Biodiversity and Conservation

Classification Systems

Why Classify Organisms?

Classification (taxonomy) is the science of grouping organisms based on shared characteristics. The purposes of classification include:

• Organising the vast diversity of life into manageable groups
• Identifying and naming organisms universally (using a standardised system)
• Revealing evolutionary relationships between organisms
• Facilitating communication among scientists worldwide
• Predicting characteristics of organisms based on their classification

The Five-Kingdom System

Proposed by Robert Whittaker (1969), this system classifies organisms into five kingdoms:

Kingdom	Cell Type	Nuclear Envelope	Cell Wall	Nutrition	Examples
Prokaryotae	Prokaryotic	Absent	Peptidoglycan	Heterotrophic/autotrophic	Bacteria, cyanobacteria
Protoctista	Eukaryotic	Present	Some have cellulose	Heterotrophic/autotrophic	Amoeba, Paramecium, algae
Fungi	Eukaryotic	Present	Chitin	Heterotrophic (absorptive)	Mushrooms, yeast, moulds
Plantae	Eukaryotic	Present	Cellulose	Autotrophic (photosynthetic)	Flowering plants, mosses, ferns
Animalia	Eukaryotic	Present	Absent	Heterotrophic (ingestive)	Insects, mammals, birds, fish

The Three-Domain System

Proposed by Carl Woese (1990) based on ribosomal RNA (rRNA) sequencing. This system recognises three domains above the kingdom level:

Domain	Description	Kingdoms Included	Cell Type
Bacteria	Prokaryotic; single circular chromosome; peptidoglycan cell wall; unbranched lipids in membrane	Eubacteria (true bacteria)	Prokaryotic
Archaea	Prokaryotic; no peptidoglycan; branched lipids in membrane; often extremophiles	Archaebacteria	Prokaryotic
Eukarya	Eukaryotic; true nucleus; membrane-bound organelles; linear chromosomes	Protoctista, Fungi, Plantae, Animalia	Eukaryotic

Key distinction between Bacteria and Archaea:

• Archaea lack peptidoglycan in their cell walls (they have pseudopeptidoglycan or other polymers)
• Archaea have branched isoprenoid lipids in their cell membranes (bacteria have unbranched fatty acids)
• Archaea are often found in extreme environments (extremophiles): thermophiles (hot), halophiles (salty), methanogens (anaerobic, produce methane)
• Archaea are more closely related to Eukarya than to Bacteria (based on rRNA sequences)

Binomial Nomenclature

Definition: Binomial nomenclature is the formal system of naming species using two Latinised names: the genus name and the specific epithet.

Rules:

1. The genus name is capitalised (e.g., Homo)
2. The specific epithet is lowercase (e.g., sapiens)
3. Both names are italicised (or underlined if handwritten)
4. The full name is written as: Genus species (e.g., Homo sapiens)
5. After the first mention in a document, the genus may be abbreviated (e.g., H. sapiens)
6. The name should describe a characteristic of the organism, its geographic origin, or honour a person

Examples:

Organism	Full Name	Meaning
Human	Homo sapiens	"Wise man"
Domestic dog	Canis lupus familiaris	Subspecies of the grey wolf
Common housefly	Musca domestica	"Domestic fly"
Rice	Oryza sativa	"Cultivated rice"
Escherichia coli	Escherichia coli	Named after Theodor Escherich; found in the colon

Taxonomic hierarchy:

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

Mnemonic: "David King Plays Chess On Fine Glass Stools"

As you move down the hierarchy, the groups become smaller and the organisms within each group are more closely related.

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Biodiversity Measurement

What is Biodiversity?

Biodiversity (biological diversity) is the variety of life at all levels of biological organisation, including:

• Genetic diversity: Variation in alleles and genes within a species or population
• Species diversity: The number of different species and their relative abundances in a community
• Ecosystem diversity: The range of different habitats and ecological processes

Species Richness and Species Evenness

Species richness: The number of different species in a community. A community with 50 species has higher species richness than one with 10 species.

Species evenness: A measure of how evenly individuals are distributed among the different species. A community where all species have similar abundances has high evenness. A community dominated by one or a few species has low evenness.

Example:

Community A: 10 species, each with 10 individuals (richness = 10, evenness = high)

Community B: 10 species, but one species has 91 individuals and the other 9 have 1 individual each (richness = 10, evenness = low)

Both communities have the same species richness (10), but Community A has higher species evenness and therefore higher overall species diversity.

Simpson's Diversity Index

Simpson's Diversity Index (D) is a quantitative measure of biodiversity that takes both species richness and species evenness into account.

$D = 1 - \frac{\sum n(n-1)}{N(N-1)}$

Where:

• $n$ = the number of individuals of a particular species
• $N$ = the total number of individuals of all species

Interpretation:

• $D$ ranges from 0 to 1
• $D = 0$: infinite diversity (theoretical)
• $D$ close to 1: high diversity (many species, evenly distributed)
• $D$ close to 0: low diversity (few species, or one species dominates)

Worked calculation:

A habitat contains the following organisms: 40 beetles, 30 ants, 20 spiders, 10 flies.

$N = 40 + 30 + 20 + 10 = 100$

$\sum n(n-1) = 40(39) + 30(29) + 20(19) + 10(9) = 1560 + 870 + 380 + 90 = 2900$

$D = 1 - \frac{2900}{100(99)} = 1 - \frac{2900}{9900} = 1 - 0.2929 = 0.7071$

Simpson's Diversity Index = 0.707 (relatively high diversity).

Worked Example: Interpreting Simpson's Index

Two woodland areas were surveyed:

Woodland A: 50 oak, 40 birch, 5 ash, 5 beech (total N = 100)

Woodland B: 25 oak, 25 birch, 25 ash, 25 beech (total N = 100)

(a) Calculate Simpson's Diversity Index for each woodland.

(b) Both woodlands have the same species richness (4 species). Which has higher biodiversity and why?

Solution

Woodland A: $N = 100$

$\sum n(n-1) = 50(49) + 40(39) + 5(4) + 5(4) = 2450 + 1560 + 20 + 20 = 4050$

$D = 1 - 4050 / (100 \times 99) = 1 - 0.4091 = 0.5909$

Woodland B: $N = 100$

$\sum n(n-1) = 25(24) \times 4 = 600 \times 4 = 2400$

$D = 1 - 2400 / (100 \times 99) = 1 - 0.2424 = 0.7576$

Woodland B has higher biodiversity (D = 0.758 vs D = 0.591) because species evenness is higher -- all four species are equally abundant. Woodland A is dominated by oak and birch (low evenness), which lowers its diversity index despite having the same richness.

Why Measure Biodiversity?

• Monitoring ecosystem health: High diversity generally indicates a healthy, stable ecosystem. Low diversity may indicate pollution, disturbance, or environmental degradation.
• Conservation priority: Areas with high biodiversity (e.g., tropical rainforests, coral reefs) are prioritised for conservation.
• Environmental assessment: Biodiversity surveys are used to assess the impact of human activities (e.g., deforestation, pollution) on ecosystems.
• Long-term monitoring: Tracking changes in biodiversity over time helps detect environmental changes and evaluate conservation strategies.

