Ecology

Ecology

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Board Coverage AQA Paper 2 | Edexcel A Paper 2 | OCR (A) Paper 2 | CIE Paper 4

1. Ecosystems

1.1 Definitions

Definition. An ecosystem is a self-sustaining system formed by the interactions of all living organisms (the biotic component) with their non-living physical and chemical environment (the abiotic component) within a defined area.

Definition. A habitat is the place where an organism lives. A niche describes the role and position of a species within its ecosystem: how it obtains food, its interactions with other species, and its abiotic requirements.

The competitive exclusion principle (Gause, 1934) states that two species cannot occupy exactly the same niche in the same habitat indefinitely. If they do, one will outcompete the other. In practice, species with similar niches coexist through resource partitioning: they exploit slightly different resources or are active at different times.

1.2 Trophic Levels

Energy flows through ecosystems in a unidirectional manner from producers to consumers:

Trophic Level	Organisms	Energy Source
Producer (autotroph)	Plants, algae, some bacteria	Sunlight (photosynthesis) or chemicals (chemosynthesis)
Primary consumer (herbivore)	Caterpillars, rabbits, zooplankton	Eat producers
Secondary consumer (carnivore)	Small birds, frogs, small fish	Eat primary consumers
Tertiary consumer (carnivore)	Hawks, large fish, lions	Eat secondary consumers
Decomposer (detritivore)	Fungi, bacteria, earthworms	Break down dead organic matter

Food chains show a single pathway of energy transfer. Food webs show the complex, interconnected network of feeding relationships in an ecosystem, reflecting the reality that most organisms eat (and are eaten by) multiple species.

1.3 Ecological Productivity

Gross primary production (GPP) is the total rate at which energy is captured by photosynthesis in a given area per unit time:

$\mathrm{GPP} = \mathrm{total\ solar\ energy\ fixed\ by\ photosynthesis\ per\ unit\ area\ per\ unit\ time}$

Net primary production (NPP) is the energy available to consumers after the producers have met their own respiratory demands:

$\mathrm{NPP} = \mathrm{GPP} - R$

where $R$ is the energy lost through plant respiration.

NPP is the fundamental measure of ecosystem productivity and determines the maximum biomass of consumers that can be supported. Tropical rainforests and coral reefs have the highest NPP; deserts and tundra have the lowest.

1.4 Energy Transfer and Ecological Efficiency

Energy is lost at each trophic level through:

• Respiration: energy used in metabolic processes, lost as heat.
• Excretion: energy in undigested/uneaten material (faeces, urine).
• Egestion: energy lost in faeces.

The proportion of energy transferred from one trophic level to the next is typically only 10%--20% (ecological efficiency). This means that energy available at each successive level is much less than at the previous level, explaining why food chains are typically limited to 3--5 trophic levels.

Pyramids of number, biomass, and energy:

• Pyramid of numbers: shows the number of organisms at each trophic level. Can be inverted (e.g., one oak tree supporting thousands of insects).
• Pyramid of biomass: shows the total dry mass of organisms at each level. Can be inverted in aquatic systems where phytoplankton reproduce rapidly and have low standing biomass but high productivity.
• Pyramid of energy: always upright, because energy is lost at each transfer and cannot be created.

warning

Common Pitfall Students often state that "90% of energy is lost" at each trophic level. The precise figure varies (typically 80%--90% is lost, 10%--20% is transferred). The key point is that the loss is substantial and cumulative, which is why food chains are short. The lost energy is not "wasted" -- it is dissipated as heat according to the second law of thermodynamics.

2. Populations

2.1 Population Growth

A population is a group of organisms of the same species occupying a particular space at a particular time. Population size is determined by four factors:

$\frac{dN}{dt} = B - D + I - E$

where $B$ = births, $D$ = deaths, $I$ = immigration, $E$ = emigration.

Exponential (logistic) growth: when resources are unlimited, populations grow exponentially:

$N_t = N_0 e^{rt}$

where $N_t$ is the population size at time $t$, $N_0$ is the initial size, and $r$ is the intrinsic rate of increase.

Logistic growth: in reality, resources are limited. Population growth slows as it approaches the carrying capacity ($K$) -- the maximum population size that the environment can sustain indefinitely:

$\frac{dN}{dt} = rN\left(1 - \frac{N}{K}\right)$

When $N \ll K$, growth is approximately exponential. When $N$ approaches $K$, growth rate declines towards zero. If $N \gt K$, the population overshoots and declines.

2.2 Population Regulation

Density-dependent factors: factors whose effect increases with population density.

• Competition for limited resources (food, territory, mates)
• Predation (predators consume more prey when prey is abundant)
• Disease (transmission rate increases with population density)
• Waste accumulation (toxic waste products build up)

These factors produce negative feedback, stabilising the population around $K$.

Density-independent factors: factors whose effect is independent of population density.

• Natural disasters (floods, fires, volcanic eruptions)
• Extreme weather events
• Human activities (deforestation, pollution)

These factors can cause sudden, unpredictable population changes regardless of size.

2.3 Survivorship Curves

Survivorship curves plot the number (or proportion) of surviving individuals against age:

• Type I: low early mortality, most individuals survive to old age, then die rapidly. Example: humans, large mammals. Characteristic of K-selected species (few offspring, high parental care).
• Type II: constant mortality rate throughout life. Example: many birds, small mammals.
• Type III: high early mortality, few individuals survive to adulthood, but those that do have high survival. Example: fish, invertebrates, plants producing many seeds. Characteristic of r-selected species (many offspring, little parental care).

3. Nutrient Cycles

3.1 General Principles

Unlike energy, nutrients are recycled within ecosystems. Nutrient cycles (biogeochemical cycles) involve the movement of elements between the biotic and abiotic components.

Key processes:

• Decomposition: detritivores (earthworms, woodlice) break down dead organic matter into smaller pieces; decomposers (bacteria, fungi) release enzymes that break down organic molecules into inorganic ions (mineralisation/amonification).
• Assimilation: plants absorb inorganic ions from the soil and incorporate them into organic molecules; animals obtain nutrients by consuming other organisms.
• Saprotrophic nutrition: fungi secrete extracellular enzymes onto dead matter, digest it externally, and absorb the products.

3.2 The Nitrogen Cycle

Nitrogen is essential for amino acids, proteins, nucleic acids, and ATP. Despite being 78% of the atmosphere, atmospheric $\mathrm{N_2}$ is unreactive and cannot be used directly by most organisms.

Key stages:

1. Nitrogen fixation: conversion of atmospheric $\mathrm{N_2}$ into ammonia ($\mathrm{NH_3}$) or ammonium ions ($\mathrm{NH_4^+}$).

   • Biological fixation: by nitrogen-fixing bacteria (e.g., Rhizobium in root nodules of legumes; Azotobacter in soil). These bacteria possess the enzyme nitrogenase, which catalyses: $\mathrm{N_2} + 6\mathrm{H}^+ + 6e^- + 16\mathrm{ATP} \to 2\mathrm{NH_3} + 16\mathrm{ADP} + 16P_i$.
   • Industrial fixation: Haber process ($\mathrm{N_2} + 3\mathrm{H_2} \rightleftharpoons 2\mathrm{NH_3}$, high temperature and pressure, iron catalyst).
   • Lightning: high energy converts $\mathrm{N_2}$ to $\mathrm{NO_x}$, which dissolves in rain as $\mathrm{NO_3^-}$.

2. Nitrification: conversion of $\mathrm{NH_4^+}$ to nitrite ($\mathrm{NO_2^-}$) by Nitrosomonas bacteria, then to nitrate ($\mathrm{NO_3^-}$) by Nitrobacter bacteria. Nitrates are the form most readily absorbed by plants.

3. Assimilation: plants absorb $\mathrm{NO_3^-}$ and $\mathrm{NH_4^+}$ through their roots and incorporate nitrogen into amino acids, proteins, and nucleic acids. Animals obtain nitrogen by eating plants or other animals.

4. Ammonification: decomposers break down proteins and urea in dead organisms and waste, releasing $\mathrm{NH_3}$ (which forms $\mathrm{NH_4^+}$ in solution).

5. Denitrification: conversion of $\mathrm{NO_3^-}$ back to $\mathrm{N_2}$ and $\mathrm{N_2O}$ by denitrifying bacteria (e.g., Pseudomonas) in anaerobic conditions (waterlogged soil). This returns nitrogen to the atmosphere, completing the cycle.

3.3 The Carbon Cycle

Carbon is the backbone of all organic molecules.

Key processes:

• Photosynthesis: $\mathrm{6CO_2} + 6\mathrm{H_2O} \to \mathrm{C_6H_{12}O_6} + 6\mathrm{O_2}$ (carbon moves from atmosphere/bicarbonate to organic molecules in producers).
• Respiration: $\mathrm{C_6H_{12}O_6} + 6\mathrm{O_2} \to 6\mathrm{CO_2} + 6\mathrm{H_2O}$ (carbon returns to atmosphere).
• Combustion: burning fossil fuels and biomass releases $\mathrm{CO_2}$.
• Decomposition: decomposers break down organic matter, releasing $\mathrm{CO_2}$.
• Fossilisation: incomplete decomposition of organic matter over millions of years forms coal, oil, and natural gas, sequestering carbon.
• Ocean exchange: $\mathrm{CO_2}$ dissolves in ocean water, forming $\mathrm{HCO_3^-}$ and $\mathrm{CO_3^{2-}}$ (carbonate buffer system). Marine organisms incorporate carbonate into shells and skeletons.

3.4 The Phosphorus Cycle

Unlike carbon and nitrogen, phosphorus has no significant gaseous phase. The cycle is sedimentary:

1. Weathering: phosphate-bearing rocks release $\mathrm{PO_4^{3-}}$ ions into soil and water.
2. Absorption by plants: plants take up $\mathrm{PO_4^{3-}}$ from soil.
3. Transfer through food chains: animals obtain phosphorus by consuming plants.
4. Decomposition: phosphorus in dead organisms and waste is returned to the soil.
5. Sedimentation and geological uplift: over geological time, phosphorus is deposited in sedimentary rocks and returned to the surface by tectonic activity.

4. Ecological Succession

4.1 Primary Succession

Primary succession is the colonisation of bare, lifeless substrate (e.g., volcanic rock, sand dunes, glacial moraine) where no soil exists.

