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Biodiversity, classification and conservation (chapter 18):

 A species is a group of organisms with similar morphological, physiological, biochemical

and behavioural features, which can breed together naturally to produce fertile offspring,
and are reproductively isolated from other species
 An ecosystem is a relatively self-contained, interacting community of organisms, and the
environment in which they live and with which they interact
 A niche is the role of an organism in an ecosystem
 Biodiversity can be defined as the degree of variation of life forms in an ecosystem,
considered at three different levels:
 The variation in ecosystems or habitats
 The number of different species in the ecosystem and their relative abundance
 Species diversity takes species richness (number of species in a community)
and a measure of the evenness of the abundance of the different species
 Ecosystems with high species diversity tend to be more stable than ones
with limited diversity (more able to resist change)
 The genetic variation within each species
 Genetic diversity is the diversity of alleles within the genes in the genome of
a single species
 Important in providing populations with the ability to adapt to changes in
biotic (caused by living organisms) and abiotic (physical characteristic of a
habitat) factors
 Sampling can be random or systematic
 Random sampling using frame quadrats:
 A quadrat is a square frame that marks off an area of ground, or water

 Samples must use random sampling technique to avoid any bias (Fig 18.8)
 Results can be used to calculate species frequency (measure of the chance of a
particular species being found in a particular quadrat) and species density (measure
of how many individuals per unit area)
 Either count the actual number of organisms (e.g. limpets on a rocky sea shore) or
estimate the percentage cover of each species (e.g. plant species in meadow)
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 Random sampling using mark-release-recapture technique:
 First a large number of animals is captured and marked in a way that will not affect
its chances of survival (e.g. patch of fur cut away or small spot of paint applied); the
number of marked animals recorded, returned to their habitat and left to mix
randomly with the rest of the population; given enough time, another large sample
is captured; number of marked and unmarked individuals is counted; the
proportion of the marked individual used to calculate an estimate of the total
number of population

 Simpson’s index of diversity:

 After collecting data about species abundance, species diversity can then be found
using Simpson’s index of diversity, D

 n is the total number of organisms of a particular species

 N is the total number of organisms of all species
 Values of D range from 0 (lowest species diversity) to 1 (highest species diversity)
 Comparisons should be made on a ‘like’ for ‘like’ basis (similar community and
organisms

 Systematic sampling is needed during investigations of species distribution in an area

where the physical conditions such as altitude, soil moisture, soil pH, light intensity or soil
type change
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 Systematic sampling using line and belt transects:
 Randomly select a starting point in a field and lat out a measuring tape in a straight
line
 Sample the organisms that are present along the line (transect), e.g. record the
identity of the organisms touching the line at set distances
 Line transect will provide qualitative data that can be represented as in Fig 18.11
 Belt transect technique by placing a quadrat at regular intervals along the line and
recording the abundance of each species within the quadrat

 Spearman’s rank correlation and Pearson’s linear correlation to analyse the relationships
between the distribution and abundance of species and abiotic or biotic factors
 Pearson’s linear correlation:
 Null hypothesis: there is no correlation (percentage cover) between A and B
 Given two species, P and Q in ten different 1 m2 quadrats:
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 Initially, plot a scatter graph (e.g. Fig P2.8, showing a possibility of a linear
correlation between them, hence to make sure, Pearson’s linear correlation test is
carried out)
 (this test can only be used if the data are interval data and are normally distributed)
 Formula given by:

The value should always work out

between -1 and +1

 The value of r lies close to 1, hence there is a positive correlation between the
numbers of species P and the numbers of species Q
 Spearman’s rank correlation:
 To find out whether there is a correlation between two sets of variables, when they
are not normally distributed
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 Initially, plot a scatter graph, to see whether there may be a correlation
 Given two species, R and S in 10 quadrats:

 Now rank each set of data, with the largest number ranked as 1; calculate the
differences in rank, D, by subtracting the rank of species S from species R; then
square each of these values; add them together to find total difference squared:

 0.93 is the correlation coefficient

 Using the values in Table P2.8 to find the critical value (0.05 baseline)
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 n = 10, the critical value = 0.65 (calculated value is much greater), hence there is a
significant correlation between the number of species R and the numbers of species
S
 Taxonomy is the study and practice of classification which involves placing the organisms in
a series of taxonomic units, or taxa, creating a hierarchy:

 The prokaryotes are divided between the domains Bacteria and Archaea (many live
in extreme conditions); eukaryotes are placed into the domain Eukarya
 Domain Bacteria:
 Prokaryotic cells (no nucleus)
 DNA exists as circular ‘chromosome’ and does not have histone proteins associated
with it
 Plasmids (smaller circular molecules of DNA) are often present
 No membrane-bound organelles (e.g. mitochondria, E.R., Golgi body, chloroplasts)
are present
 Ribosomes (70 S) are smaller than in eukaryotic cells
 Cell wall is always present and contains peptidoglycans
 Cells divide in binary fission (not mitosis)
 Usually exist as single cells or small group of cells
 Domain Archaea (archaeans):
 Prokaryotic cells (no nucleus)
 DNA exists as circular ‘chromosome’ and does not have histone proteins associated
with it
 Plasmids are often present
 No membrane-bound organelles are present
 Ribosomes (70 S) are smaller than in eukaryotic cells, but have features similar to
those of eukaryotic ribosomes
 Cell wall is always present, but does not contain peptidoglycans
 Cells divide in binary fission (not mitosis)
 Usually exist as single cells or small group of cells
 Metabolism similar to bacteria, but transcription common with eukaryotes
 Domain Eukarya:
 Cells with nuclei and membrane-bound organelles
 DNA in the nucleus arranged in linear chromosomes with histone proteins
 Ribosomes (80 S) in the cytosol larger than prokaryotes’; chloroplasts and
mitochondrial DNA have 70 S ribosomes
 Chloroplast and mitochondrial DNA is circular as in prokaryotes
 May be unicellular, colonial and multicellular organisms
 Cell division by mitosis
 Method of reproduction: asexual and sexual
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 4 kingdoms of Eukarya: kingdom Protoctista, Fungi, Plantae and Animalia
 Kingdom Protoctista:
 Any eukaryote that is not fungus, plant or animal is a protoctist
 Features:
 Eukaryotic
 Mostly single-celled, or exist as groups of similar cells
 Protozoa – having animal-like cells (no cell wall)
 Algae – having plant-like cells (cellulose cell walls and chloroplasts)
 Kingdom Fungi:
 Eukaryotic
 No chlorophyll (no photosynthesis)
 Heterotrophic nutrition – use organic compounds made by other organisms as their
source of energy and source of molecules for metabolism
 Reproduce by means of spores
 Simple body form (may be unicellular or made up of long threads called hypae
(with or without cross walls))
 Have cell walls made up of chitin or other substances (not cellulose)
 Does not have cilia or flagella
 Kingdom Plantae:
 Multicellular eukaryotes with cells that are differentiated to form tissues and
organs
 Few types of specialised cells
 Some cells have chloroplasts and photosynthesise
 Cells have large, often permanent vacuoles for support
 Autotrophic nutrition
 Cell walls are always present (made of cellulose)
 Cells may have flagella
 Kingdom Animalia:
 Multicellular eukaryotes with many different types of specialised cells
 Cells that are differentiated to form tissues and organs
 No chloroplasts (no photosynthesis)
 Small and temporary cell vacuoles ( e.g. lysosomes and vacuoles)
 Heterotrophic nutrition
 No cell walls
 Communication is by the nervous system
 Cells may have cilia or flagella
 Viruses:
 Acellular – no cellular structure like bacteria and fungi
 No features traditionally use for classification
 Infectious but has no metabolism
 Their taxonomic system is based on the type of nucleic acid they contain (DNA or
RNA), and whether the nucleic acid is single-stranded or double-stranded (DNA and
RNA)
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 Major threats to the biodiversity of aquatic and terrestrial ecosystems:
 Habitat loss and degradation of the environment
 E.g. clearing of land for agriculture housing, transport and industry removes
vegetation, leading to loss of habitats completely or habitat fragmentation
(divided into small areas); deforestation causes severe land degradation due
to soil erosion once the vegetation is removed
 Climate change
 Industrialisation and combustion of fossil fuels led an increase in the
concentrations of carbon dioxide and methane in the atmosphere
(greenhouse gases), causing disruptions in migration patterns of aquatic life,
acidification of oceans (coral reefs and molluscs), increase in ocean
temperature causes coral bleaching, rise in sea levels, and increase in
frequency of natural catastrophes
 Excessive use of fertilisers and industrial and domestic forms of pollution
 Enters food chain and causes disruptions, due to severe impacts on different
species
 Non-biodegradable plastics
 Fertilisers provide extra nutrients for producers (e.g. algae), algal bloom
causing eutrophication and increases toxicity; reduces biodiversity of coral
reefs
 Air pollution – acid rain (combustion of high sulfur content fuels), causing
destruction of vegetation and acidification of aquatic ecosystems,
decreasing biodiversity
 Overexploitation and unsustainable use of resources
 E.g. overfishing, removal of valuable trees by logging companies and
poaching
 Effects of invasive alien species on native species, especially endemics
 Reasons for the need to maintain biodiversity:
 Moral and ethical issues
 Ecological reasons
 The higher the diversity of an ecosystem, the less likely for it to be
unbalanced by change in environmental conditions or threats
 All organisms in an ecosystem interact in many ways, if one key species
disappears, the whole community will be affected
 Loss of drugs and fuels derived from living organisms
 Aesthetic reasons
 Ecotourism (wildlife) provides many countries’ income and employment
 Social and commercial reasons
 Decrease in genetic variety due to selective breeding of uniform, high
yielding crops and genetic modified crops – leading to major impacts due to
diseases
 Diversity of microbes as a source of many useful products: antibiotics and
enzymes