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Evolution Evidence

Types of Evidence for Evolution

Type of Evidence	Description	Example
Fossil record	Sequential appearance of organisms in rock layers; transitional forms show intermediate traits	Archaeopteryx (reptile-bird transition); Tiktaalik (fish-tetrapod transition)
Comparative anatomy	Structural similarities across species indicating common ancestry	Pentadactyl limb in humans, bats, whales, cats
Molecular biology	DNA and protein sequence similarities reflect evolutionary relationships	Cytochrome c is nearly identical across all eukaryotes; humans share 98-99% DNA with chimpanzees
Biogeography	Geographic distribution of species matches continental drift patterns	Marsupials in Australia vs placentals elsewhere
Embryology	Embryos of related species resemble each other in early developmental stages	Pharyngeal pouches in fish, chick, and human embryos

The Fossil Record

Fossils are the preserved remains or traces of organisms that lived in the past. They form when organisms are buried rapidly under sediment, preventing decomposition and scavenging.

Types of fossils:

Type	Description
Body fossils	Preserved remains of the organism itself (bones, teeth, shells, amber-trapped insects)
Trace fossils	Evidence of organism activity (footprints, burrows, coprolites/fossilised faeces)
Casts and moulds	Impressions left in sediment when the organism decays; mineral-filled impressions form casts
Amber fossils	Organisms trapped and preserved in tree resin
Permineralisation	Minerals fill the pores of bones and shells, preserving the structure

Limitations of the fossil record:

• The fossil record is incomplete (fossilisation requires specific conditions that are rare)
• Soft-bodied organisms rarely fossilise (bias towards organisms with hard parts)
• Only a tiny fraction of organisms that ever lived have been fossilised
• Many fossils have not yet been discovered
• Geological activity (erosion, metamorphism, subduction) can destroy fossils

Dating fossils:

• Relative dating: Determines the age of a fossil relative to other fossils based on its position in rock layers (deeper layers are older). Uses index fossils (widespread, short-lived species).
• Absolute dating: Determines the approximate age of a fossil in years. Radiometric dating uses the known decay rate of radioactive isotopes (e.g., carbon-14 dating for organic material up to approximately 50,000 years; potassium-argon dating for volcanic rocks up to billions of years).

Comparative Anatomy

Homologous structures:

Structures in different species that share a common evolutionary origin but may serve different functions.

• Example: The pentadactyl limb (five-digit limb) in humans (grasping), bats (flying), whales (swimming), and cats (walking). All share the same basic bone arrangement (humerus, radius, ulna, carpals, metacarpals, phalanges) derived from a common ancestor, but are modified for different functions.

Analogous structures:

Structures that serve similar functions but have different evolutionary origins and different underlying anatomy.

• Example: The wing of a bird (modified forelimb with bones) and the wing of an insect (exoskeleton extension with no bones). Both are used for flight but evolved independently (convergent evolution).

Vestigial organs:

Structures that are remnants of functional organs in ancestral species but have lost their original function.

• Human appendix: remnant of a large caecum used for digesting cellulose in herbivorous ancestors
• Pelvic bones in whales and snakes: remnants of walking ancestors
• Human tailbone (coccyx): remnant of a tail
• Wings of flightless birds (ostrich, kiwi)

Molecular Biology Evidence

DNA sequence comparison:

• More closely related species share a higher percentage of DNA sequence
• Humans and chimpanzees share approximately 98-99% of their DNA
• The molecular clock hypothesis: mutations accumulate at a roughly constant rate over time; by comparing sequence differences, the time since two species diverged from a common ancestor can be estimated

Protein sequence comparison:

• Cytochrome c (a protein involved in the electron transport chain) is highly conserved across species
• The number of amino acid differences in cytochrome c correlates with evolutionary distance
• Fewer differences = more closely related

Universal genetic code:

• Nearly all organisms use the same genetic code (the same codons code for the same amino acids)
• This is strong evidence for a common ancestor of all life

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Natural Selection and Speciation

Darwin's Theory of Natural Selection

1. Variation: Individuals within a population exhibit heritable variation in traits
2. Overproduction: Populations produce more offspring than the environment can support
3. Competition: There is competition for limited resources (food, mates, territory)
4. Differential survival and reproduction: Individuals with traits better suited to the environment have higher survival and reproductive success
5. Accumulation: Favourable traits increase in frequency over generations

Types of Natural Selection

Type	Description	Effect on Population	Example
Stabilising selection	Favouring intermediate phenotypes; extremes selected against	Reduced variation; mean unchanged	Human birth weight (very low and very high have higher mortality)
Directional selection	Favouring one extreme phenotype	Mean shifts in one direction	Peppered moth (dark form favoured during industrial pollution)
Disruptive selection	Favouring both extremes; intermediate selected against	Bimodal distribution; increased variation	African seedcracker finch (large and small beaks favoured, intermediate disadvantageous)

Speciation

Definition: Speciation is the formation of new species through the evolution of reproductive isolation between populations.

Reproductive isolation mechanisms:

Type	Examples
Prezygotic	Geographical isolation, habitat isolation, temporal isolation (different breeding seasons), behavioural isolation (different courtship displays), mechanical isolation (incompatible reproductive structures), gametic isolation (sperm cannot fertilise egg)
Postzygotic	Hybrid inviability (offspring do not survive), hybrid sterility (offspring are sterile, e.g., mules), hybrid breakdown (first-generation hybrids are fertile but subsequent generations are not)

Allopatric speciation (geographic isolation):

1. A population is divided by a geographic barrier (mountain range, river, ocean, desert)
2. The two subpopulations are prevented from interbreeding (gene flow is interrupted)
3. Each subpopulation experiences different selection pressures, mutations, and genetic drift
4. Over many generations, the two populations diverge genetically and phenotypically
5. Reproductive isolation mechanisms accumulate
6. Even if the populations come back into contact, they can no longer interbreed to produce fertile offspring -- they are now separate species

Allopatric speciation is the most common mode of speciation, particularly on islands (island biogeography) and in habitats fragmented by human activity.

Sympatric speciation (same geographic area):

New species arise without geographic separation. Mechanisms include:

• Polyploidy: Common in plants. An error in meiosis produces a gamete with a full extra set of chromosomes. When this gamete fuses with a normal gamete, the offspring is polyploid (e.g., 3n triploid). The polyploid individual is reproductively isolated from the parent population because it cannot produce fertile offspring with diploid individuals. This is a major mechanism of speciation in flowering plants (approximately 30-70% are polyploid).
• Ecological speciation: Different populations exploit different ecological niches within the same area (e.g., different host plants for insects)
• Sexual selection: Different mating preferences or displays lead to reproductive isolation

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info on speciation, always clearly identify the geographic barrier, explain how gene flow is interrupted, describe the different selection pressures on each population, and explain how reproductive isolation arises.

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Human Impact on Biodiversity

Current Extinction Crisis

The current rate of species extinction is estimated to be 100-1000 times higher than the natural background extinction rate. Many scientists refer to the current era as the "sixth mass extinction."

The five main causes are remembered by the acronym HIPPO:

H -- Habitat Destruction

• Deforestation: Clearing forests for agriculture, logging, urbanisation, and infrastructure. Tropical rainforests are particularly affected (approximately 10 million hectares lost per year).
• Habitat fragmentation: Large continuous habitats are broken into smaller, isolated patches. This reduces total habitat area, isolates populations (reducing gene flow), increases edge effects, and makes populations more vulnerable to extinction.
• Draining wetlands: Wetlands are among the most productive ecosystems; draining for agriculture or development destroys habitat for many species.
• Urbanisation and infrastructure development: Roads, buildings, and other infrastructure replace natural habitats.

I -- Invasive Species

An invasive (non-native) species is one that has been introduced (intentionally or accidentally) to an area outside its natural range and causes ecological or economic harm.