Stages (example: sand dune succession):

1. Pioneer species: salt-tolerant plants (e.g., Lyme grass, sea couch grass) colonise the bare sand. They are tolerant of harsh conditions (salinity, drought, lack of nutrients) and stabilise the sand with their roots.
2. Soil formation: pioneer plants die and decompose, adding organic matter. Soil depth and nutrient content increase.
3. Colonisation by more demanding species: as conditions improve, less hardy species colonise. Mosses and lichens may precede higher plants.
4. Intermediate communities: a series of seres (seral stages) replaces the previous community. Each stage modifies the environment, making it less suitable for itself and more suitable for the next stage.
5. Climax community: the final, stable community in equilibrium with the climate. In the UK, this is typically oak or ash woodland. The climax community is self-sustaining and persists until a major disturbance.

4.2 Secondary Succession

Secondary succession occurs on previously colonised land where the existing community has been disturbed or removed (e.g., after a forest fire, flood, or deforestation), but soil remains.

Secondary succession proceeds faster than primary succession because soil and seed banks already exist. The stages are similar but start from an intermediate point.

4.3 Deflected Succession

Deflected succession occurs when succession is prevented from reaching the natural climax by human activity or other factors. Examples: regular mowing of grassland prevents succession to woodland; grazing by livestock maintains heathland; managed farmland is maintained at a plagioclimax.

5. Human Impacts on Ecosystems

5.1 Pollution

Eutrophication: the enrichment of water bodies with nutrients (nitrates and phosphates), primarily from agricultural fertiliser runoff and sewage discharge.

Stages of eutrophication:

1. Nitrates and phosphates enter a lake or river.
2. Algae grow rapidly (algal bloom), forming a dense layer on the surface.
3. Light cannot penetrate the algal layer, so submerged plants die.
4. Dead algae and dead plants are decomposed by bacteria.
5. Bacterial respiration consumes dissolved oxygen.
6. Hypoxia (very low dissolved oxygen) causes fish and other aerobic organisms to die.
7. Anaerobic decomposers take over, producing toxic substances (hydrogen sulfide, methane).

Biochemical oxygen demand (BOD) measures the amount of oxygen consumed by microorganisms in decomposing organic matter in a water sample over 5 days. High BOD indicates heavy pollution. Clean water has a BOD of approximately $2\ \mathrm{mg\ dm^{-3}}$; polluted water may exceed $20\ \mathrm{mg\ dm^{-3}}$.

5.2 Pesticides and Bioaccumulation

Pesticides are chemicals used to control pests (insects, weeds, fungi). Problems:

• Bioaccumulation: pesticides accumulate in the fatty tissues of organisms; concentration increases at each trophic level (biomagnification).
• Non-target effects: pesticides may harm beneficial species (pollinators, predators of pests).
• Resistance: overuse selects for resistant pest populations.

Example: DDT (dichlorodiphenyltrichloroethane) was widely used as an insecticide. Its persistence, bioaccumulation, and biomagnification caused eggshell thinning in birds of prey (ospreys, peregrine falcons), leading to population declines. DDT was banned in most countries following Rachel Carson's Silent Spring (1962).

5.3 Deforestation

Removal of forests for agriculture, logging, and urbanisation has consequences:

• Loss of biodiversity (habitat destruction, species extinction).
• Increased $\mathrm{CO_2}$ (loss of photosynthesis, release from burning).
• Soil erosion (loss of tree roots that bind soil).
• Disruption of the water cycle (less transpiration, reduced rainfall).
• Loss of indigenous knowledge and cultural heritage.

6. Global Warming

6.1 The Greenhouse Effect

The greenhouse effect is the process by which certain gases in the atmosphere (greenhouse gases) absorb and re-radiate infrared radiation emitted by the Earth's surface, warming the planet.

Natural greenhouse effect: essential for life; without it, Earth's average temperature would be approximately $-18\ ^\circ\mathrm{C}$ instead of +15\ ^^\circ\mathrm{C}.

Enhanced greenhouse effect: anthropogenic (human-caused) increases in greenhouse gas concentrations are intensifying the warming effect.

Key greenhouse gases:

Gas	Pre-industrial concentration	Current concentration	Contribution
$\mathrm{CO_2}$	$\approx 280\ \mathrm{ppm}$	$\approx 420\ \mathrm{ppm}$	$\approx 60\%$
$\mathrm{CH_4}$	$\approx 700\ \mathrm{ppb}$	$\approx 1900\ \mathrm{ppb}$	$\approx 20\%$
$\mathrm{N_2O}$	$\approx 270\ \mathrm{ppb}$	$\approx 330\ \mathrm{ppb}$	$\approx 6\%$

Sources: $\mathrm{CO_2}$ from fossil fuel combustion and deforestation; $\mathrm{CH_4}$ from agriculture (rice paddies, cattle), landfill, and fossil fuel extraction; $\mathrm{N_2O}$ from agricultural fertilisers and industrial processes.

6.2 Consequences of Global Warming

• Rising temperatures: global average temperature has risen by approximately $1.1\ ^\circ\mathrm{C}$ since pre-industrial times.
• Melting ice caps and glaciers: contributing to sea level rise (approximately $3.6\ \mathrm{mm\ yr^{-1}}$).
• Sea level rise: thermal expansion of seawater plus ice melt threatens low-lying coastal areas.
• Ocean acidification: increased $\mathrm{CO_2}$ absorption lowers ocean pH, threatening coral reefs and shellfish.
• Changes in weather patterns: more frequent extreme weather events (heatwaves, storms, droughts, flooding).
• Disruption of ecosystems: species ranges shift towards the poles and to higher altitudes; phenological mismatches (timing of flowering, migration, breeding become desynchronised).

7. Maintaining Biodiversity

7.1 Why Biodiversity Matters

Biodiversity provides ecosystem services: pollination of crops, water purification, soil formation, nutrient cycling, carbon sequestration, flood control, and raw materials (food, medicine, timber). High biodiversity also increases ecosystem resilience: diverse ecosystems are better able to withstand and recover from disturbances.

7.2 Conservation Strategies

In situ conservation: protecting species in their natural habitat.

• National parks and nature reserves: legal protection from development, agriculture, and hunting. Examples: Yellowstone National Park (USA), Serengeti National Park (Tanzania).
• Marine protected areas (MPAs): restrict fishing and other extractive activities.
• SSSIs (Sites of Special Scientific Interest): designated areas with important wildlife or geological features.
• Management techniques: controlled burning, grazing, coppicing, and rotational clearance to maintain specific habitats and prevent succession from reducing diversity.

Ex situ conservation: protecting species outside their natural habitat.

• Zoos and captive breeding programmes: breed endangered species in captivity for eventual reintroduction. Examples: California condor, Arabian oryx.
• Seed banks: store seeds of threatened plant species at low temperature and low humidity for long-term preservation. Example: the Millennium Seed Bank (Kew, UK).
• Botanical gardens: maintain living collections of threatened plant species.

International agreements:

• CITES (Convention on International Trade in Endangered Species): regulates or bans international trade in endangered species.
• Convention on Biological Diversity (CBD): commits nations to conserving biodiversity, using it sustainably, and sharing benefits from genetic resources.
• Rio Convention (1992): three linked conventions on biodiversity, climate change, and desertification.

warning

warning They are complementary strategies. In situ is generally preferred because it conserves the entire ecosystem and evolutionary processes, but ex situ is essential as a backup for species whose habitat has been destroyed or whose population is too small to survive in the wild.

8. Quantitative Ecology

8.1 Calculating Net Primary Production

NPP is the rate at which energy is stored as biomass by producers, after accounting for their own respiration. It is typically measured in $\mathrm{kJ\ m^{-2}\ yr^{-1}}$ or as dry biomass in $\mathrm{g\ m^{-2}\ yr^{-1}}$.

Worked Example 1. A meadow receives $2.0 \times 10^6\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$ of solar radiation. The plants absorb 40% of this. The gross primary production (GPP) is 2.5% of the absorbed radiation. Plant respiration accounts for 60% of GPP. Calculate NPP and the overall ecological efficiency.

Absorbed radiation $= 0.40 \times 2.0 \times 10^6 = 8.0 \times 10^5\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$.

$\mathrm{GPP} = 0.025 \times 8.0 \times 10^5 = 20000\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$.

$\mathrm{NPP} = \mathrm{GPP} - R = 20000 - 0.60 \times 20000 = 20000 - 12000 = 8000\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$.

Overall ecological efficiency (from total solar to NPP) $= \frac◆LB◆8000◆RB◆◆LB◆2.0 \times 10^6◆RB◆ = 0.004 = 0.4\%$.

Worked Example 2. An area of tropical rainforest has $\mathrm{GPP} = 22000\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$ and $\mathrm{NPP} = 15000\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$. A desert has $\mathrm{GPP} = 1200\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$ and $\mathrm{NPP} = 400\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$. Compare the ecological efficiencies.

Rainforest: fraction lost to respiration $= \frac{22000 - 15000}{22000} = 0.318 = 31.8\%$.

Desert: fraction lost to respiration $= \frac{1200 - 400}{1200} = 0.667 = 66.7\%$.

The desert ecosystem is less efficient at converting GPP to NPP because a larger proportion of captured energy is lost to respiration. This is partly because desert plants invest more energy in root systems and water acquisition mechanisms.

8.2 Population Growth Modelling

Worked Example 1. A population of bacteria has an initial size $N_0 = 100$ and an intrinsic rate of increase $r = 0.693\ \mathrm{h^{-1}}$. Calculate the population size after 5 hours, assuming unlimited resources (exponential growth).

$N_t = N_0 e^{rt} = 100 \times e^{0.693 \times 5} = 100 \times e^{3.465} = 100 \times 31.99 = 3199$

Note: $r = 0.693\ \mathrm{h^{-1}}$ corresponds to a doubling time of $t_d = \frac◆LB◆\ln 2◆RB◆◆LB◆r◆RB◆ = \frac{0.693}{0.693} = 1\ \mathrm{hour}$. In 5 hours, the population doubles 5 times: $100 \times 2^5 = 3200$ (consistent with the exponential calculation, within rounding).

Worked Example 2. A population of rabbits has carrying capacity $K = 500$ and intrinsic rate of increase $r = 1.2\ \mathrm{yr^{-1}}$. If the current population is $N = 100$, what is the current rate of population growth?

$\frac{dN}{dt} = rN\left(1 - \frac{N}{K}\right) = 1.2 \times 100 \times \left(1 - \frac{100}{500}\right) = 120 \times 0.8 = 96\ \mathrm{individuals\ yr^{-1}}$

When $N = 250$ (half of $K$), the growth rate is maximised:

$\frac{dN}{dt} = 1.2 \times 250 \times 0.5 = 150\ \mathrm{individuals\ yr^{-1}}$

The maximum growth rate always occurs at $N = K/2$.

