a variety of diseases from staphylococcal food poisoning to toxic shock syndrome, and now
resistant to penicillin, methicillin and vancomycin. These bacteria are effectively untreatable at present. The
best solution is to minimise the use of antibiotics so that the resistant strain has no selective advantage, and
may die out.
HGS Biology A-level notes
NCM/2/16
A Level Biology Unit 5
page 16
Lactose tolerance in humans.
Some people are lactose intolerant, and feel ill (including diarrhoea and vomiting) when they drink milk. In
fact globally most human adults are lactose intolerant and this is the normal condition: lactose tolerance in
adults is a mutation. All infant mammals make lactase to digest lactose in their mother’s milk, and they all
stop producing lactase after they are weaned (its production is switched off at about age four in most
humans).
Around 10,000 years ago humans gradually changed from being mainly hunter-gatherers to being mainly
farmers, and for the first time animal milk was available as a food source. Humans who, through a chance
mutation, could drink milk without feeling ill were at an advantage, as they could supplement their normal
diet with milk in harsh times (and farming was very unreliable in the early days). By natural selection they
survived and their genes spread in their populations. As a result, in human societies that adopted pastoral
(animal) farming (such as most Europeans, northern Indians and some Africans), people are generally
lactose tolerant today, while the rest (most Asians, Africans, native Americans and Australians) remain
lactose intolerant as adults.
HIV resistance in humans.
The AIDS virus HIV first arose in human populations in the 1930s in West Africa, where it spread from
primates through the practice of killing and eating “bush meat”. Since then it has gradually spread around
the world. Why is HIV so fatal to humans, but has so little effect on chimps? It turns out that chimps are
resistant because they have a protein (called CCL3) that stops HIV entering and infecting white blood cells.
Humans have this protein too, and it seems that the more copies of the gene for CCL3 you have, the more
resistant you are to HIV. Chimps have
on average 11 copies of the CCL3 gene,
African humans have on average 6
copies, and non-African humans have on
average 2 copies. In Africa people who,
by chance, have many copies are
favoured and will reproduce, while
those with few copies die young without
reproducing. So natural selection in
humans explains the frequency of the
CCL3 gene. A thousand years in the
future, if we have not developed a medical cure for HIV, the whole human population will probably have
evolved to possess around 11 copies of CCL3.
HGS Biology A-level notes
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A Level Biology Unit 5
page 17
Speciation – The Origin of New Species
We’ve seen how species can change through natural selection, but how does this change lead to new
species? The simple answer is that new species are formed when an existing species splits into two separate
groups. Remember the definition of a species: members of the same species can breed together to produce
fertile offspring but cannot breed with members of other species. So for the two groups to become two
different species they must be reproductively isolated, so that there is no mixing of genes between them
If members of the two groups can still interbreed If interbreeding between the two groups is
then there will be gene flow between them and they somehow prevented, then there is no gene flow and
will not be reproductively isolated. They will remain the two groups are reproductively isolated. They
members of the same species.
could become different species.
There are many ways that reproductive isolation can come about, but they are grouped into two methods:
allopatric speciation and sympatric speciation.
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Allopatric Speciation
Allopatric speciation happens when two populations of the same species become geographically separated
(allopatric literally means “different fatherland”). This is by far the most common kind of speciation.
1. Start with an interbreeding population of one species.
2. The population becomes divided by a physical barrier such as water,
mountains, desert, or just a large distance. This can happen in various ways:
 When some of the population migrates or is dispersed to a new area, such
as an isolated island or the other side of a mountain or large river. The
dispersal must be over an unusually large distance so that it is not
repeated and the new group remains isolated. Land birds, insect and plant
seeds can be carried unusually large distances in a storm and small animals
can unintentionally “raft” across oceans on fallen trees. Isolated islands like
Madagascar, Hawaii and the Galapagos were colonised this way.
 When the geography changes catastrophically e.g. an earthquake could
create an impassable rift; the lava flow from a volcano could create an
impassable barrier, rising sea level could create islands; or falling sea level
could isolate lakes.
 When the geography changes gradually e.g. erosion could create a deep
valley like the Grand Canyon; plate tectonic movements cause whole
continents to move apart (which explains why similar species are found in
South America and Africa).
The isolated population could be as small as a few seeds or a single pregnant
female. The populations must be reproductively isolated, so that there is no
gene flow between the groups.
3. If the environments (abiotic or biotic) are different in the two places (and
they almost certainly will be), then different characteristics will be selected by
natural selection and the two populations will evolve differently. Even if the
environments are similar, the populations may still change by random genetic
drift, especially if the population is small (unit 10). The allele frequencies in
the two populations will become different.
4. Much later, if the barrier is now removed and the two populations meet
again, they are now so different that they can no longer interbreed. They
therefore remain reproductively isolated and are two distinct species. They
may both be different from the original species, if it still exists elsewhere.