Impacts:

• Outcompete native species for resources (food, space, light)
• Prey on native species (e.g., introduced rats on oceanic islands prey on ground-nesting birds and their eggs)
• Introduce new diseases to which native species have no immunity
• Alter ecosystem processes (e.g., introduced nitrogen-fixing plants change soil chemistry)
• Hybridise with native species, reducing genetic purity

Examples:

• Cane toad (Rhinella marina) in Australia: introduced to control cane beetles, but became a major pest, poisoning predators and competing with native species
• Kudzu vine in the southeastern United States: introduced for erosion control, now covers millions of acres, smothering native vegetation
• Zebra mussel in the Great Lakes: transported in ballast water, outcompetes native mussels, clogs water intake pipes

P -- Pollution

• Eutrophication: Excess nutrients (nitrates and phosphates from agricultural fertilisers, sewage) enter water bodies, causing algal blooms. Algae die and are decomposed by bacteria that consume dissolved oxygen, causing hypoxia and killing fish and other aquatic organisms.
• Pesticides and herbicides: DDT (dichlorodiphenyltrichloroethane) accumulates in food chains (biomagnification), causing eggshell thinning in birds of prey (e.g., bald eagles, peregrine falcons).
• Heavy metals: Lead, mercury, cadmium contaminate soil and water; biomagnify in food chains; cause neurological damage.
• Plastic pollution: Entangles and is ingested by marine organisms; microplastics enter food chains; persists for hundreds of years.
• Oil spills: Coat marine organisms, reducing insulation and buoyancy; toxic components cause liver damage and reproductive failure.

P -- Population Growth

The human population has grown from approximately 1 billion in 1800 to over 8 billion today. Population growth drives:

• Increased demand for food (leading to agricultural expansion and habitat destruction)
• Increased demand for energy (leading to fossil fuel extraction and climate change)
• Increased resource consumption
• Increased waste production
• Urbanisation and infrastructure development

O -- Overexploitation

• Overfishing: Approximately 34% of fish stocks are overfished. Atlantic cod, bluefin tuna, and many shark species are critically depleted.
• Bushmeat hunting: Unsustainable hunting of wild animals for food in tropical regions threatens primates and other mammals.
• Poaching: Illegal hunting of elephants (ivory), rhinos (horn), tigers (body parts), and pangolins (scales).
• Collection for trade: Overharvesting of plants for medicine, ornamental plants, and the pet trade.

Climate Change

Burning fossil fuels releases $\mathrm{CO}_2$, $\mathrm{CH}_4$ (methane), and $\mathrm{N}_2\mathrm{O}$ (nitrous oxide) -- greenhouse gases that trap infrared radiation, increasing global temperatures.

Consequences for biodiversity:

• Range shifts: Species move towards the poles or to higher elevations to track suitable temperature conditions. Species that cannot move fast enough or have nowhere to go (e.g., Arctic species) are at risk.
• Phenological mismatch: The timing of biological events (flowering, migration, breeding) shifts at different rates for different species, disrupting food webs. For example, if insects emerge earlier due to warming but the birds that feed on them do not adjust their breeding time, the birds may miss the peak food supply for their chicks.
• Ocean acidification: Dissolved $\mathrm{CO}_2$ forms carbonic acid, lowering ocean pH. This impairs the ability of corals, molluscs, and other calcifying organisms to build their calcium carbonate shells and skeletons.
• Coral bleaching: Increased water temperature causes corals to expel their symbiotic algae (zooxanthellae), depriving them of their primary food source and colour. If temperatures remain high, corals die.
• Increased frequency of extreme events: Droughts, floods, hurricanes, and wildfires become more frequent and severe, destroying habitats and killing organisms.

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Conservation Strategies

In Situ Conservation

In situ conservation means protecting species in their natural habitats. This is generally the preferred approach because it preserves the entire ecosystem, including ecological interactions and evolutionary processes.

Strategy	Description
National parks	Large areas designated for the protection of ecosystems and wildlife; restricted human activities
Nature reserves	Areas set aside for the conservation of specific species or habitats; may allow limited human use
Marine protected areas (MPAs)	Designated ocean areas where extractive activities are restricted or prohibited
Wildlife corridors	Strips of habitat connecting isolated habitat patches; allow gene flow and migration between populations
Legal protection	Laws protecting endangered species from hunting, trade, or habitat destruction (e.g., Wildlife Protection Ordinance in Hong Kong)

Advantages of in situ conservation:

• Preserves the entire ecosystem and ecological interactions
• Species continue to evolve and adapt in their natural environment
• Large-scale protection is more sustainable than protecting individual species
• Maintains ecosystem services (water purification, carbon sequestration, pollination)

Ex Situ Conservation

Ex situ conservation means protecting species outside their natural habitats. Used when in situ conservation is not possible (e.g., species is critically endangered in the wild, habitat is destroyed).

Strategy	Description
Zoos and captive breeding	Breeding endangered species in captivity; maintaining genetic diversity; reintroduction programmes
Botanical gardens	Cultivating and conserving rare and endangered plant species
Seed banks	Storing seeds of plant species at low temperatures and low humidity for long-term preservation (e.g., Millennium Seed Bank at Kew)
Cryopreservation	Freezing gametes, embryos, or tissues at ultra-low temperatures (liquid nitrogen, -196 degrees C) for long-term storage
Tissue culture	Growing plant tissue in vitro for conservation and mass propagation

Advantages of ex situ conservation:

• Provides a safety net for species on the brink of extinction
• Allows controlled breeding to maximise genetic diversity
• Can be used for research and education
• Seeds and tissues can be stored long-term with minimal space

Disadvantages:

• Does not preserve the natural habitat or ecosystem
• Captive-bred animals may lose behaviours needed for survival in the wild
• Limited space and resources
• Risk of disease in captive populations
• Genetic diversity may decline in small captive populations

International Agreements

Agreement	Description
CITES (1975)	Convention on International Trade in Endangered Species of Wild Fauna and Flora; regulates international trade in species listed in three appendices based on threat level
CBD (1992)	Convention on Biological Diversity; three goals: conservation, sustainable use, fair sharing of benefits from genetic resources
Ramsar Convention (1971)	Protection of wetlands of international importance, especially as waterfowl habitat
Kyoto Protocol (1997) / Paris Agreement (2015)	International agreements to reduce greenhouse gas emissions and combat climate change

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Ecological Succession

Definition

Ecological succession is the sequential, directional process of change in the species composition and community structure of an ecosystem over time. Succession occurs because each stage of community modifies the environment, making it more suitable for the next stage.

Primary Succession

Definition: Colonisation of bare, lifeless substrate where no soil previously existed.

Stages:

1. Pioneer species: Lichens are typically the first organisms to colonise bare rock. Lichens are mutualistic associations of fungi and algae. They can survive on bare rock because they require no soil, absorb water and minerals directly from the rock surface, and can tolerate extreme conditions (desiccation, temperature extremes).
2. Soil formation: Lichens secrete acids that slowly break down the rock surface, beginning the process of soil formation. When lichens die, their organic matter contributes to the developing soil.
3. Mosses and liverworts: As a thin layer of soil accumulates, mosses and liverworts colonise the area. They further contribute organic matter when they die.
4. Grasses and herbs: As the soil deepens, grasses and herbaceous plants colonise. Their roots help bind the soil and retain water. More organic matter accumulates, improving soil fertility.
5. Shrubs and small trees: As soil becomes deeper and more nutrient-rich, shrubs and small trees establish.
6. Climax community: After hundreds or thousands of years, a relatively stable, self-sustaining community becomes established (e.g., temperate deciduous forest in temperate regions, tropical rainforest in tropical regions). The species composition remains relatively constant, though individual organisms are continually replaced.