8.3 Ecological Footprint Calculations

The ecological footprint measures the area of land and water required to produce the resources consumed and to absorb the waste produced by a population, expressed in global hectares (gha) per person.

Worked Example. If the average person in a country has an ecological footprint of $5.0\ \mathrm{gha}$ and the country's biocapacity is $3.2\ \mathrm{gha}$ per person:

Ecological deficit $= 5.0 - 3.2 = 1.8\ \mathrm{gha}$ per person.

This means the country is consuming resources faster than they can be regenerated, running an ecological deficit. It is meeting the shortfall by importing resources, depleting its own natural capital, or emitting waste that cannot be absorbed (e.g., $\mathrm{CO_2}$ exceeding absorption capacity).

warning

Common Pitfall Students sometimes calculate ecological efficiency as the fraction of solar energy that reaches producers, rather than the fraction transferred between trophic levels. The ecological efficiency between trophic levels is the fraction of energy at one level that is incorporated into biomass at the next level (typically 10--20%), not the fraction of total solar radiation captured by producers (typically less than 3%).

9. Advanced Nutrient Cycle Analysis

9.1 Quantifying the Nitrogen Cycle

Worked Example. A farmer applies $150\ \mathrm{kg\ ha^{-1}}$ of ammonium nitrate fertiliser ($\mathrm{NH_4NO_3}$, molar mass $= 80\ \mathrm{g\ mol^{-1}}$). Calculate the mass of nitrogen applied per hectare.

Molar mass of $\mathrm{NH_4NO_3} = 2(14) + 4(1) + 3(16) = 80\ \mathrm{g\ mol^{-1}}$.

Mass fraction of nitrogen $= \frac{28}{80} = 0.35 = 35\%$.

Mass of nitrogen applied $= 150 \times 0.35 = 52.5\ \mathrm{kg\ ha^{-1}}$.

If only 50% of applied nitrogen is taken up by crops (the rest is lost through leaching, denitrification, or volatilisation), the effective nitrogen available to crops is $26.25\ \mathrm{kg\ ha^{-1}}$. The excess $26.25\ \mathrm{kg\ ha^{-1}}$ contributes to eutrophication if it enters water bodies.

9.2 BOD Calculations in Detail

Biochemical oxygen demand (BOD) measures the amount of oxygen (in $\mathrm{mg\ dm^{-3}}$) consumed by microorganisms in decomposing organic matter in a water sample over 5 days at $20\ ^\circ\mathrm{C}$.

Worked Example. A water sample is taken from a river upstream and downstream of a sewage outfall.

Measurement	Upstream	Downstream
Dissolved $\mathrm{O_2}$ initially ($\mathrm{mg\ dm^{-3}}$)	9.2	8.8
Dissolved $\mathrm{O_2}$ after 5 days ($\mathrm{mg\ dm^{-3}}$)	7.8	2.1

Upstream $\mathrm{BOD} = 9.2 - 7.8 = 1.4\ \mathrm{mg\ dm^{-3}}$.

Downstream $\mathrm{BOD} = 8.8 - 2.1 = 6.7\ \mathrm{mg\ dm^{-3}}$.

The downstream BOD is nearly 5 times higher, indicating significant organic pollution from the sewage outfall. The dissolved oxygen level downstream after 5 days ($2.1\ \mathrm{mg\ dm^{-3}}$) is below the level required by most fish species ($> 5\ \mathrm{mg\ dm^{-3}}$), suggesting the river downstream is undergoing hypoxia.

9.3 The Carbon Cycle: Quantitative Analysis

Worked Example. An area of forest covers $10\ \mathrm{km^2}$. The average NPP of the forest is $1200\ \mathrm{g\ C\ m^{-2}\ yr^{-1}}$. The average rate of decomposition returns 900 $\mathrm{g\ C\ m^{-2}\ yr^{-1}}$ to the atmosphere as $\mathrm{CO_2}$.

Total NPP $= 1200 \times 10^7 = 1.2 \times 10^{10}\ \mathrm{g\ C\ yr^{-1}} = 12000\ \mathrm{tonnes\ C\ yr^{-1}}$.

Net carbon sequestration $= \mathrm{NPP} - \text{decomposition} = (1200 - 900) \times 10^7 = 3000\ \mathrm{tonnes\ C\ yr^{-1}}$.

If the forest is cleared, this sequestration is lost. Additionally, burning releases the stored carbon in biomass back to the atmosphere. If the forest biomass contains $5000\ \mathrm{tonnes\ C\ km^{-2}}$, clearing 10 $\mathrm{km^2}$ releases 50000 tonnes of carbon, equivalent to $50000 \times \frac{44}{12} = 183333\ \mathrm{tonnes\ CO_2}$.

10. Fieldwork Techniques and Data Analysis

10.1 Random Sampling with Quadrats

Worked Example. A student uses a $0.5\ \mathrm{m} \times 0.5\ \mathrm{m}$ quadrat to estimate the population density of daisies in a $100\ \mathrm{m} \times 50\ \mathrm{m}$ field. They place 10 quadrats randomly and count: 12, 8, 15, 6, 10, 14, 9, 11, 7, 13 daisies.

Mean daisies per quadrat $= \frac{12 + 8 + 15 + 6 + 10 + 14 + 9 + 11 + 7 + 13}{10} = \frac{105}{10} = 10.5$

Mean density $= \frac◆LB◆10.5◆RB◆◆LB◆0.5 \times 0.5◆RB◆ = 42\ \mathrm{daisies\ m^{-2}}$.

Estimated total population $= 42 \times 100 \times 50 = 210000$ daisies.

Standard deviation $= \sqrt◆LB◆\frac◆LB◆\sum(x_i - \bar{x})^2◆RB◆◆LB◆n-1◆RB◆◆RB◆ = \sqrt◆LB◆\frac{(12-10.5)^2 + (8-10.5)^2 + ... + (13-10.5)^2}{9}◆RB◆ = \sqrt◆LB◆\frac{70.5}{9}◆RB◆ = \sqrt{7.83} = 2.80$.

Standard error $= \frac◆LB◆s◆RB◆◆LB◆\sqrt{n}◆RB◆ = \frac◆LB◆2.80◆RB◆◆LB◆\sqrt{10}◆RB◆ = 0.89\ \mathrm{daisies\ per\ quadrat}$.

The 95% confidence interval is approximately $\bar{x} \pm 2 \times \mathrm{SE} = 10.5 \pm 1.78$, or 8.72 to 12.28 daisies per quadrat. Converting to total population: 174400 to 245600 daisies.

10.2 The Lincoln Index (Capture-Mark-Recapture)

For mobile organisms that cannot be counted directly, the Lincoln index estimates population size:

$N = \frac◆LB◆n_1 \times n_2◆RB◆◆LB◆n_3◆RB◆$

where:

• $n_1$ = number captured and marked in the first sample
• $n_2$ = number captured in the second sample
• $n_3$ = number of marked individuals recaptured in the second sample

Worked Example. A researcher studying woodlice captures 80 individuals, marks them, and releases them. One week later, she captures 60 individuals, of which 12 are marked.

$N = \frac◆LB◆80 \times 60◆RB◆◆LB◆12◆RB◆ = 400$

Estimated population size $= 400$ woodlice.

Assumptions of the Lincoln index:

• Marked and unmarked individuals have the same probability of capture (marks do not affect behaviour).
• The proportion of marked to unmarked individuals in the population does not change between sampling (no births, deaths, immigration, or emigration).
• Marks are not lost.
• Samples are random.

warning

Common Pitfall The Lincoln index assumes a closed population between the two sampling events. If organisms are born, die, migrate in, or migrate out between samples, the estimate will be inaccurate. If no marked individuals are recaptured ($n_3 = 0$), the method fails entirely.

11. Climate Change and Ocean Acidification

11.1 Ocean Acidification: Quantitative Analysis

The ocean absorbs approximately 25--30% of anthropogenic $\mathrm{CO_2}$ emissions. Dissolved $\mathrm{CO_2}$ reacts with water:

$\mathrm{CO_2(aq)} + \mathrm{H_2O} \rightleftharpoons \mathrm{H_2CO_3} \rightleftharpoons \mathrm{H^+} + \mathrm{HCO_3^-} \rightleftharpoons 2\mathrm{H^+} + \mathrm{CO_3^{2-}}$

Increased $\mathrm{CO_2}$ drives this equilibrium to the right, increasing $[\mathrm{H^+}]$ (decreasing pH) and decreasing $[\mathrm{CO_3^{2-}}]$.

Worked Example. Pre-industrial ocean surface pH was approximately 8.18. Current pH is approximately 8.07. Calculate the change in $[\mathrm{H^+}]$.

Pre-industrial: $[\mathrm{H^+}] = 10^{-8.18} = 6.61 \times 10^{-9}\ \mathrm{mol\ dm^{-3}}$.

Current: $[\mathrm{H^+}] = 10^{-8.07} = 8.51 \times 10^{-9}\ \mathrm{mol\ dm^{-3}}$.

Change: $\frac{8.51 - 6.61}{6.61} \times 100\% = 28.7\%$ increase in $[\mathrm{H^+}]$.

A change of 0.11 pH units represents a 29% increase in hydrogen ion concentration, illustrating that even small changes in pH reflect significant chemical changes.

Biological consequences: decreased $[\mathrm{CO_3^{2-}}$ reduces the saturation state of calcium carbonate ($\mathrm{CaCO_3}$), making it more difficult for marine organisms to build and maintain their shells and skeletons. Coral reefs, pteropods, and some phytoplankton species are particularly vulnerable. If $\mathrm{CO_3^{2-}}$ concentration falls below the aragonite saturation threshold, coral skeletons begin to dissolve.

12. Practical Ecology: Measuring Abiotic Factors

12.1 Key Abiotic Measurements

Factor	Instrument	Unit
Temperature	Thermometer / data logger	$^\circ\mathrm{C}$
Light intensity	Light meter (lux meter)	Lux or $\mathrm{W\ m^{-2}}$
Soil / water pH	pH meter / pH indicator paper	pH
Dissolved oxygen	Dissolved oxygen probe	$\mathrm{mg\ dm^{-3}}$ or % saturation
Soil moisture	Soil moisture meter	% volumetric water content
Wind speed	Anemometer	$\mathrm{m\ s^{-1}}$
Humidity	Hygrometer	% relative humidity
Water flow rate	Flow meter	$\mathrm{m^3\ s^{-1}}$

12.2 Reliability and Validity in Ecological Investigations

Reliability: results are consistent when the investigation is repeated. Improved by: using large sample sizes, taking multiple measurements at each site, using standardised techniques, and controlling variables.