 Roles of conserved areas, zoos, ‘frozen zoos’, botanic gardens and seed banks in protecting
endangered species:
 Conserved areas (national parks and marine parks) – controlled by the government of a
country and protected by legislation:
 Maintaining the natural habitat, hence all the ‘life support systems’ are provided
 Protecting of the whole ecosystems threatened by human developments
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 Limiting human activities (strict limits on hunting, grazing farm animals or other
activities that might affect animals and plants living there)
 Alien species and invasive plants removed
 Raises awareness of important issues (education)
 Incentives to indigenous people
 Population monitoring
 Zoos:
 Captive breeding programmes
 Reintroduction programmes (difficulty in readjusting to the wild)
 Increase in genetic diversity
 (assisted reproduction is a solution to interbreeding problems)
 Sperm bank (transferring of species in between zoos):
 Collection and freezing of semen from males
 Checked for sperm activity; diluted with a buffer solution and albumen;
stored into straws, into liquid nitrogen
 Artificial insemination (AI) – embryo transfer and surrogacy – solves the problem of males
and females who do not show any courtship behaviour and will not mate:
 Straw placed into warm water causing ‘active’ sperms; placed into a catheter; and
inserted into the vagina; through the cervix into the uterus, leading to ovulation
 Following AI, the resulting embryo ‘flushed out’ of the uterus and transferred to
other females (surrogate mothers) that have had hormonal treatment to prepare
them for pregnancy
 Embryo transfer protects the endangered animal from the risks of pregnancy and
means that she can be a source of many offspring
 In vitro fertilisation (IVF):
 Oocytes (eggs) are collected by inserting a needle into the ovaries and withdrawing
some mature follicles; kept in culture medium for a short time; mixed with semen
in vitro; then divides to form embryos; frozen (similar to sperm) until a surrogate
mother becomes available
 The resulting oocytes divide to form embryos; cultured then placed into a female
species
 Eggs (oocytes) and embryos are stored much like sperm
 ‘Frozen zoo’:
 Holds genetic resources in the form of sperm, eggs and embryos from many
endangered animals until they might be needed
 Materials can be kept for a long period of time
 Botanic garden:
 Seeds or cutting are collected from species in the wild; used to build up the
population of plants to be reintroduced to their natural habitats
 Roles of botanic gardens:
 Protect endangered plant species
 Research methods of reproduction and growth
 Research conservation methods for new habitats
 Reintroduce species to habitats where it is extinct or rare
 Educate public on the roles of plants
 Seed bank:
 National and international organisations collect and store seeds from the world’s
plants (seeds from the same species collected from different sites, to contain a
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good proportion of the total gene pool for that species) to prevent losses in genetic
diversity in crop plants in cases of disasters
 Culling (killing of animals) and contraceptive methods (birth control and chemical
contraceptives – targeting zona pellucid (layer of glycoproteins around the egg) by
stimulating an immune response producing antibodies against it) used to prevent
overpopulation of protected and non-protected species
 Explain the reasons for controlling alien or invasive species:
 Successful predators with few controls
 Compete effectively with native organisms that occupy the same niche
 Introduce diseases that spread to similar organisms that have never been exposed
to the pathogens
 May cover large areas of water, blocks sunlight from reaching aquatic plants,
reducing the oxygen concentration of the water, killing the fishes
 Outcompetes native species by reducing the space in which they can grow
 E.g. the Burmese pythons which invaded the Everglades National Park in Florida,
which feeds on a wide variety of mammals and birds, competing with native
predators, where humans are its only predator
 Convention on International Trade in Endangered Species of Wild Flora and Fauna (CITES):
 Controls the trade in endangered species, and any products such as furs, skins and
ivory – countries signing an agreement
 Does this by considering the evidence presented to it about endangered species
and assigns them to one of the three Appendices (most endangered, less
endangered and request of the country)
 Species are reviewed by expert committees and the list is growing
 World Wide Fund for Nature (WWF):
 Campaign group for wildlife
 Largest non-governmental organisation (NGO) specialising in conservation
 Funds conservation projects, publicises environmental issues and campaigns to save
ecosystems from degradation and species from extinction
 Restoring degraded habitats:
 Conservation involves restoring degraded areas by natural catastrophes or human
activities
 Famers decide to plant trees on land that is no longer needed for food and
production or has become degraded by overuse
 Replanting of mangrove forests to coastal erosions, providing protections against
storm damages
 Tree planting projects by NGOs
 Reclamation projects such as Eden Project in Cornwall UK

Genetic engineering (Chapter 19):

 Genetic engineering involves the extraction of genes from one organism, or the synthesis
of genes, in order to place them in another organism (of the same or another species) such
that the receiving organism expresses the gene product
 Recombinant DNA: DNA made by joining pieces from two or more different sources
creating a transgenic organism or a genetically modified organism (GMO)
 An overview of gene transfer:
1. The gene that is required is identified, may be cut from a chromosome; made from
mRNA by reverse transcription or synthesised from nucleotides