Characteristics of primary succession:

• Occurs on substrate with no pre-existing soil (e.g., volcanic rock, sand dunes, land exposed by retreating glacier)
• Very slow process (centuries to millennia)
• Begins with lichens or autotrophic bacteria as pioneer species
• Soil development is a key early process

Secondary Succession

Definition: Recolonisation of an area where an existing community has been disturbed or removed but soil remains intact.

Stages:

1. Disturbance: The existing community is removed or severely damaged (e.g., by fire, flooding, deforestation, abandonment of farmland).
2. Pioneer species: Grasses and fast-growing herbaceous plants are typically the first colonisers (soil already exists).
3. Intermediate species: Shrubs and fast-growing trees colonise the area.
4. Climax community: The area eventually returns to a community resembling the original (though not necessarily identical).

Characteristics of secondary succession:

• Occurs where soil already exists
• Much faster than primary succession (decades to centuries rather than millennia)
• Begins with grasses and herbs rather than lichens
• The climax community may or may not be the same as the original community

Comparison of Primary and Secondary Succession

Feature	Primary Succession	Secondary Succession
Starting substrate	Bare rock, sand, lava (no soil)	Previously occupied land with intact soil
Pioneer species	Lichens, autotrophic bacteria	Grasses, fast-growing herbs
Soil at start	Absent	Present
Speed	Very slow (centuries to millennia)	Faster (decades to centuries)
Example	Colonisation of volcanic island (Surtsey, Iceland)	Regrowth after forest fire or abandoned farmland

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Biogeochemical Cycles

The Carbon Cycle

Carbon is the fundamental element of all organic molecules. The carbon cycle describes the movement of carbon between the atmosphere, biosphere, oceans, and geosphere.

Key processes:

Process	Description	Carbon Flux
Photosynthesis	Plants, algae, and cyanobacteria convert atmospheric $\mathrm{CO}_2$ into organic compounds (glucose) using light energy	Removes $\mathrm{CO}_2$ from the atmosphere
Respiration	All living organisms break down organic molecules, releasing $\mathrm{CO}_2$ as a by-product	Returns $\mathrm{CO}_2$ to the atmosphere
Combustion	Burning fossil fuels (coal, oil, natural gas) and biomass releases stored carbon as $\mathrm{CO}_2$	Returns $\mathrm{CO}_2$ to the atmosphere
Decomposition	Decomposers break down dead organic matter, releasing $\mathrm{CO}_2$	Returns $\mathrm{CO}_2$ to the atmosphere
Ocean absorption	Oceans dissolve $\mathrm{CO}_2$ from the atmosphere (forming carbonic acid, bicarbonate, and carbonate ions)	Removes $\mathrm{CO}_2$ from the atmosphere
Sedimentation	Dead marine organisms (with calcium carbonate shells) settle to the ocean floor, forming limestone over geological time	Removes carbon from the short-term cycle
Fossilisation	Organic matter is buried and compressed over millions of years, forming fossil fuels (coal, oil, natural gas)	Stores carbon long-term
Deforestation	Removal of trees reduces photosynthesis; burning releases stored carbon	Returns $\mathrm{CO}_2$ to the atmosphere

Carbon reservoirs:

Reservoir	Approximate Amount (GtC)
Atmosphere	Approximately 750
Oceans	Approximately 38,000
Terrestrial biosphere	Approximately 560
Fossil fuels	Approximately 4,000
Sedimentary rocks	Approximately 75,000,000

The Nitrogen Cycle

Nitrogen is essential for amino acids, proteins, nucleic acids, and ATP. The atmosphere is approximately 78% $\mathrm{N}_2$ gas, but this form is unavailable to most organisms because the triple bond in $\mathrm{N}_2$ is very strong and requires significant energy to break.

Key processes:

Process	Description	Organisms Involved
Nitrogen fixation	Atmospheric $\mathrm{N}_2$ is converted to ammonia ($\mathrm{NH}_3$)	Nitrogen-fixing bacteria (e.g., Rhizobium in root nodules of legumes; Azotobacter; cyanobacteria); lightning
Nitrification	Ammonia ($\mathrm{NH}_3$) is converted to nitrite ($\mathrm{NO}_2^-$) then to nitrate ($\mathrm{NO}_3^-$)	Nitrosomonas (ammonia to nitrite); Nitrobacter (nitrite to nitrate)
Absorption	Plants absorb nitrate ($\mathrm{NO}_3^-$) (and some ammonium, $\mathrm{NH}_4^+$) through their roots	Plant root cells
Assimilation	Plants incorporate nitrogen into amino acids, proteins, nucleic acids, and other organic compounds	Plants
Feeding	Animals obtain nitrogen by eating plants or other animals	Animals
Decomposition / ammonification	Decomposers break down dead organisms and urea/excreted waste, releasing ammonia ($\mathrm{NH}_3$)	Decomposer bacteria and fungi
Denitrification	Nitrate ($\mathrm{NO}_3^-$) is converted back to $\mathrm{N}_2$ gas, returning it to the atmosphere	Denitrifying bacteria (e.g., Pseudomonas, Paracoccus)

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warning atmosphere. Plants cannot use atmospheric nitrogen directly. They can only absorb nitrogen in the form of nitrate ($\mathrm{NO}_3^-$) or ammonium ($\mathrm{NH}_4^+$) ions through their roots. Atmospheric nitrogen must first be fixed by bacteria or lightning.

The Water Cycle

The water cycle describes the continuous movement of water between the atmosphere, land, and oceans, driven by solar energy and gravity.

Worked Example: Nitrogen Cycle Process Identification

For each description, identify the nitrogen cycle process and the organism(s) involved:

(a) Atmospheric N$_2$ is converted to NH$_3$ in root nodules of legumes.

(b) NH$_3$ is converted to NO$_2^-$ then to NO$_3^-$ in the soil.

(c) NO$_3^-$ is converted back to N$_2$ gas in waterlogged soil.

(d) Dead organisms are broken down, releasing NH$_3$.

Solution

(a) Nitrogen fixation by Rhizobium (nitrogen-fixing bacteria in root nodules). The enzyme nitrogenase catalyses this energy-intensive reaction.

(b) Nitrification by Nitrosomonas (ammonia to nitrite) followed by Nitrobacter (nitrite to nitrate). These are chemoautotrophic bacteria that obtain energy from the oxidation reactions.

(c) Denitrification by Pseudomonas (denitrifying bacteria). This occurs under anaerobic conditions (waterlogged soil) and returns nitrogen to the atmosphere, reducing soil fertility.

(d) Ammonification (decomposition) by decomposer bacteria and fungi. They break down proteins and nucleic acids in dead organisms and urea in waste, releasing ammonia into the soil.

Key processes:

Process	Description
Evaporation	Water changes from liquid to vapour from oceans, lakes, rivers, and soil
Transpiration	Water vapour is released from plant leaves through stomata (approximately 10% of atmospheric moisture)
Condensation	Water vapour cools and condenses into tiny water droplets or ice crystals, forming clouds
Precipitation	Water returns to Earth's surface as rain, snow, sleet, or hail
Surface runoff	Water flows over the land surface into rivers, lakes, and oceans
Infiltration	Water soaks into the ground surface, moving downwards through soil and rock
Percolation	Water moves deeper through permeable rocks to become groundwater
Groundwater flow	Groundwater moves slowly through aquifers (permeable rock layers) and eventually reaches the surface via springs or into rivers and oceans

Human impacts on the water cycle:

• Deforestation: Reduces transpiration; increases surface runoff and soil erosion; decreases groundwater recharge
• Urbanisation: Impermeable surfaces (concrete, tarmac) increase surface runoff and reduce infiltration; this can lead to flooding and reduced groundwater levels
• Agriculture: Irrigation removes water from rivers and groundwater; can lead to water depletion and salinisation of soil
• Climate change: Alters precipitation patterns; increases evaporation in some regions; causes more extreme droughts and floods

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Common Pitfalls

1. Confusing species richness with species diversity: Species richness counts the number of species but ignores their relative abundances. Simpson's Diversity Index accounts for both richness and evenness. A community with high richness but very low evenness (one dominant species) can have lower diversity than a community with moderate richness but high evenness.