Validity: the investigation measures what it claims to measure. Improved by: using appropriate sampling methods, controlling confounding variables, and ensuring measurements are taken at the same time of day and under similar weather conditions.

Correlation vs causation: an observed correlation between two variables (e.g., light intensity and plant height) does not establish causation. Controlled experiments or manipulation of one variable while holding others constant are needed to establish causal relationships.

Practice Problems

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Problem 1

A lake receives runoff containing nitrates and phosphates from surrounding agricultural land. Describe the process of eutrophication and explain its ecological consequences.

Answer. Nitrates and phosphates enter the lake, providing excess nutrients. This stimulates rapid growth of algae, forming a dense algal bloom on the surface. The algal layer blocks light from reaching submerged plants, which can no longer photosynthesise and die. Dead algae and dead plants are decomposed by aerobic bacteria, whose populations increase dramatically. These bacteria consume dissolved oxygen from the water through respiration, causing dissolved oxygen levels to fall (hypoxia). When oxygen levels drop too low, fish and other aerobic organisms die. Anaerobic bacteria then dominate decomposition, producing toxic substances (hydrogen sulfide, methane) that further degrade water quality. The ecological consequences include loss of biodiversity (death of fish, invertebrates, and plants), disruption of food webs, and potentially irreversible ecosystem damage.

If you get this wrong, revise: Eutrophication

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Problem 2

If 10,000 J of energy is available at the producer level of a food chain, calculate the energy available at each subsequent trophic level, assuming an ecological efficiency of 15%.

Answer. At each trophic level, 15% of the energy from the previous level is transferred.

Producer level: $10000\ \mathrm{J}$.

Primary consumer: $10000 \times 0.15 = 1500\ \mathrm{J}$.

Secondary consumer: $1500 \times 0.15 = 225\ \mathrm{J}$.

Tertiary consumer: $225 \times 0.15 = 33.75\ \mathrm{J}$.

The remaining 85% at each level is lost through respiration, excretion, egestion, and heat. After four trophic levels, only 0.34% of the original energy remains available, illustrating why long food chains are rare and why top predators are always relatively few in number.

If you get this wrong, revise: Energy Transfer and Ecological Efficiency

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Problem 3

Describe the role of microorganisms in the nitrogen cycle. In your answer, name the specific groups of bacteria involved and the chemical transformations they catalyse.

Answer. Nitrogen-fixing bacteria (Rhizobium in root nodules, Azotobacter free-living in soil) convert atmospheric $\mathrm{N_2}$ into $\mathrm{NH_3}$/$\mathrm{NH_4^+}$ using the enzyme nitrogenase, an energy-intensive process requiring 16 ATP per molecule of $\mathrm{N_2}$ fixed. Nitrifying bacteria (Nitrosomonas converts $\mathrm{NH_4^+}$ to $\mathrm{NO_2^-}$; Nitrobacter converts $\mathrm{NO_2^-}$ to $\mathrm{NO_3^-}$) make nitrogen available in the form most readily absorbed by plant roots. Denitrifying bacteria (Pseudomonas, Paracoccus) convert $\mathrm{NO_3^-}$ back to $\mathrm{N_2}$ gas under anaerobic conditions (waterlogged soil), returning nitrogen to the atmosphere. Decomposers break down proteins and urea in dead organic matter and excretory waste, releasing $\mathrm{NH_4^+}$ through ammonification. These microbial processes collectively maintain the nitrogen cycle, ensuring continuous availability of nitrogen for living organisms despite constant losses through denitrification.

If you get this wrong, revise: The Nitrogen Cycle

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Problem 4

Explain the difference between primary and secondary succession, giving an example of each. Why does secondary succession generally proceed faster?

Answer. Primary succession occurs on bare, lifeless substrate where no soil exists (e.g., volcanic lava, glacial moraine, sand dunes). It begins with the colonisation by pioneer species (lichens, salt-tolerant grasses) that can tolerate harsh conditions and begin the slow process of soil formation through the accumulation of organic matter from dead organisms. Example: succession on sand dunes beginning with Lyme grass and progressing through marram grass, herbs, shrubs, and eventually woodland. Secondary succession occurs on previously colonised land where the existing community has been removed but soil remains (e.g., after a forest fire, abandoned farmland, or clearance). It proceeds faster because soil (with its nutrients, seed bank, and microorganisms) is already present, so the pioneer stage is bypassed and colonisation by higher-order species can begin immediately. Example: regeneration of forest after a wildfire, where grasses and shrubs colonise quickly, followed by tree seedlings.

If you get this wrong, revise: Primary Succession

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Problem 5

Evaluate the relative advantages and disadvantages of in situ and ex situ conservation strategies for maintaining biodiversity.

Answer. In situ conservation (protecting species in their natural habitat) preserves the entire ecosystem, including ecological interactions (food webs, pollination, competition), which cannot be replicated in captivity. It allows natural evolutionary processes (adaptation, selection) to continue. National parks and reserves can also provide economic benefits through ecotourism. However, in situ conservation is vulnerable to habitat destruction, climate change, and political instability, and requires large areas of land. Ex situ conservation (zoos, seed banks, botanical gardens) provides a safety net for species whose habitat has been destroyed or whose wild population is critically low. Seed banks are cost-effective and can store genetic diversity for centuries. Captive breeding can prevent imminent extinction. However, ex situ conservation cannot replicate natural selection pressures, may lead to loss of behaviours learned in the wild, suffers from reduced genetic diversity in small captive populations (inbreeding depression), and is extremely expensive for large animals. The most effective approach combines both: in situ as the primary strategy, with ex situ as a backup.

If you get this wrong, revise: Conservation Strategies

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Problem 6

Explain the mechanism of the enhanced greenhouse effect and discuss the evidence linking human activities to global warming.

Answer. The greenhouse effect occurs when greenhouse gases ($\mathrm{CO_2}$, $\mathrm{CH_4}$, $\mathrm{N_2O}$, water vapour) in the atmosphere absorb infrared radiation re-emitted by the Earth's surface and re-radiate it in all directions, including back towards the surface, warming the planet. The enhanced greenhouse effect refers to the additional warming caused by increased atmospheric concentrations of these gases due to human activities. Evidence: (1) Atmospheric $\mathrm{CO_2}$ has risen from approximately $280\ \mathrm{ppm}$ (pre-industrial) to over $420\ \mathrm{ppm}$ (2024), directly correlated with fossil fuel combustion (ice core data show current levels are unprecedented in the last 800,000 years). (2) Global average temperature has risen by approximately $1.1\ ^\circ\mathrm{C}$ since 1850, with the rate of increase accelerating. (3) Isotopic analysis of atmospheric $\mathrm{CO_2}$ shows an increasing proportion of $^{13}\mathrm{C}$-depleted carbon, consistent with fossil fuel combustion (fossil fuels are depleted in $^{13}\mathrm{C}$). (4) Ocean acidification (pH has decreased by approximately 0.1 units since pre-industrial times) is consistent with increased $\mathrm{CO_2}$ absorption. (5) Atmospheric $\mathrm{CH_4}$ and $\mathrm{N_2O}$ have risen in parallel with agricultural and industrial expansion. These lines of evidence together establish a causal link between human activities and global warming.

If you get this wrong, revise: The Greenhouse Effect

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Problem 7

A student uses the capture-mark-recapture method to estimate the population size of woodlice in a garden. In the first sample, she captures 50 woodlice, marks them, and releases them. In the second sample (one week later), she captures 40 woodlice, of which 8 are marked. (a) Calculate the estimated population size. (b) List three assumptions of this method and explain how a violation of each would affect the estimate. (c) The student repeats the study with a larger sample size. Explain why this improves the reliability of the estimate.

Answer. (a) $N = \frac◆LB◆n_1 \times n_2◆RB◆◆LB◆n_3◆RB◆ = \frac◆LB◆50 \times 40◆RB◆◆LB◆8◆RB◆ = 250$ woodlice.

(b) Assumption 1: marks are not lost between samples. If marks are lost, $n_3$ decreases, causing overestimation of $N$ (denominator is smaller). Assumption 2: marked individuals mix randomly with the population. If marked individuals remain clustered near the release point, the probability of recapture is higher in that area, potentially causing either over- or under-estimation depending on where the second sample is taken. Assumption 3: the population is closed (no births, deaths, immigration, or emigration). Deaths of marked individuals reduce $n_3$, causing overestimation. Immigration of unmarked individuals increases the population but not $n_3$, also causing overestimation.

(c) Larger sample sizes reduce the effect of random sampling error. The estimate $N = \frac{n_1 n_2}{n_3}$ has uncertainty that is inversely related to $n_3$. With only 8 recaptures, random variation could substantially change the estimate. If $n_3 = 7$ instead of 8, $N = 286$ instead of 250 -- a 14% change. Larger samples give smaller proportional changes.

If you get this wrong, revise: The Lincoln Index (Capture-Mark-Recapture)

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Problem 8

An agricultural ecosystem has the following energy values (in $\mathrm{kJ\ m^{-2}\ yr^{-1}}$):

Trophic Level	Energy intake	Energy lost in faeces	Energy lost in respiration
Wheat (producer)	25000	0	8000
Aphid (primary)	2000	800	700
Ladybird (secondary)	300	120	120

(a) Calculate the ecological efficiency between each trophic level. (b) Calculate NPP of the wheat. (c) Explain why the ecological efficiency is less than 100% at each level.

Answer. (a) Energy available to aphids (assimilated by wheat minus wheat respiration, stored as NPP): $\mathrm{NPP} = 25000 - 8000 = 17000\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$.

Ecological efficiency (wheat to aphid) $= \frac{2000}{17000} \times 100\% = 11.8\%$.

Energy assimilated by aphids $= 2000 - 800 = 1200\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$.

Ecological efficiency (aphid to ladybird) $= \frac{300}{1200} \times 100\% = 25.0\%$.

(b) $\mathrm{NPP} = \mathrm{GPP} - R = 25000 - 8000 = 17000\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$.

(c) Ecological efficiency is less than 100% because: (1) not all biomass at one level is consumed by the next (some wheat is not eaten by aphids); (2) not all consumed material is digested and absorbed (faeces contain undigested material); (3) much of the assimilated energy is used for respiration (metabolism, movement, heat production) and is lost as heat. Only the remaining energy is converted to new biomass (growth and reproduction) available to the next trophic level.

If you get this wrong, revise: Ecological Productivity and Quantitative Ecology

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Problem 9

Explain how the nitrogen cycle would be disrupted by the application of large quantities of nitrogen fertiliser to agricultural land. In your answer, describe the effects on (a) the soil nitrogen cycle, (b) aquatic ecosystems downstream, and (c) the soil microbiome.