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A Level Biology Unit 5
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Sympatric Speciation
Sympatric speciation happens when two populations of the same species become reproductively isolated
even though they share the same geographical location (sympatric literally means “same fatherland”). It is
much rarer than allopatric speciation. How can two groups of the same species in the same place be
reproductively isolated?
1. Ecological isolation. Populations can become reproductively isolated if they develop different niches
within the same area. A well-described example of this is the fruit fly Rhagoletis pomonella in the United
States. The original species lives on hawthorn bushes, but a new population has arisen that feeds on
apple trees instead. This new population arose from a mutant fly that was able to digest apples and now
the population of “apple flies” has a new niche in apple orchards so are effectively isolated from the
“hawthorn flies”. This isolation means the two populations are evolving independently and have already
altered their breeding seasons to match the different fruiting seasons of the two plants. They have
become two separate species in the same geographical area.
2. Behavioural isolation. Populations can become reproductively isolated if they develop different
courtship behaviours. Normally courtship behaviour (such as plumage, dance displays and songs in
birds) allows members of the same species to identify themselves and synchronise mating. Mutant birds
with a different-coloured plumage will be reproductively isolated from other birds in the same area
because they will not attract mates.
3. Temporal isolation. Populations can become reproductively isolated if the timing of their
reproductive season changes. Examples include plants that flower at different times, insects that pupate
at different times or mammals that come into oestrus at different times.
4. Mechanical isolation. Populations can become reproductively isolated if their anatomy or chemistry
changes so that mating is impossible. For example plants can’t interbreed if their flowers are different
shapes so the same insects can’t visit them to transfer pollen. As we saw in unit 3, pollen grains are
stimulated to germinate on the stigma by particular chemicals that are unique to that species. If the
chemicals on a plant stigma change, pollen will not germinate and that plant will be reproductively
isolated (though it may be able to self-fertilise).
5. Genetic isolation. Populations can become reproductively isolated if their genes change so that
embryos cannot develop, even if mating is possible. The chromosomes of the embryo may not
replicate; mitosis may not take place correctly or genes required for embryo development may not be
present. Mating does not lead to viable offspring, so the two populations are reproductively isolated.
6. Hybrid sterility. This is a particular example of genetic isolation, where a hybrid is born but is sterile,
so can’t itself reproduce. This stops the flow of genes so the two parent groups are still genetically
isolated. This is why the states that members of the same species can breed together to produce fertile
offspring. A famous example of hybrid sterility is the mule. A mule is the offspring of a male donkey
(n=31) and a female horse (n=32).
Mules therefore have 63 chromosomes, which can’t form
homologous pairs in meiosis, so mules can’t make gametes and are infertile.
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Summary of Speciation
1. A population becomes separated into two groups that are reproductively isolated, so that there is no
gene flow between the groups. The isolation can be geographical (allopatric) or some other method
(sympatric).
2. The two groups’ environments are different, so natural selection favours different characteristics.
3. The allele frequencies in the two groups will change in different ways.
4. Eventually the two populations will be unable to interbreed, so will be different species.
Populations of the same species that are currently isolated are called subspecies (or sometimes breeds,
varieties or races) and they may in time become distinct species, or they may remain an interbreeding
single species. It is meaningless to say that one species is absolutely better than another species, only that it
is better adapted to that particular environment. A species may be well-adapted to its environment, but if
the environment changes, then the species must evolve or die. In either case the original species will
become extinct. Since all environments change eventually, it is the fate of all species to become extinct
(including our own).
Deep Time and the Origin of Life
It takes time to evolve 100 million species and it is now known that the earth is 4,600 million years old. Life
(in the form of prokaryotic cells) arose quite quickly, and has existed for around 4,000 million years. These
huge spans of time are almost impossible to comprehend, and are often referred to as deep time. This
chart illustrates some of the events in the history of the Earth.
No one knows how life arose in the first place, but the conditions in the early Earth were very different
from now, and experiments have shown that biochemicals like amino acids and nucleotides could be
synthesised from inorganic molecules under primordial conditions. We saw in unit 1 how lipid bilayers can
form spontaneously, so perhaps that’s how cellular life arose.
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Biodiversity
Biodiversity simply means the variety of all the life on Earth. The 1992 United Nations Earth Summit in Rio
de Janeiro defined biodiversity as "the variability among living organisms from all sources, including, 'inter alia',
terrestrial, marine, and other aquatic ecosystems, and the ecological complexes of which they are part: this includes
diversity within species, between species and of ecosystems". This definition is adopted by the United Nations
Convention on Biological Diversity. There are thus three levels of biodiversity:
All three levels of biodiversity are important because all living organisms are inter-related and depend upon
each other in numerous ways. All three levels are also linked, for example genetic diversity is necessary to
maintain species diversity, and vice versa.