2. Writing that the three-domain system replaced the five-kingdom system: The three-domain system is a higher-level classification that sits above the kingdom level. The five-kingdom system is still valid within the domain Eukarya. They are complementary, not contradictory.

3. Confusing allopatric and sympatric speciation: Allopatric speciation requires geographic separation. Sympatric speciation occurs without geographic separation. Polyploidy is the most common mechanism of sympatric speciation and is important in plants, not animals.

4. Writing that all mutations are harmful: Most mutations are neutral or harmful, but some are beneficial and provide the raw material for natural selection. The mutation rate itself is not "directed" -- mutations occur randomly.

5. Confusing bioaccumulation with biomagnification: Bioaccumulation is the accumulation of a substance within a single organism over its lifetime. Biomagnification is the increasing concentration of a substance at each successive trophic level in a food chain. Both terms may appear in the same question.

6. Writing that nitrogen gas can be directly absorbed by plants: Plants can only absorb nitrogen in the form of nitrate ($\mathrm{NO}_3^-$) or ammonium ($\mathrm{NH}_4^+$). Atmospheric $\mathrm{N}_2$ must first be fixed by nitrogen-fixing bacteria or lightning.

7. Confusing primary and secondary succession: Primary succession occurs on bare, lifeless substrate with no soil (e.g., volcanic rock). Secondary succession occurs where soil already exists after a disturbance (e.g., after a forest fire). The key difference is the presence or absence of soil at the start.

8. Writing that carbon in fossil fuels is part of the short-term carbon cycle: Fossil fuel carbon is part of the long-term carbon cycle (geological timescale). Burning fossil fuels releases carbon that has been locked away for millions of years, which is why it disrupts the current carbon balance.

9. Confusing in situ and ex situ conservation: In situ conservation protects species in their natural habitat (national parks, reserves). Ex situ conservation protects species outside their natural habitat (zoos, seed banks, botanical gardens). DSE questions often require both to be discussed.

10. Forgetting the role of decomposers in nutrient cycles: Decomposers (bacteria and fungi) are essential in all nutrient cycles. They break down dead organic matter and waste, releasing nutrients back into the soil in forms that plants can absorb. Without decomposers, nutrients would remain locked in dead organisms and the cycles would stop.

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Problem Set

Problem 1: Calculate Simpson's Diversity Index for a pond community with the following organisms: 60 water boatmen, 30 pond skaters, 5 dragonfly nymphs, 3 mayfly nymphs, and 2 water beetles.

If you get this wrong, revise: Biodiversity Measurement -- Simpson's Diversity Index

Solution

$N = 60 + 30 + 5 + 3 + 2 = 100$

$\sum n(n-1) = 60(59) + 30(29) + 5(4) + 3(2) + 2(1) = 3540 + 870 + 20 + 6 + 2 = 4438$

$D = 1 - \frac{4438}{100(99)} = 1 - \frac{4438}{9900} = 1 - 0.4483 = 0.5517$

This indicates moderate diversity. The pond is dominated by water boatmen (60% of individuals), which lowers evenness and therefore the diversity index. A more even distribution would increase D.

Problem 2: Describe the role of bacteria in the nitrogen cycle. Explain why plants cannot use atmospheric nitrogen directly.

If you get this wrong, revise: Biogeochemical Cycles -- The Nitrogen Cycle

Solution

Bacteria play essential roles:

• Nitrogen-fixing bacteria (Rhizobium in root nodules; Azotobacter free-living; cyanobacteria): convert N$_2$ to NH$_3$ (nitrogen fixation).
• Nitrifying bacteria (Nitrosomonas: NH$_3$ to NO$_2^-$; Nitrobacter: NO$_2^-$ to NO$_3^-$): nitrification.
• Denitrifying bacteria (Pseudomonas): convert NO$_3^-$ back to N$_2$ (denitrification, anaerobic).
• Decomposer bacteria: break down dead organisms and waste, releasing NH$_3$ (ammonification).

Plants cannot use atmospheric N$_2$ because the triple bond between nitrogen atoms (~945 kJ/mol) is extremely strong and requires significant energy to break. Plants lack the enzyme nitrogenase. They can only absorb nitrogen as NO$_3^-$ or NH$_4^+$ ions through their roots.

Problem 3: A species of tree frog is endangered due to deforestation. Discuss the relative merits of in situ and ex situ conservation strategies for this species.

If you get this wrong, revise: Conservation Strategies -- In Situ Conservation; Ex Situ Conservation

Solution

In situ (establishing a protected area): Preserves the entire ecosystem, including the frog's food sources, breeding sites, and microhabitat. Allows natural evolutionary processes. Wildlife corridors connect fragmented habitats, enabling gene flow. Most sustainable long-term approach. Limitation: habitat may already be too degraded; enforcement challenges.

Ex situ (captive breeding in zoos): Provides immediate protection from habitat destruction. Allows controlled breeding for genetic diversity. Tissue samples can be cryopreserved. Limitation: maintaining correct microhabitat conditions in captivity is difficult; captive-bred frogs may lose survival behaviours; limited space.

Best approach: A combination -- in situ addresses the root cause (habitat protection) as the long-term goal, while ex situ provides a safety net to prevent extinction during habitat restoration.

Problem 4: A river changes course over thousands of years, dividing a population of beetles into two separate populations. Describe how this could lead to allopatric speciation.

If you get this wrong, revise: Natural Selection and Speciation -- Allopatric Speciation

Solution

1. The river creates a geographic barrier, physically separating the population and preventing gene flow.

2. Each subpopulation experiences different environmental conditions (vegetation, predators, climate).

3. Different selection pressures favour different traits (e.g., darker colouration on one bank, lighter on the other).

4. Over generations, natural selection and genetic drift cause allele frequencies to diverge in each population.

5. Reproductive isolation mechanisms accumulate (e.g., different mating behaviours, mechanical isolation, hybrid inviability).

6. Even if the river dries up, the populations can no longer interbreed successfully. They are now separate species (allopatric speciation).

Problem 5: Explain the difference between primary and secondary succession, giving an example of each.

If you get this wrong, revise: Ecological Succession -- Primary Succession; Secondary Succession

Solution

Primary succession occurs on bare, lifeless substrate with no soil (e.g., newly formed volcanic rock, sand dunes). Pioneer species are lichens and autotrophic bacteria. Soil forms gradually from rock weathering and organic matter accumulation. It is very slow (centuries to millennia). Example: colonisation of volcanic island Surtsey (Iceland).

Secondary succession occurs where soil already exists after a disturbance (e.g., forest fire, abandoned farmland). Pioneer species are grasses and fast-growing herbs. It is much faster (decades) because soil and some organisms already exist. Example: regrowth after a forest fire.

Problem 6: Distinguish between stabilising, directional, and disruptive selection, providing an example of each.

If you get this wrong, revise: Natural Selection and Speciation -- Types of Natural Selection

Solution

Stabilising selection favours intermediate phenotypes and selects against extremes. The mean is unchanged but variation decreases. Example: human birth weight (very low and very high have higher mortality).