Answer. (a) Excess nitrogen fertiliser (as $\mathrm{NH_4NO_3}$ or $\mathrm{NH_4^+}$) increases the concentration of ammonium and nitrate in the soil far above natural levels. This can inhibit nitrogen-fixing bacteria (because they have no selective advantage when fixed nitrogen is abundant) and stimulate denitrifying bacteria, increasing \mathrm{N_2\mathrm{O} emissions (a potent greenhouse gas). The natural balance between fixation, nitrification, and denitrification is disrupted.

(b) Excess nitrates are highly soluble and readily leach from the soil into groundwater and rivers. This causes eutrophication downstream: nitrates act as nutrients for algae, causing algal blooms that block light and deplete dissolved oxygen when decomposed, killing aquatic organisms. High nitrate concentrations in drinking water are also a health concern (methemoglobinemia, or "blue baby syndrome," in infants).

(c) High concentrations of ammonium-based fertilisers can lower soil pH over time (ammonium nitrification releases $\mathrm{H^+}$). Acidification inhibits many soil microorganisms, reducing the diversity and activity of decomposers, mycorrhizal fungi, and other beneficial soil organisms. This reduces soil fertility in the long term, creating a dependency on continued fertiliser application.

If you get this wrong, revise: The Nitrogen Cycle and Advanced Nutrient Cycle Analysis

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13. Population Dynamics: Advanced Models

13.1 Exponential vs Logistic Growth

Exponential growth occurs when resources are unlimited:

$N_t = N_0 e^{rt}$

Where $N_t$ = population size at time $t$, $N_0$ = initial population size, $r$ = intrinsic rate of increase, $t$ = time.

Exponential growth produces a J-shaped curve. It is unrealistic in nature because resources are always finite.

Logistic growth incorporates a carrying capacity ($K$):

$\frac{dN}{dt} = rN \left(1 - \frac{N}{K}\right)$

The logistic equation produces an S-shaped (sigmoidal) curve:

• When $N \ll K$: growth is approximately exponential ($1 - N/K \approx 1$).
• When $N = K/2$: population growth rate is maximum.
• When $N \approx K$: growth rate approaches zero (population stabilises).

13.2 Worked Example: Population Growth

A population of bacteria starts with 100 cells and has an intrinsic growth rate of $r = 0.5\ \mathrm{h^{-1}}$. The carrying capacity is $10^6$ cells.

Using the exponential model: $N_t = 100 \times e^{0.5 \times 10} = 100 \times e^5 = 100 \times 148.4 = 14,840$ cells after 10 hours.

Using the logistic model (at $t = 10\ \mathrm{h}$, assuming $N \ll K$): the result is approximately the same because the population is far below $K$.

At $t = 30\ \mathrm{h}$: exponential model gives $N = 100 \times e^{15} = 3.27 \times 10^8$ cells (exceeds $K$, unrealistic). The logistic model would cap the population at $K = 10^6$.

13.3 Survivorship Curves

Survivorship curves plot the proportion of individuals surviving against age:

Type	Shape	Characteristics	Examples
Type I	Convex (steep decline at old age)	Low mortality in early and middle life; most individuals survive to old age	Humans, elephants, large mammals
Type II	Straight diagonal (constant mortality rate)	Constant probability of death at all ages	Many birds, small mammals, annual plants
Type III	Concave (steep decline early)	High mortality in early life; those that survive the juvenile period have low mortality	Fish, marine invertebrates, trees (produce many seeds, few survive)

14. Advanced Ecological Interactions

14.1 Niche Concepts

Fundamental niche: the full range of environmental conditions (temperature, pH, food, habitat) in which a species could survive and reproduce, in the absence of competitors.

Realised niche: the actual range of conditions a species occupies in nature, restricted by competition, predation, and other biotic interactions.

Competitive exclusion principle (Gause's principle): two species cannot coexist indefinitely in the same habitat if they occupy exactly the same niche. One species will outcompete the other, leading to competitive exclusion.

Resource partitioning: to avoid competitive exclusion, similar species divide the available resources (e.g., different feeding heights, different active times, different prey sizes). This allows coexistence by reducing niche overlap.

14.2 Predator-Prey Dynamics

Predator and prey populations show cyclical fluctuations (the Lotka-Volterra model):

• When prey population increases, predator population increases (more food available).
• When predator population increases, prey population decreases (more predation).
• When prey population decreases, predator population decreases (less food available).
• When predator population decreases, prey population recovers.

The predator population cycle typically lags behind the prey cycle because there is a time delay between the change in prey availability and the predator population response (predators need time to reproduce).

The classic example is the snowshoe hare and lynx cycle in the Canadian Arctic, recorded by the Hudson's Bay Company from fur trapping records over nearly 100 years.

14.3 Ecological Succession: Mechanisms

Primary succession occurs on bare, lifeless substrate (e.g., volcanic rock, sand dunes, glacial moraine):

1. Pioneer species: lichens and algae colonise bare rock. Lichens secrete acids that weather the rock, beginning soil formation.
2. Mosses and ferns colonise the thin soil.
3. Grasses and herbs establish, adding organic matter when they die.
4. Shrubs replace grasses.
5. Fast-growing trees (e.g., birch, pine) colonise.
6. Climax community (e.g., oak-hickory forest in temperate regions) is reached. This is a stable, self-sustaining community that does not change significantly unless disrupted.

Secondary succession occurs in an area where an existing community has been disturbed (e.g., after a forest fire, flood, or farming abandonment). Soil is already present, so succession proceeds faster than primary succession.

15. Human Impacts: Advanced Analysis

15.1 Eutrophication: Quantitative Analysis

Worked Example. A lake receives agricultural runoff containing $5\ \mathrm{mg\ L^{-1}}$ of nitrate ($\mathrm{NO_3^-}$). The lake has a volume of $2.5 \times 10^6\ \mathrm{m^3}$ and an outflow rate of $10^4\ \mathrm{m^3\ day^{-1}}$.

Concentration of nitrate entering lake per day $= 5\ \mathrm{mg\ L^{-1}} \times 10^4\ \mathrm{m^3\ day^{-1}} \times 10^3\ \mathrm{L\ m^{-3}} = 5 \times 10^7\ \mathrm{mg\ day^{-1}} = 50\ \mathrm{kg\ day^{-1}}$.

Assuming the lake is well-mixed and outflow has the same concentration as the lake:

At steady state: input rate $=$ output rate.

$50\ \mathrm{kg\ day^{-1}} = C_{\text{lake}} \times 10^4\ \mathrm{m^3\ day^{-1}} \times 10^3\ \mathrm{L\ m^{-1}}$.

$C_{\text{lake}} = \frac◆LB◆50\ \mathrm{kg}◆RB◆◆LB◆10^7\ \mathrm{L}◆RB◆ = \frac◆LB◆50000\ \mathrm{mg}◆RB◆◆LB◆10^7\ \mathrm{L}◆RB◆ = 5\ \mathrm{mg\ L^{-1}}$.

If the safe level for nitrate in drinking water is $11.3\ \mathrm{mg\ L^{-1}}$ (EU standard), this lake is currently within the safe limit but close. An increase in agricultural intensity could push it above the safe level.

15.2 Deforestation and the Carbon Cycle

Tropical rainforests store approximately $200\ \mathrm{t\ ha^{-1}}$ of carbon in biomass. Deforestation releases this carbon as $\mathrm{CO_2}$ when trees are burned or when dead biomass decomposes.

Worked Example. If $10\ \mathrm{million\ ha}$ of tropical rainforest are cleared per year:

Carbon released $= 10 \times 10^6 \times 200\ \mathrm{t\ C\ yr^{-1}} = 2 \times 10^9\ \mathrm{t\ C\ yr^{-1}}$.

As $\mathrm{CO_2}$: mass of $\mathrm{CO_2} = 2 \times 10^9 \times \frac{44}{12} = 7.3 \times 10^9\ \mathrm{t\ CO_2\ yr^{-1}}$.

Global $\mathrm{CO_2}$ emissions from fossil fuels are approximately $36 \times 10^9\ \mathrm{t\ CO_2\ yr^{-1}}$. Deforestation contributes an additional approximately $20\%$ to global $\mathrm{CO_2}$ emissions.

15.3 Indicator Species

Indicator species are organisms whose presence, absence, or abundance reflects the environmental quality of a habitat:

Environment	Indicator Species	What It Indicates
Freshwater (clean)	Stonefly larvae, mayfly larvae, caddisfly larvae	Low pollution, high dissolved $\mathrm{O_2}$
Freshwater (moderate pollution)	Freshwater shrimp, bloodworm	Some organic pollution
Freshwater (heavy pollution)	Rat-tailed maggot, sludgeworm	High organic pollution, low dissolved $\mathrm{O_2}$
Air quality	Lichens (especially crustose lichens)	Lichens are sensitive to $\mathrm{SO_2}$; their absence indicates air pollution
Soil quality	Earthworms	High earthworm count indicates healthy, well-aerated soil with high organic content

Biological Oxygen Demand (BOD) is a quantitative measure of water pollution: it measures the amount of $\mathrm{O_2}$ required by microorganisms to decompose organic matter in a water sample over 5 days ($\mathrm{BOD_5}$).

• Clean water: $\mathrm{BOD_5} < 5\ \mathrm{mg\ L^{-1}}$.
• Moderately polluted: $\mathrm{BOD_5} = 5$--$10\ \mathrm{mg\ L^{-1}}$.
• Severely polluted: $\mathrm{BOD_5} > 10\ \mathrm{mg\ L^{-1}}$.

16. Conservation Biology: Advanced Topics

16.1 The Species-Area Relationship

The species-area relationship describes how the number of species in a habitat increases with habitat area:

$S = cA^z$

Where $S$ = number of species, $A$ = area, $c$ = constant (depends on the type of organism and habitat), $z$ = slope (typically $0.2$--$0.35$ for islands).

This relationship has important implications for habitat fragmentation:

If a forest is reduced to 10% of its original area: $S' = c(0.1A)^z = 0.1^z \times cA^z = 0.1^{0.3} \times S = 0.50 \times S$.

The new area will contain approximately 50% of the original number of species, even though only 10% of the habitat remains. This is because smaller areas support smaller populations, which are more vulnerable to extinction (demographic stochasticity, environmental stochasticity, genetic drift).