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Genetic Diversity
The gene pool of a species is defined as all the genes in that species. Members of the same species all have
the same genes, but different combinations of alleles. New alleles arise through mutation and existing alleles
are recombined by meiosis and random fertilisation during sexual reproduction so that every individual
within a species is genetically unique.
Genetic diversity of a species is defined as the number of different alleles within a species’ gene pool. We
can also talk about the genetic diversity of a particular gene, in which case it is the number of different
alleles of that gene in a population. By using modern genome sequencing techniques on a sample of
individuals in a population we can actually quantify the genetic diversity.
Genetic diversity is important because it is the basis of evolution and survival of a species. A species with a
high genetic diversity is likely to have some individuals with the characteristics required to survive a change
in the environment, so some members of the species will survive. Low genetic diversity means a species will
be unable to cope with environmental changes and so is more likely to become extinct. Genetic diversity is
generally higher in large populations and lower in small populations.
Genetic Erosion
Genetic Erosion refers to the loss of genetic diversity in wild and domesticated species. Genetic diversity is
dramatically reduced by selective breeding, since only a small number of alleles are selected. This means
that all domesticated farm animals and crops have low genetic diversity and are susceptible to disease and
other environmental changes. The issue is considered so serious that the United Nations Food and
Agriculture Organization (FAO) has set up a Commission on
Genetic Resources for Food and Agriculture to oversee the
management of animal genetic resources worldwide.
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Species Diversity
All the organisms living in a habitat are collectively called its community, and species diversity means the
variety of species in a community. Species diversity is useful because it tell us about the complexity, quality
and stability of an ecosystem.
The simplest measurement is just to count the number of species in the samples - the species richness.
However richness alone is not a good measure of diversity because it doesn’t take into account the size of
each species population – its abundance. For example a wild meadow and a wheat field might both have 25
species, but in the meadow the species are equally abundant, while in the wheat field 95% of all the plants
are the single species of wheat.
A good measure of diversity takes into account the species richness and their abundance. One common
measure is the Simpson Diversity Index (D):
Simpson
Diversity
Index
D
N(N  1)
 n( n  1)
where N = total number of individuals (total abundance)
n = number of individuals in each species
The higher the index, the higher the species diversity. A community where one species is dominant over
others has a lower diversity than one where the species are more equitable. For example these two
communities each have 100 individuals in 3 species:
(a)
species
A
B
C
total
abundance
90
5
5
100
n(n-1)
8010
20
20
D=
(100 × 99)
= 1.23
8050
8050
(b)
species
abundance
n(n-1)
A
34
1122
(100 × 99)
B
33
1056
D=
= 3.06
3234
C
33
1056
total
100
3234
So (b) is more diverse than (a). A few dominant species tend to decrease the diversity index.
Harsh habitats tend to have low species diversity, as only a few species are adapted to the harsh
environment. Mild habitats support a high species diversity. The many plant species will lead to high
productivity (due to a lot of photosynthesis), which will support a large, complex food web.
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Conservation
Human activities are reducing biodiversity at all three levels. Ecosystem diversity is reduced by
deforestation, mining and building; species diversity is reduced by farming, hunting and habitat destruction;
and genetic diversity is reduced by selective breeding and competition with humans. Understanding our
impact on biodiversity has led to conservation – the attempt to conserve biodiversity worldwide.
Conservation applies to all three levels. The global gene pool is a resource for learning more about life on
Earth, and some genes may be able to provide us with useful products for medicine and biotechnology. To
maintain the gene pool we need to preserve species diversity and to conserve species diversity we must
provide suitable niches for all species by preserving habitat diversity.
Conservationists recognise that humans need to exploit the natural world in order to survive. So the aim of
conservation today is not to preserve pristine untouched nature, but is the management of our
environment to keep the land as a productive resource, but in a sustainable way that maintains biodiversity
and will continue to do so in the future for all our descendants.
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Justifying Conservation
Why is conservation important? There are ethical and economic reasons.
Ethical reasons
In conservation there are no simple answers and decisions are based on a balance between opposing views,
for example:

the needs of humans to use and exploit nature for our survival

the needs of other animals to live their lives without human interference

the needs of humans to enjoy the natural beauty of untouched nature

the needs of our descendants to enjoy or use ecosystems as we do

the needs of everyone on the planet to avoid catastrophes such as global warming or mass extinctions
Economic reasons
Conservation is expensive, and, in order to persuade governments and businesses to take an interest, the
concept of Ecosystem Services has been devised. The aim of ecosystem services is to teach politicians and
other non-scientists some basic ecology and make them more aware of the benefits of the natural world
and so hopefully to encourage them to put effort and money into conserving them. Ecosystem services are
grouped into four categories:
1. Supporting services. These include the basic functions of all ecosystems, such as nutrient cycling,
primary production (photosynthesis), decay and soil formation. These functions underlie everything else.