Directional selection favours one extreme phenotype, shifting the mean in one direction. Example: peppered moth during industrial pollution (dark form favoured).

Disruptive selection favours both extremes and selects against intermediates, potentially splitting the population. Example: African seedcracker finch (large and small beaks favoured, intermediate disadvantageous).

Problem 7: Explain the process of eutrophication and its effects on aquatic ecosystems.

If you get this wrong, revise: Human Impact -- Pollution (Eutrophication)

Solution

1. Excess nutrients (nitrates and phosphates from fertilisers, sewage) enter a water body.
2. Nutrient enrichment causes rapid algal growth (algal bloom).
3. The algal layer blocks light, killing submerged aquatic plants.
4. Algae die and are decomposed by bacteria, which consume dissolved oxygen through aerobic respiration.
5. Dissolved oxygen levels drop (hypoxia or anoxia).
6. Fish and other aquatic organisms die.
7. Decomposition of dead organisms further consumes oxygen, worsening the problem.

Problem 8: Explain what is meant by bioaccumulation and biomagnification, using mercury as an example.

If you get this wrong, revise: Human Impact -- Pollution (Bioaccumulation vs Biomagnification)

Solution

Bioaccumulation is the accumulation of a substance within a single organism over its lifetime. Mercury absorbed from water or food accumulates in the body tissues (especially the liver and brain) faster than it can be excreted.

Biomagnification is the increasing concentration of a substance at each successive trophic level. Mercury concentration increases from plankton to small fish to large fish to birds of prey. At each level, organisms consume many prey items, accumulating all the mercury those prey contained.

Key distinction: bioaccumulation is within one organism; biomagnification is across the food chain. Mercury is particularly problematic because it is fat-soluble, persistent, and toxic to the nervous system.

Problem 9: Describe three types of fossil evidence that support the theory of evolution.

If you get this wrong, revise: Evolution Evidence -- The Fossil Record

Solution

1. Transitional fossils: Show intermediate characteristics between ancestral and descendant groups. Example: Archaeopteryx (feathered dinosaur with teeth and long bony tail -- intermediate between reptiles and birds); Tiktaalik (fish with limb-like fins -- intermediate between fish and tetrapods).

2. Sequential appearance in rock layers: Fossils in deeper (older) rock layers are simpler and less similar to modern organisms, while fossils in shallower (younger) layers are more complex and similar to modern organisms. This demonstrates gradual change over time.

3. Biogeographic patterns: Fossil distributions match continental drift patterns (e.g., identical Mesosaurus fossils found in both South America and Africa, supporting that these continents were once joined).

Problem 10: Explain two ways in which climate change threatens biodiversity, and suggest one conservation strategy to mitigate each threat.

If you get this wrong, revise: Human Impact -- Climate Change; Conservation Strategies

Solution

1. Range shifts: As temperatures rise, species move towards poles or to higher elevations to track suitable conditions. Species that cannot move fast enough or have nowhere to go (e.g., Arctic species) are at risk of extinction. Mitigation: Establish wildlife corridors connecting protected areas, allowing species to migrate in response to changing conditions.

2. Ocean acidification: Dissolved CO$_2$ forms carbonic acid, lowering ocean pH. This impairs the ability of corals, molluscs, and other calcifying organisms to build calcium carbonate shells and skeletons, threatening coral reef ecosystems. Mitigation: Reduce CO$_2$ emissions (transition to renewable energy); establish marine protected areas to reduce additional stress on coral reefs.

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Invasive Species

What is an Invasive Species?

An invasive (non-native) species is one that has been introduced to an area outside its natural range and that causes ecological, economic, or human health harm. Not all introduced species become invasive -- many fail to establish, and some integrate without causing significant damage.

Impact of Invasive Species

Impact Type	Description	Example
Predation	Invasive predators can devastate native wildlife populations that have evolved without such predation pressure	Cats and rats in New Zealand; brown tree snake in Guam (eliminated 10 of 12 native bird species)
Competition	Invasive species outcompete native species for resources (food, light, water, nesting sites)	Grey squirrel outcompeting red squirrel in the UK (grey carries squirrelpox virus)
Disease	Invasive species can introduce diseases to which native species have no immunity	Dutch elm disease fungus; chytrid fungus devastating amphibian populations globally
Habitat alteration	Invasive plants can change soil chemistry, fire regimes, and water cycles	Water hyacinth blocking waterways; kudzu smothering native vegetation in the southeastern US
Hybridisation	Invasive species can hybridise with native species, reducing genetic purity of native populations	Introduced mallard ducks hybridising with native duck species

Case Study: Water Hyacinth (Eichhornia crassipes)

Feature	Detail
Origin	Amazon basin, South America
Introduction	Introduced as an ornamental plant; now found in tropical and subtropical regions worldwide
Growth rate	Extremely rapid; can double in population size in approximately 2 weeks under optimal conditions
Problems caused	Blocks waterways; reduces light and oxygen for aquatic life; interferes with fishing and transport; increases water loss through transpiration; creates breeding grounds for mosquitoes (malaria risk)
Control methods	Physical removal; biological control (weevils Neochetina eichhorniae and N. bruchi); herbicides (limited effectiveness)

Case Study: Cane Toad (Rhinella marina) in Australia

The cane toad was introduced to Australia in 1935 to control cane beetles. It failed to control the beetles but became a major invasive species:

• Toxic bufotoxins kill native predators (snakes, lizards, crocodiles, dingoes)
• Competes with native species for food and habitat
• Reproduces rapidly (up to 30,000 eggs per clutch, multiple clutches per year)
• No natural predators in Australia
• Population has spread across northern and eastern Australia
• Current population: over 200 million
• Control methods: physical removal, trapping, community campaigns, research into biological control

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Conservation Genetics

Genetic Bottlenecks

A genetic bottleneck occurs when a population undergoes a drastic reduction in size, losing a significant portion of its genetic diversity.

Consequences of reduced genetic diversity:

1. Reduced adaptive potential: With less genetic variation, the population is less able to adapt to changing environmental conditions
2. Increased homozygosity: Recessive deleterious alleles become more common (inbreeding depression)
3. Inbreeding depression: Mating between closely related individuals increases homozygosity, expressing harmful recessive alleles; reduced fertility, higher juvenile mortality, increased susceptibility to disease
4. Reduced evolutionary potential: Less raw material for natural selection to act upon

The 50/500 Rule

Number	Purpose
50	Minimum to prevent short-term inbreeding depression
500	Minimum to maintain long-term evolutionary potential

Genetic Rescue

Genetic rescue involves introducing individuals from a different population to increase genetic diversity in a small, inbred population.

• Successful example: Florida panther (introduced Texas individuals to increase genetic diversity; improved survival and reproductive success)
• Risks: Outbreeding depression (if populations are too genetically distinct, the hybrid offspring may have reduced fitness)

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Climate Change and Conservation

Effects of Climate Change on Biodiversity

Effect	Mechanism	Affected Species/Ecosystems
Range shifts	Species move towards poles or to higher elevations to track suitable temperature conditions	Arctic species; alpine plants; montane amphibians
Ocean acidification	Dissolved $\mathrm{CO}_2$ lowers ocean pH; impairs calcification in corals, molluscs, and planktonic organisms	Coral reefs; pteropods; shellfish
Altered phenology	Seasonal events shift in timing; may create mismatches between species interactions	Pollinators and flowering plants; migratory birds and food availability
Increased extreme weather	More frequent droughts, floods, storms damage habitats and kill organisms directly	Coral reefs; forests; coastal ecosystems
Sea level rise	Coastal habitats are inundated; saltwater intrusion into freshwater ecosystems	Mangroves; salt marshes; low-lying islands
Changing rainfall patterns	Altered distribution of freshwater and food resources	Savanna ecosystems; wetlands; migratory species

Conservation Strategies for Climate Change

Strategy	Description
Protected area networks	Connected reserves that allow species to migrate in response to changing climate (corridors)
Assisted migration	Deliberately moving species to more suitable habitat as their current range becomes uninhabitable
Ex situ conservation	Captive breeding programmes, seed banks, and gene banks as a safety net for species that cannot survive in the wild
Habitat restoration	Restoring degraded ecosystems to increase resilience and absorb climate refugees
Reducing greenhouse emissions	The most important long-term strategy; transitioning to renewable energy; reducing deforestation

tip

tip Ready to test your understanding of Biodiversity and Conservation? The diagnostic test contains the hardest questions within the DSE specification for this topic, each with a full worked solution.