16.2 Island Biogeography

MacArthur and Wilson's island biogeography theory (1967) predicts that the number of species on an island is determined by the balance between immigration rate and extinction rate:

• Immigration rate decreases with the number of species already present (most new arrivals are already present) and increases with island size (larger target) and proximity to the mainland (shorter distance).
• Extinction rate increases with the number of species present (more competition) and decreases with island size (larger populations are less vulnerable to extinction).

At equilibrium: immigration rate $=$ extinction rate. Larger, closer islands have more species; smaller, more distant islands have fewer species.

16.3 In Situ vs Ex Situ Conservation

Method	Description	Advantages	Disadvantages
In situ (on-site)	Protecting species in their natural habitat (national parks, nature reserves, SSSIs)	Preserves the entire ecosystem and evolutionary processes; cheaper in the long term	Vulnerable to habitat degradation, climate change, poaching
Ex situ (off-site)	Protecting species outside their natural habitat (zoos, botanical gardens, seed banks, cryopreservation)	Provides a safety net against extinction; allows captive breeding and reintroduction	Expensive; animals may lose natural behaviours; genetic diversity may be reduced in small captive populations

Seed banks store seeds at $-20$ degrees C and low humidity, extending their viability from years to centuries. The Millennium Seed Bank at Kew (UK) stores seeds from 40,000 species, representing approximately 25% of the world's plant species. Seeds are periodically germinated to test viability and to regenerate stocks.

Reintroduction programmes have had notable successes:

• Arabian oryx: extinct in the wild by 1972, reintroduced from captive populations to Oman and Saudi Arabia.
• California condor: population reduced to 27 individuals in 1987, captive breeding increased numbers to over 400, with many released back into the wild.
• Large blue butterfly: extinct in the UK by 1979, reintroduced from Swedish populations after its ecological requirements (a specific species of ant) were understood.

17. Energy Flow and Ecological Efficiency

17.1 Trophic Levels and Energy Transfer

Energy enters ecosystems as sunlight (in most ecosystems) and is transferred through trophic levels. At each transfer, approximately 90% of the energy is lost (as heat through respiration, as uneaten material, as faeces and urine). Only approximately 10% is incorporated into the biomass of the next trophic level.

Gross Primary Production (GPP): the total amount of energy fixed by photosynthesis per unit area per unit time.

Net Primary Production (NPP): GPP minus the energy lost through plant respiration ($R$).

$\text{NPP} = \text{GPP} - R$

NPP is the energy available to herbivores (primary consumers).

Net Secondary Production (NSP): the energy incorporated into herbivore biomass.

$\text{NSP} = \text{energy consumed} - \text{energy lost in faeces} - \text{energy lost in respiration}$

17.2 Ecological Efficiency Calculations

Worked Example. A field receives $2.0 \times 10^6\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$ of sunlight. The plants (producers) have a GPP of $1.2 \times 10^4\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$ and a respiration rate of $4.0 \times 10^3\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$.

$\text{NPP} = 1.2 \times 10^4 - 4.0 \times 10^3 = 8.0 \times 10^3\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$.

Photosynthetic efficiency $= \frac◆LB◆\text{GPP}◆RB◆◆LB◆\text{light received}◆RB◆ = \frac◆LB◆1.2 \times 10^4◆RB◆◆LB◆2.0 \times 10^6◆RB◆ = 0.006 = 0.6\%$.

This very low efficiency is typical -- most sunlight is reflected, transmitted, or absorbed by non-photosynthetic structures, and much of the absorbed light is at wavelengths that chlorophyll cannot use.

If the primary consumers eat the entire NPP ($8.0 \times 10^3\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$) but assimilate only 20% (the rest is lost as faeces), and they respire 60% of the assimilated energy:

$\text{NSP} = 8000 \times 0.20 \times (1 - 0.60) = 8000 \times 0.20 \times 0.40 = 640\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$.

Trophic efficiency from producer to primary consumer $= \frac{640}{8000} = 8\%$.

17.3 Pyramids of Number, Biomass, and Energy

Pyramid Type	What It Shows	Limitations
Pyramid of numbers	Number of organisms at each trophic level	Can be inverted (e.g., one oak tree supporting many insects)
Pyramid of biomass	Dry mass of organisms at each trophic level	Can be inverted in aquatic ecosystems (phytoplankton have low standing biomass but high turnover)
Pyramid of energy	Energy flow per unit area per unit time	Never inverted; the most fundamental and useful representation

Inverted pyramids of biomass in aquatic ecosystems occur because phytoplankton reproduce and are consumed very rapidly (high turnover rate). At any given instant, their biomass is low, but the total energy they fix and transfer to zooplankton over a year is much greater than their standing biomass suggests.

18. Succession: Worked Examples

18.1 Sand Dune Succession

Sand dune succession is a classic example of primary succession:

1. Embryo dunes: pioneer plants such as sea couch grass and marram grass colonise the bare sand. Their long roots stabilise the sand and trap more sand, allowing the dune to grow.
2. Fore dunes: as sand accumulates, conditions become less harsh (more moisture, less wind). Plants such as sea spurge and sea holly colonise.
3. Yellow dunes: marram grass dominates. It has rolled leaves (reduces water loss), deep roots (anchors in sand), and can tolerate burial by sand.
4. Grey dunes: as organic matter accumulates from dead plant material, the soil becomes more fertile and retains more water. Fixed dune communities develop with species such as restharrow, bird's-foot trefoil, and vetches.
5. Dune slack: behind the dunes, a hollow may fill with fresh water (rainwater above the saline groundwater), forming a dune slack with wetland species (willow, rushes, orchids).
6. Climax community: eventually, shrubs and trees (oak, birch, pine) colonise, forming a woodland climax community.

18.2 Measuring Succession

Changes during succession can be measured by:

Variable	How to Measure	Expected Trend
Species richness	Quadrat sampling	Generally increases (though may peak and decline at climax)
Species diversity (Simpson's index)	Quadrat sampling	Generally increases
Soil depth	Soil corer	Increases (organic matter accumulates)
Soil organic matter content	Soil samples, combustion method	Increases
Soil moisture content	Gravimetric method (weigh, dry, reweigh)	Increases (soil retains more water as organic content increases)
pH	pH meter or indicator	May decrease (organic acids) or increase (calcium from plant material)

19. Climate Change: Mechanisms and Evidence

19.1 The Greenhouse Effect

Solar radiation (mostly visible light and short-wave infrared) passes through the atmosphere and warms the Earth's surface. The Earth re-radiates this energy as long-wave infrared radiation. Greenhouse gases in the atmosphere absorb and re-emit some of this long-wave radiation back towards the surface, warming the lower atmosphere.

Greenhouse Gas	Pre-industrial Concentration	Current Concentration	Contribution to Warming
$\mathrm{CO_2}$	$280\ \mathrm{ppm}$	$> 420\ \mathrm{ppm}$	$\approx 60\%$
Methane ($\mathrm{CH_4}$)	$700\ \mathrm{ppb}$	$> 1900\ \mathrm{ppb}$	$\approx 20\%$
Nitrous oxide ($\mathrm{N_2O}$)	$270\ \mathrm{ppb}$	$> 330\ \mathrm{ppb}$	$\approx 6\%$
CFCs	0	Variable	$\approx 14\%$

19.2 Evidence for Anthropogenic Climate Change

• Ice core data: bubbles trapped in Antarctic ice preserve samples of the ancient atmosphere. $\mathrm{CO_2}$ concentration has fluctuated between 180 and $280\ \mathrm{ppm}$ over the last 800,000 years (glacial-interglacial cycles) but has risen to $> 420\ \mathrm{ppm}$ in the last 150 years -- far above the natural range.
• Global temperature records: average global temperature has risen by approximately $1.1$ degrees C since 1850, with the rate of warming accelerating since the 1970s.
• Ocean acidification: oceans have absorbed approximately 30% of anthropogenic $\mathrm{CO_2}$, forming carbonic acid and lowering ocean pH by approximately 0.1 units (a 26% increase in $\mathrm{H^+}$ concentration). This impairs shell formation in marine organisms (corals, molluscs).
• Sea level rise: thermal expansion of seawater and melting of land ice have raised global sea level by approximately 20 cm since 1900, with the rate accelerating.

19.3 Biological Consequences of Climate Change

Impact	Description
Range shifts	Species move towards the poles or to higher altitudes as temperatures rise (e.g., butterfly ranges shifting north in Europe)
Phenological mismatch	Timing of events (flowering, migration, breeding) changes at different rates, disrupting ecological interactions (e.g., pollinators may emerge before plants flower)
Coral bleaching	Elevated sea temperatures cause corals to expel their symbiotic zooxanthellae, leading to coral death
Increased disease	Warmer temperatures extend the range of disease vectors (e.g., malaria mosquitoes) and pathogen development rates
Ocean acidification	Reduces calcification in marine organisms with calcium carbonate shells or skeletons

20. Ecological Techniques: Advanced Fieldwork

20.1 Random Sampling with Quadrats

Procedure:

1. Lay out two tape measures at right angles to create a coordinate grid across the study area.
2. Use random number tables (or a calculator) to generate pairs of random coordinates.
3. Place the quadrat (typically $0.5 \times 0.5\ \mathrm{m}$ or $1 \times 1\ \mathrm{m}$) at each coordinate.
4. Record the species present and their abundance (percentage cover or number of individuals) in each quadrat.
5. Repeat for at least 10--20 quadrats (more quadrats = more reliable results).

Minimum quadrat number: a species-area curve (accumulation curve) is plotted: the cumulative number of species recorded is plotted against the number of quadrats sampled. When the curve levels off (no new species are found with additional quadrats), a sufficient number of quadrats has been sampled.

20.2 Systematic Sampling Along a Transect

Line transect: a tape measure is laid across the study area. Species touching the line are recorded at regular intervals (e.g., every metre).

Belt transect: a quadrat is placed at regular intervals along the tape measure. This combines the spatial information of a transect with the quantitative data of quadrat sampling.

Interrupted belt transect: a quadrat is placed at fixed intervals along a transect. Particularly useful for studying zonation (e.g., changes in species distribution from the top to the bottom of a rocky shore).

20.3 Capture-Mark-Release-Recapture

Used to estimate the population size of mobile animals:

1. Capture a sample of animals (e.g., using pitfall traps, sweep nets, mammal traps).
2. Mark each captured animal (e.g., with non-toxic paint, leg rings, RFID tags).
3. Release the marked animals back into the population.
4. Recapture a second sample after sufficient time for marked animals to mix back into the population.
5. Record the total number captured ($n_2$) and the number of marked recaptures ($m_2$).