2. Regulating services. These are also basic functions of all ecosystems, framed so as to emphasise their
importance in regulating the natural world. They include the carbon cycle (including its impact on
climate change); decay (including sewage treatment to provide clean water); predator-prey interactions
(used to control pests and pathogens).
3. Provisioning services. These are all the useful products humans obtain from the natural world,
including: food; water; raw materials for building, clothing and industry; minerals (including fossil fuels,
metal ores, jewels and raw materials for the chemical industry); medicinal resources (including
pharmaceuticals and microbes); genetic resources (i.e. genes that can be used in biotechnology); and
energy (including biomass fuels, natural gas, hydro-electric power, etc.).
4. Cultural services. These are the non-material benefits nature provides for people, including recreation
(e.g. sports and tourism); education and cultural (e.g. inspiration for literature or art).
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In-Situ Conservation
In-situ conservation means conserving whole natural ecosystems and the various species they contain. In
practice this means setting up Protected Areas, such as National Parks. In-situ conservation automatically
means protecting all three levels of biodiversity – ecosystem, species and genetic.
The International Union for the Conservation of Nature (IUCN) oversees the
organisation and classification of Protected Areas worldwide. Almost every country in the
world has set up Protected Areas to conserve local habitats and their wildlife. There are
over 161,000 protected areas in the world with more added daily, representing about
15% of the world's land surface area and 1% of the world's oceans. There are laws forbidding or controlling
human activities like building, hunting, farming, mining, industry and other exploitation of Protected Areas,
though the specific limitations vary enormously depending of the area. Tourism and education are generally
encouraged, though with strict controls.
In the UK Protected Areas include: National Parks (NP); Environmentally Sensitive Areas (ESA); Sites of
Special Scientific Interest (SSSI); Marine Nature Reserves (MNR); National Nature Reserves (NNR); Local
Nature Reserves; Ramsar Wetland Sites (RWS); and World Heritage Sites (WHS). There are 15 National
Parks in the UK, and, in contrast to National Parks in other countries, considerable human activity is
allowed in National Parks, including farming and towns. The aim is to allow economic development while
still protecting the countryside.
Advantages of in-situ conservation
 When a habitat is conserved the whole community is conserved with it, including invertebrates, plants,
fungi and microbes.
 Large numbers of animals and plants can be conserved in-situ, with a correspondingly large genetic
diversity.
 Young animals learn natural skills from families and social groups in their natural environment.
 Reserves are safe environments to re-introduce animals from captive (ex-situ) breeding programs.
 Reserves can be popular tourist destinations, which helps to fund them and to educate visitors.
Disadvantages of in-situ conservation
 Many important protected areas are in poor countries, and it can be expensive to maintain and protect
a large area.
 Commercial and political interests (e.g. poachers, loggers, farmers, miners) often compete with
conservation interest, and often win.
 Tourist income can be limited as parks can be expensive to visit.
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Ex-Situ Conservation
Ex-situ conservation means conserving species away from their natural habitats.
In practice this means collecting specimens in zoos, aquaria, botanical gardens,
seed banks and gene banks. Zoos were originally established for entertainment,
but now serve the more useful functions of education and conservation.
International breeding programs allow endangered species to reproduce safely
in captivity and, where possible, released into the wild. Zoos keep electronic
studbooks containing genealogical and genetic data on their animals. These studbooks allow the best
matings to be arranged between animals held in different zoos, to maximise genetic diversity.
Endangered plants may be grown in botanical gardens, and can also be preserved in seed banks, where
samples of seeds are dried and preserved cryogenically at -40°C. Large numbers of seeds can be preserved
this way for centuries without losing their fertility. The Millennium Seed
Bank (MSB), run by the Royal Botanic Gardens, Kew, currently (2015) holds
nearly 2 billion seeds from 34,088 wild plant species. Their aim is to
conserve the seeds from 75,000 species of plants (25% of known plants) by 2020, including all the UK’s
native plants. There is now an attempt to preserve endangered animal species in gene banks, by storing
embryos cryogenically.
Advantages of ex-situ conservation
 Animals that endangered in the wild can be protected in zoos.
 We-managed breeding programs can maintain and even improve genetic diversity.
 Animals in zoos have a longer life expectancy than in the wild.
 Since zoos are cheap and easily-accessible, they attract large numbers of visitors, which helps to raise
funds and provides an excellent opportunity to educate many people in the importance of conservation
work.
Disadvantages of ex-situ conservation
 Only a small number of animals and plants can be conserved ex-situ, with a correspondingly limited
genetic diversity.
 The zoo environment can be small and unnatural for large animals and they do not have the same social
interactions. Some of these limitations can be addressed in larger wildlife parks.
 Young animals do not learn natural skills from observing families and peers in their natural environment.
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