Unit tests probe edge cases and common misconceptions. Integration tests combine Biodiversity and Conservation with other biology topics to test synthesis under exam conditions.

See Diagnostic Guide for instructions on self-marking and building a personal test matrix.

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Ecological Succession

Primary Succession

Primary succession occurs on bare, lifeless substrate where no soil exists -- for example, on newly formed volcanic rock, sand dunes, or land exposed by retreating glaciers.

Stage	Description	Pioneer Species / Key Features
Bare substrate	No soil; rock, sand, or ash surface; hostile environment (no organic matter, no water retention, extreme temperatures)	None initially
Colonisation	Pioneer species colonise: lichens, algae, mosses. Lichens secrete acids that weather the rock, beginning soil formation. Wind-blown spores and seeds arrive	Lichens (symbiosis of fungi and algae); cyanobacteria
Soil development	As pioneer organisms die and decompose, organic matter accumulates, forming a thin layer of humus. This improves water retention and nutrient content	Mosses, liverworts
Herbaceous stage	Grasses and small herbaceous plants colonise the developing soil. Their roots further stabilise the soil and add more organic matter	Grasses, ferns, small herbs
Shrub stage	Shrubs and small woody plants appear. They outcompete the grasses for light and nutrients	Shrubs (e.g., gorse, bramble), small trees
Climax community	A stable, self-sustaining community dominated by large trees. The community remains relatively stable unless disrupted by a major disturbance	Oak forest, tropical rainforest, depending on climate

Secondary Succession

Secondary succession occurs on previously occupied land where the existing community has been disturbed or destroyed, but the soil remains intact.

Feature	Description
Trigger	Fire, flooding, deforestation, abandonment of farmland, hurricane damage
Starting point	Soil already present (with seeds, spores, and organic matter), so succession is faster than primary succession
Early colonisers	Grasses and herbaceous plants (not lichens, since soil already exists)
Intermediate species	Shrubs and fast-growing trees (e.g., birch, pine)
Climax community	Slower-growing, shade-tolerant trees eventually dominate (e.g., oak, beech)
Time scale	Typically 50-200 years to reach climax community (compared to hundreds to thousands of years for primary succession)

Plagioclimax

A plagioclimax is a stable community that is prevented from reaching its natural climax community by human activity or other persistent factors.

Example	Description
Grazed grassland (e.g., the South Downs)	Regular sheep/cattle grazing prevents shrubs and trees from establishing; the grassland is maintained artificially
Heather moorland	Managed burning prevents tree colonisation; heather is maintained as the dominant vegetation
Managed forest / plantation	Regular harvesting and replanting prevents natural succession from occurring
Mown lawns and parks	Regular mowing prevents the natural succession to scrub and woodland

Key Terms

Term	Definition
Pioneer species	The first organisms to colonise a bare substrate; typically hardy, tolerant of extreme conditions, fast-growing, and able to fix nitrogen (if applicable)
Climax community	The final, stable community in succession; dominated by slow-growing, long-lived species; relatively self-sustaining
Sere	The sequence of stages in succession from pioneer to climax
Deflected succession	Succession that is diverted from its natural course by human activity or other factors (producing a plagioclimax)

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Biogeography

Continental Drift and Species Distribution

The theory of continental drift (proposed by Alfred Wegener, 1912; confirmed by plate tectonics in the 1960s) explains many patterns in species distribution.

Evidence from Biogeography	Description
Matching fossils	Identical fossil species (e.g., Mesosaurus, Glossopteris) found on continents now separated by oceans (South America, Africa, India, Antarctica, Australia) -- these organisms could not have crossed the oceans, so the continents must have once been joined
Endemic species on islands	Oceanic islands (volcanic origin) have unique species that evolved from colonisers that arrived by wind or sea -- they resemble species on the nearest mainland but are distinct
Australian fauna	Australia has been isolated for ~30-40 million years; its unique marsupial fauna (kangaroos, koalas, wombats, platypus) evolved in the absence of placental mammal competition
Convergent evolution	Similar habitats on different continents have produced ecologically equivalent but evolutionarily unrelated species (e.g., cacti in Americas vs. euphorbias in Africa; marsupial moles in Australia vs. placental moles elsewhere)

Island Biogeography (MacArthur and Wilson, 1967)

The theory of island biogeography predicts species richness on islands based on two opposing processes:

Factor	Effect on Species Richness
Island size (area)	Larger islands have higher species richness (more habitats, larger populations less prone to extinction, larger "target" for colonisation)
Distance from mainland	Islands closer to the mainland have higher species richness (easier for species to colonise)

$S = cA^z$

Where:

• $S$ = number of species
• $A$ = island area
• $c$ = constant (depends on the taxonomic group and biogeographic region)
• $z$ = constant (typically 0.2-0.35)

At equilibrium, the rate of colonisation equals the rate of extinction, and the number of species remains relatively stable.

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Sampling Techniques in Detail

Random Sampling

1. Mark out a study area using a tape measure
2. Use random number tables or a random number generator to select coordinates for sampling points
3. Place a quadrat at each selected coordinate
4. Record the species present and/or their abundance within the quadrat
5. Repeat for multiple quadrats (typically 10-30) to obtain a representative sample

Systematic Sampling

1. Mark out a transect line (a straight line across the study area, from one side to the other)
2. Place quadrats at regular intervals along the transect (e.g., every 2 metres)
3. This is useful for studying how species distribution changes along an environmental gradient (e.g., from sea shore inland, from edge to centre of a woodland)

Quadrat Size Guidelines

Habitat	Recommended Quadrat Size
Grassland	0.5 m $\times$ 0.5 m or 1 m $\times$ 1 m
Heathland / moorland	1 m $\times$ 1 m or 2 m $\times$ 2 m
Woodland (ground flora)	1 m $\times$ 1 m
Rocky shore (small organisms)	0.25 m $\times$ 0.25 m

Calculating Species Diversity

Species richness: The number of different species in a given area (a simple count).

Simpson's Diversity Index (SDI):

$D = 1 - \sum \left( \frac{n}{N} \right)^2$

Where:

• $n$ = number of individuals of a particular species
• $N$ = total number of individuals of all species
• $D$ ranges from 0 (no diversity, only one species) to approaching 1 (maximum diversity, many species with equal abundance)

Interpretation:

• $D$ close to 0: low diversity; the community is dominated by one or a few species; ecosystem is less stable and more vulnerable to disturbance
• $D$ close to 1: high diversity; many species with similar abundances; ecosystem is more stable and resilient

Capture-Mark-Release-Recapture

Used to estimate the population size of mobile animals (e.g., insects, small mammals, fish).