$N = \frac◆LB◆n_1 \times n_2◆RB◆◆LB◆m_2◆RB◆$

Where $N$ = estimated population size, $n_1$ = number captured and marked in the first sample, $n_2$ = number captured in the second sample, $m_2$ = number of marked individuals in the second sample.

20.4 Assumptions and Limitations of CMRR

Assumption	Why It May Not Hold	Effect on Estimate
Marked individuals mix randomly into the population	Marked individuals may avoid or be attracted to traps (trap-happy or trap-shy behaviour)	$N$ is inaccurate
Marks are not lost and do not affect survival	Marks may wear off, be removed by grooming, or increase predation risk	$m_2$ is underestimated; $N$ is overestimated
The population is closed (no births, deaths, immigration, emigration between sampling)	Births, deaths, or migration may occur between sampling periods	$N$ is inaccurate
The probability of capture is equal for all individuals	Some species/sexes/ages may be more easily captured	$N$ is biased

20.5 Worked Example: CMRR Calculation

A biologist captures 50 woodlice and marks them. One week later, she captures 40 woodlice, of which 10 are marked.

$N = \frac◆LB◆50 \times 40◆RB◆◆LB◆10◆RB◆ = 200$ woodlice.

The estimated population size is 200.

Confidence interval: if a different second sample might have produced different results, the estimate has uncertainty. For a rough estimate, the standard error can be approximated by:

$\text{SE} \approx \sqrt◆LB◆\frac◆LB◆n_1 \times n_2 \times (n_1 - m_2) \times (n_2 - m_2)◆RB◆◆LB◆m_2^3◆RB◆◆RB◆$

$\text{SE} = \sqrt◆LB◆\frac◆LB◆50 \times 40 \times 40 \times 30◆RB◆◆LB◆1000◆RB◆◆RB◆ = \sqrt◆LB◆\frac{2400000}{1000}◆RB◆ = \sqrt{2400} = 49$.

Approximate 95% confidence interval: $200 \pm 98$, or 102 to 298.

This wide range reflects the uncertainty inherent in CMRR estimates with relatively small sample sizes.

21. Primary and Secondary Productivity: Worked Problems

21.1 Calculating Net Primary Productivity

Worked Example. A forest has a biomass of $20,000\ \mathrm{kg\ ha^{-1}}$. Over one year, the biomass increased by $2,500\ \mathrm{kg\ ha^{-1}}$, and the plants respired $8,000\ \mathrm{kg\ ha^{-1}}$ of carbon (measured as $\mathrm{CO_2}$ equivalent).

$\text{NPP} = \text{biomass increase} = 2,500\ \mathrm{kg\ ha^{-1}\ yr^{-1}}$.

$\text{GPP} = \text{NPP} + R = 2,500 + 8,000 = 10,500\ \mathrm{kg\ ha^{-1}\ yr^{-1}}$.

Photosynthetic efficiency $= \frac◆LB◆\text{GPP}◆RB◆◆LB◆\text{light energy received}◆RB◆$.

If the forest receives $1.0 \times 10^{10}\ \mathrm{kJ\ ha^{-1}\ yr^{-1}}$ of light energy, and the energy content of plant biomass is approximately $18\ \mathrm{kJ\ g^{-1}}$:

$\text{GPP (energy)} = 10,500 \times 18 = 189,000\ \mathrm{kJ\ ha^{-1}\ yr^{-1}}$.

Photosynthetic efficiency $= \frac◆LB◆189\,000◆RB◆◆LB◆1.0 \times 10^{10}◆RB◆ = 0.0019 = 0.19\%$.

21.2 Comparing Ecosystems

Ecosystem	NPP ($\mathrm{kg\ ha^{-1}\ yr^{-1}}$)	Reason
Tropical rainforest	22,000	High temperature, abundant water, year-round growing season
Temperate deciduous forest	11,000	Seasonal climate limits growing season
Temperate grassland	6,000	Less biomass than forest; drought may limit growth
Desert	500	Water is severely limiting
Open ocean	2,000	Nutrient limitation (especially nitrogen and iron); most production is by phytoplankton
Coral reef	2,500	High productivity despite nutrient-poor waters (efficient nutrient recycling)
Estuary	15,000	Nutrient-rich (from river input); high light penetration

22. Human Impacts on Ecosystems: Quantitative Analysis

22.1 Eutrophication: Step-by-Step

1. Nutrient input: fertilisers (nitrates and phosphates) are leached from agricultural land or discharged in sewage into rivers and lakes.
2. Algal bloom: the high nutrient concentration causes rapid growth of algae (phytoplankton) at the water surface, forming a dense green bloom.
3. Light blocked: the algal bloom prevents light from reaching submerged plants (macrophytes), which die.
4. Death and decomposition: dead algae and dead plants sink to the bottom, where they are decomposed by aerobic bacteria.
5. Oxygen depletion: the aerobic bacteria consume dissolved $\mathrm{O_2}$ from the water during decomposition, causing the BOD (biochemical oxygen demand) to increase.
6. Hypoxia/anoxia: dissolved $\mathrm{O_2}$ levels drop below that required by fish and other aquatic organisms, which die (fish kills).
7. Further decomposition: dead fish and other organisms are decomposed, further increasing BOD and accelerating $\mathrm{O_2}$ depletion.
8. Recovery: only when the nutrient input is stopped and the ecosystem can slowly recover.

22.2 Indicator Species

Indicator	Clean Water	Moderate Pollution	Heavy Pollution
Mayfly nymphs (Ephemeroptera)	Present	May be present	Absent
Stonefly nymphs (Plecoptera)	Present	Absent	Absent
Freshwater shrimp (Gammarus)	Present	May be present	Absent
Bloodworms (Chironomus)	Absent or rare	Present	Abundant
Sludge worms (Tubificidae)	Absent	Present	Abundant
Rat-tailed maggots (Eristalis)	Absent	Present	Abundant
Algae/diatoms	Diverse community	Fewer species	Dominated by pollution-tolerant species
Lichens (air quality)	Xanthoria (moderate $\mathrm{SO_2}$) absent	Xanthoria present	Only crustose lichens or none

22.3 Calculating Biodiversity Indices

Shannon diversity index ($H$):

$H = -\sum p_i \ln p_i$

Where $p_i$ is the proportion of individuals belonging to species $i$.

Example: A woodland has 4 species with the following abundances: A = 50, B = 30, C = 15, D = 5. Total = 100.

Species	$n_i$	$p_i$	$\ln p_i$	$p_i \ln p_i$
A	50	0.50	$-0.693$	$-0.347$
B	30	0.30	$-1.204$	$-0.361$
C	15	0.15	$-1.897$	$-0.285$
D	5	0.05	$-2.996$	$-0.150$

$H = -(-0.347 - 0.361 - 0.285 - 0.150) = 1.14$

A higher $H$ value indicates greater biodiversity. The maximum possible value for 4 species (with equal abundance) is $\ln 4 = 1.386$.

Simpson's diversity index ($D$):

$D = 1 - \sum p_i^2$

Using the same data:

$D = 1 - (0.25 + 0.09 + 0.0225 + 0.0025) = 1 - 0.365 = 0.635$

Values range from 0 (no diversity) to approaching 1 (infinite diversity).

22.4 Climate Change: Evidence and Consequences

Evidence:

Evidence	Data
Atmospheric $\mathrm{CO_2}$ concentration	280 ppm (pre-industrial) $\to$ > 420 ppm (2024); measured at Mauna Loa Observatory since 1958
Global mean temperature	Increased by approximately 1.1 degrees C since 1850 (IPCC AR6, 2021)
Sea level rise	Approximately 20 cm since 1900; accelerating (currently $\approx 3.6\ \mathrm{mm\ yr^{-1}}$)
Arctic sea ice extent	Declined by approximately 13% per decade since satellite records began (1979)
Ocean acidification	pH has decreased from 8.21 to 8.10 (approximately 26% increase in $[\mathrm{H^+}]$) since pre-industrial times

Consequences for ecosystems:

1. Range shifts: species migrate towards the poles or to higher altitudes to track their optimal temperature. Species at the poles or mountain tops have nowhere to go.
2. Phenological mismatch: the timing of biological events (flowering, migration, breeding) changes at different rates for different species, disrupting food webs (e.g., insects emerging before their food plant has flowered).
3. Coral bleaching: increased ocean temperature causes coral to expel their zooxanthellae (symbiotic algae), losing their energy source and colour. Mass bleaching events are increasing in frequency.
4. Extreme weather events: more frequent and severe droughts, floods, and storms disrupt ecosystems and reduce agricultural productivity.
5. Permafrost thaw: releases methane (a potent greenhouse gas, approximately 25x more effective than $\mathrm{CO_2}$ at trapping heat), creating a positive feedback loop.

23. Ecological Techniques and Fieldwork

23.1 Sampling Methods

Method	When to Use	Procedure	Limitations
Random sampling (quadrats)	Relatively uniform habitat; sessile (non-moving) organisms	Lay out a grid; use random numbers to select quadrat positions; count/estimate percentage cover within each quadrat	Time-consuming; only works for organisms that can be counted in quadrats
Systematic sampling (transects)	Gradient exists (e.g., altitude, distance from sea, soil moisture)	Place quadrats at regular intervals along a line (belt transect or line transect)	May miss important features between sampling points
Mark-release-recapture	Mobile animals	Capture, mark, release, wait, recapture. $N = \frac◆LB◆n_1 \times n_2◆RB◆◆LB◆n_3◆RB◆$	Assumes: no death/migration/immigration; marks do not affect survival; marks are not lost; random mixing

23.2 Mark-Release-Recapture: Worked Example

A biologist captures 50 woodlice and marks them with non-toxic paint. The next day, she captures 40 woodlice, of which 8 are marked.

$N = \frac◆LB◆n_1 \times n_2◆RB◆◆LB◆n_3◆RB◆ = \frac◆LB◆50 \times 40◆RB◆◆LB◆8◆RB◆ = 250$

Estimated population size $= 250$ woodlice.

23.3 Measuring Abundance

Measure	Description	When to Use
Density	Number of individuals per unit area ($\mathrm{m^{-2}}$)	When individuals can be counted (e.g., plants, slow-moving animals)
Frequency	Proportion of quadrats in which a species is present	When individuals are hard to count but presence/absence is easy to record
Percentage cover	Percentage of ground covered by a species (visual estimate)	For plants, especially when they form a continuous cover (e.g., grass)

23.4 Simpson's Diversity Index: Worked Example

A sample from a grassland contains the following species abundances:

Species	Number ($n_i$)	$n_i/N$ ($p_i$)	$p_i^2$
Ryegrass	120	0.60	0.360
White clover	40	0.20	0.040
Dandelion	25	0.125	0.0156
Plantain	10	0.05	0.0025
Daisy	5	0.025	0.000625
Total	200	1.000	0.419

$D = 1 - \sum p_i^2 = 1 - 0.419 = 0.581$

This indicates moderate biodiversity. A pristine ancient woodland might have $D > 0.9$; a heavily grazed monoculture pasture might have $D < 0.2$.