Lincoln-Petersen Index:

$N = \frac{M \times C}{R}$

Where:

• $N$ = estimated total population size
• $M$ = number of animals captured and marked in the first sample
• $C$ = total number of animals captured in the second sample
• $R$ = number of marked animals recaptured in the second sample

Assumptions:

1. The proportion of marked to unmarked animals in the second sample is the same as in the total population
2. Marks are not lost and do not affect the animal's survival or behaviour
3. The population is closed (no births, deaths, immigration, or emigration between samples)
4. All individuals have an equal chance of being captured (random mixing)
5. Sufficient time has passed for marked individuals to mix back into the population

Common Pitfalls

• Quadrats must be placed randomly, not subjectively (e.g., placing quadrats only where there are many plants introduces sampling bias)
• Simpson's Diversity Index takes both species richness AND evenness into account, unlike species richness alone. Two communities can have the same number of species but very different diversity indices if one is dominated by a single species
• The capture-mark-release-recapture method assumes a closed population. If animals are born, die, or migrate between the two samples, the estimate will be inaccurate

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Classification Systems

The Three-Domain System (Carl Woese, 1990)

Based on molecular evidence (rRNA sequencing), Woese proposed three domains above the kingdom level:

Domain	Cell Type	Description	Examples
Bacteria	Prokaryotic	Unicellular; no nucleus; no membrane-bound organelles; cell wall contains peptidoglycan; circular DNA; 70S ribosomes	E. coli, Staphylococcus, Cyanobacteria
Archaea	Prokaryotic	Unicellular; no nucleus; no membrane-bound organelles; cell wall does NOT contain peptidoglycan (contains pseudopeptidoglycan or other polymers); often found in extreme environments; some genes have introns (like eukaryotes)	Methanogens; halophiles; thermophiles; Sulfolobus
Eukarya	Eukaryotic	Unicellular or multicellular; nucleus and membrane-bound organelles; linear DNA with introns; 80S ribosomes; cytoskeleton; sexual reproduction common	Animals, plants, fungi, protists

The Five-Kingdom System (Whittaker, 1969)

Kingdom	Cell Type	Cell Wall	Nutrition	Examples
Prokaryotae (Monera)	Prokaryotic	Peptidoglycan	Various (autotrophic, heterotrophic, saprotrophic)	Bacteria, cyanobacteria
Protoctista (Protista)	Eukaryotic	Some have cellulose	Various	Amoeba, paramecium, algae, seaweed
Fungi	Eukaryotic	Chitin	Saprotrophic (extracellular digestion)	Mushrooms, yeasts, moulds, Penicillium
Plantae	Eukaryotic	Cellulose	Autotrophic (photosynthesis)	Mosses, ferns, conifers, flowering plants
Animalia	Eukaryotic	No cell wall	Heterotrophic (ingestion)	Insects, fish, amphibians, reptiles, birds, mammals

Binomial Nomenclature

• Devised by Carl Linnaeus (1758)
• Each species is given a two-part Latin name:
  • Genus name (capitalised, e.g., Homo)
  • Species name (lowercase, e.g., sapiens)
• The full name is written in italics (or underlined if handwritten): Homo sapiens
• This system is universal (used worldwide) and avoids confusion caused by common names (e.g., "puma", "cougar", "mountain lion" all refer to Puma concolor)

Classification Hierarchy

$\text{Domain} \rightarrow \text{Kingdom} \rightarrow \text{Phylum} \rightarrow \text{Class} \rightarrow \text{Order} \rightarrow \text{Family} \rightarrow \text{Genus} \rightarrow \text{Species}$

Mnemonic: "Dear King Philip Came Over For Good Soup"

Each level is called a taxon (plural: taxa). Species within the same genus are more closely related than species in different genera; species within the same family are more closely related than those in different families, and so on.

Viruses -- Classification Debate

Viruses are NOT classified in any of the three domains because:

Feature	Living Organisms	Viruses
Cell structure	Have cells (prokaryotic or eukaryotic)	Acellular (no cell structure); consist of genetic material (DNA or RNA) enclosed in a protein coat (capsid); some have a lipid envelope
Metabolism	Carry out metabolic reactions (respiration, etc.)	No metabolism of their own; do not carry out respiration, nutrition, or excretion
Reproduction	Reproduce independently (cell division, sexual reproduction)	Can only replicate inside a host cell; they are obligate intracellular parasites
Response to stimuli	Can respond to environmental stimuli	No response to stimuli
Homeostasis	Maintain a stable internal environment	No homeostasis

Extremophiles

Extremophiles are organisms, predominantly archaea, that thrive in extreme environments:

Type	Environment	Example
Thermophiles	High temperature (45-80 degrees C or higher)	Thermus aquaticus (source of Taq polymerase for PCR); archaea near deep-sea hydrothermal vents
Hyperthermophiles	Very high temperature (above 80 degrees C)	Pyrolobus fumarii (grows at 113 degrees C)
Halophiles	High salt concentration	Halobacterium (turns salt lakes pink due to bacteriorhodopsin pigment)
Acidophiles	Low pH (acidic environments, pH < 3)	Acidithiobacillus ferrooxidans (lives in acid mine drainage, pH ~1.5)
Alkaliphiles	High pH (alkaline environments, pH > 9)	Natronomonas (lives in soda lakes)
Barophiles (piezophiles)	High pressure	Archaea and bacteria in deep ocean trenches (>1000 atmospheres)

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Biodiversity and Ecosystem Stability

Relationship Between Biodiversity and Stability

Higher biodiversity generally leads to greater ecosystem stability:

1. Productivity stability: Ecosystems with higher species diversity tend to have more stable productivity (total biomass production) over time, because if one species declines, others can compensate
2. Resistance: High-diversity ecosystems are more resistant to change (e.g., more resistant to invasion by alien species, because more ecological niches are already filled)
3. Resilience: High-diversity ecosystems recover more quickly after disturbance (e.g., fire, drought), because there are more species with different traits that can survive and re-establish the community
4. Trophic stability: In diverse food webs, each species has multiple food sources and multiple predators, so the loss of one species is less likely to cause a cascade of extinctions

The Intermediate Disturbance Hypothesis

• Proposed by Joseph Connell (1978)
• Ecosystems with intermediate levels of disturbance have the HIGHEST species diversity
• Low disturbance: competitive exclusion reduces diversity (the best competitor dominates and excludes others)
• High disturbance: only the most tolerant or opportunistic species survive (pioneer species)
• Intermediate disturbance: prevents competitive exclusion by periodically reducing the dominance of the strongest competitors, allowing a wider variety of species to coexist

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Common Pitfalls

• Archaea and Bacteria are BOTH prokaryotes, but they are in DIFFERENT domains. They differ in cell wall composition (peptidoglycan vs. pseudopeptidoglycan), rRNA sequences, and membrane lipid structure
• Viruses are NOT considered living organisms. They do not have cells, do not carry out metabolism, and cannot reproduce independently. They are not classified in any domain or kingdom
• The binomial name always has TWO parts: genus (capitalised) and species (lowercase). Both parts should be italicised (or underlined). The genus name can be abbreviated to its initial letter after the first use (e.g., H. sapiens)
• "Endemic" and "native" are different terms. "Endemic" means a species is found naturally in only ONE geographic area and nowhere else. "Native" means a species occurs naturally in an area (but may also occur elsewhere). For example, kangaroos are endemic to Australia; oak trees are native to many countries but not endemic to any single one**
• Species richness and species diversity are NOT the same thing. Species richness is a simple count of the number of species. Species diversity (e.g., Simpson's Diversity Index) takes both species richness AND evenness (relative abundance of each species) into account**