23.5 Primary and Secondary Succession: Worked Example

Primary succession on sand dunes:

Stage	Dominant Species	Soil Characteristics	Distance from sea
Embryo dune	Lyme grass, marram grass	Sandy, low water retention, low organic matter, high salinity	0--50 m
Fore dune	Marram grass, sea couch	Slightly more organic matter; nitrogen fixation by cyanobacteria begins	50--100 m
Yellow dune	Marram grass, sand sedge	Accumulation of organic matter; soil begins to form	100--200 m
Grey dune (fixed dune)	Grasses, herbs, lichens	Soil develops; more water retention; lower pH	200--400 m
Dune heath	Heather, gorse, bracken	Acidic soil; more organic matter	400--600 m
Dune scrub/woodland	Birch, pine, oak (climax community)	Well-developed soil; stable community	> 600 m

Each stage modifies the environment, making it more suitable for the next stage (autogenic succession). The climax community is the most stable and diverse community that can be sustained under the prevailing climate and soil conditions.

24. Ecological Interactions

24.1 Interspecific Relationships

Relationship	Effect on A	Effect on B	Example
Mutualism (+/+)	Both benefit	Both benefit	Mycorrhizae (fungi on plant roots: fungus provides minerals; plant provides carbohydrates); pollination (insect gets nectar; plant gets pollinated); zooxanthellae in coral (algae provide sugars via photosynthesis; coral provides shelter and $\mathrm{CO_2}$)
Commensalism (+/0)	One benefits; other unaffected	Unaffected	Barnacles on a whale (barnacles get transport and food; whale is unaffected); epiphytes (orchids growing on tree branches)
Parasitism (+/-)	Parasite benefits; host is harmed	Harmed	Tapeworm in human intestine; Plasmodium in red blood cells; fleas on mammals; dodder on plants
Predation (+/-)	Predator benefits; prey is killed	Killed	Lion hunting zebra; hawk hunting mouse
Herbivory (+/-)	Herbivore benefits; plant is damaged	Damaged (but not killed)	Caterpillar eating leaves; rabbit eating grass
Competition (-/-)	Both are harmed	Both are harmed	Two species competing for the same limiting resource (food, light, water, space)

24.2 Niche

A niche describes the role and position of a species within its ecosystem, including:

• Habitat niche: where the organism lives (e.g., tropical forest canopy).
• Trophic niche: what it eats (e.g., insectivore).
• Activity niche: when and how it is active (e.g., nocturnal hunter).

Competitive exclusion principle: two species cannot coexist in the same niche (one will outcompete the other). If two species appear to occupy the same niche, closer inspection usually reveals niche differentiation (resource partitioning).

24.3 The Niche Concept and Species Coexistence

Principle	Description	Example
Competitive exclusion	Two species with identical niches cannot coexist; one will exclude the other	Paramecium caudatum and P. aurelia grown together: P. aurelia outcompetes P. caudatum
Resource partitioning	Coexisting species divide the available resources to reduce competition	Darwin's finches on the Galapagos: different beak sizes allow different species to specialise on different seed sizes
Fundamental niche	The full range of conditions and resources a species could theoretically use	A species' potential range if no competitors were present
Realised niche	The actual range of conditions and resources a species uses in the presence of competitors	Usually smaller than the fundamental niche due to competition

24.4 Ecological Pyramids

Pyramid Type	Description	Limitations
Pyramid of numbers	Number of organisms at each trophic level	Can be inverted (e.g., one tree supporting many insects)
Pyramid of biomass	Total dry mass of organisms at each trophic level (per unit area)	Can be inverted in aquatic systems (phytoplankton have low standing biomass but high productivity due to rapid turnover)
Pyramid of energy	Total energy at each trophic level per unit area per unit time	Never inverted; energy is always lost at each trophic level (10% rule)

25. Energy Flow and Productivity Calculations

25.1 The 10% Rule

Approximately 10% of energy is transferred from one trophic level to the next. The remaining 90% is lost as:

• Heat (respiration by the organism at each level).
• Uneaten material (bones, teeth, fibrous plant material).
• Energy in excreted waste (urea, faeces).
• Inefficiencies in digestion and absorption.

Implications of the 10% rule:

• A food chain with 4 trophic levels (producer $\to$ primary consumer $\to$ secondary consumer $\to$ tertiary consumer) retains only approximately $0.1\%$ of the energy at the producer level.
• This is why food chains are typically short (3--4 trophic levels).
• There are many more producers than top predators.

Example:

• If the producer level captures 100,000\ \mathrm{kJ\ m^{-2}\ yr^{-1} of light energy.
• Primary consumers receive approximately $10,000\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$.
• Secondary consumers receive approximately $1,000\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$.
• Tertiary consumers receive approximately $100\ \mathrm{kJ\ m^{-2}\ yr^{-1}}$.

25.2 Calculating NPP from Biomass Data

To convert biomass to energy:

1. Dry the sample to constant mass (remove all water).
2. Weigh the dry biomass.
3. Multiply by the energy content per unit dry mass (approximately 18\ \mathrm{kJ\ g^{-1} for plant material).

Example: A forest produces 2,500\ \mathrm{kg\ ha^{-1}\ yr^{-1} of dry biomass.

\mathrm{NPP} = 2,500\ \times 18 = 45,000\ \mathrm{kJ\ ha^{-1}\ yr^{-1}

$\mathrm{GPP} = \mathrm{NPP} + R = 45,000 + 18,000 = 63,000\ \mathrm{kJ\ ha^{-1}\ yr^{-1}}$

Ecological efficiency (efficiency of energy transfer from producers to primary consumers):

If primary consumers consume 5,000\ \mathrm{kg\ ha^{-1}\ yr^{-1} of plant biomass:

$\text{Efficiency} = \frac◆LB◆5,000 \times 18◆RB◆◆LB◆63,000◆RB◆ \times 100 = 14.3\%$

26. Succession in Detail

26.1 Primary vs Secondary Succession

Feature	Primary Succession	Secondary Succession
Starting point	Bare rock, sand, or volcanic ash (no soil)	Previously colonised land where the community has been removed (soil already present)
Soil	Must form from scratch (weathering of rock, pioneer species, humus accumulation)	Already present; may need enrichment
Pioneer species	Lichens, algae, mosses (can survive on bare rock)	Fast-growing plants (weeds, grasses, ruderal species)
Time scale	Hundreds to thousands of years	Decades to centuries
Example	Sand dune succession; volcanic island colonisation	Abandoned farmland; forest after fire; deforested land

26.2 Sand Dune Succession (Classic Example)

Stage	Species	Changes to Environment
Embryo dune	Salt-tolerant grasses (e.g., Spartina, Lyme grass)	Traps sand; raises dune surface; adds organic matter
Fore dune	Marram grass; sea couch grass	Deep roots stabilise sand; more organic matter; soil begins to form
Yellow dune	Marram grass dominant; some herbs	More soil accumulation; reduced salt spray; more water retention
Grey dune	Diverse grassland; herbs; mosses; lichens	Thicker soil; less sand movement; higher nutrient content
Dune slack	Water collects in hollows; reeds, rushes, willow	Wetland community develops
Climax community	Deciduous woodland (oak, birch, hazel)	Stable, self-sustaining community

26.3 Deflected Succession

Deflected succession occurs when human activity prevents the natural climax community from developing:

Example	Description
Grazing (sheep/cattle)	Prevents tree seedlings from establishing; maintains grassland
Mowing (lawns, parks)	Prevents tall vegetation and trees; maintains short grass
Burning (heathland management)	Prevents scrub and tree invasion; maintains heather moorland

27. Eutrophication: Step-by-Step

27.1 Process

Step	What Happens	Consequence
1. Nutrient enrichment	Nitrates and phosphates enter water (from agricultural fertiliser runoff, sewage, detergents)	Increased nutrient concentration
2. Algal bloom	Algae and cyanobacteria grow rapidly (exponential growth) in the nutrient-rich water	Thick green layer on water surface; blocks light
3. Light blocked	Upper layers of algae prevent light reaching deeper water	Submerged plants (macrophytes) cannot photosynthesise; they die
4. Death and decomposition	Dead algae and dead plants sink to the bottom; saprobiotic bacteria decompose them	Bacteria population increases; bacteria respire aerobically
5. Oxygen depletion	Bacterial respiration consumes dissolved oxygen (DO) from the water	DO drops below levels needed by fish and invertebrates
6. Death of aerobic organisms	Fish and invertebrates die from hypoxia (low $\mathrm{O_2}$)	Only anaerobic organisms survive; water becomes stagnant and foul-smelling (hydrogen sulfide from anaerobic respiration)

27.2 Indicators of Eutrophication

Indicator	What to Measure	Expected Values
Biochemical oxygen demand (BOD)	Amount of $\mathrm{O_2}$ consumed by bacteria in a water sample over 5 days at 20$\degree\mathrm{C}$	Clean water: BOD < 5 mg/L; Polluted water: BOD > 10 mg/L; Severely polluted: BOD > 20 mg/L
Dissolved oxygen (DO)	$\mathrm{O_2}$ concentration in water (measured with an oxygen probe)	Clean water: 8--12 mg/L; Eutrophic water: < 4 mg/L (hypoxic)
Nitrate concentration	Nitrate levels in water (colorimetric test)	Clean: < 1 mg/L; Eutrophic: > 5 mg/L
Species diversity	Number and variety of invertebrate species (biotic index)	Clean water: high diversity (mayfly nymphs, stonefly larvae -- sensitive to pollution); Polluted water: low diversity (only tolerant species like bloodworms, sludgeworms)

28. Climate Change and Biology

28.1 The Greenhouse Effect

Greenhouse Gas	Sources	Current Concentration	Warming Potential (vs $\mathrm{CO_2}$)
Carbon dioxide ($\mathrm{CO_2}$)	Fossil fuel combustion; deforestation	~420 ppm	1 (reference)
Methane ($\mathrm{CH_4}$)	Agriculture (rice paddies, cattle); landfill; natural gas leaks	~1.9 ppm	~25--80 (depending on time frame)
Nitrous oxide ($\mathrm{N_2O}$)	Agricultural fertiliser use; industrial processes	~0.33 ppm	~265
Chlorofluorocarbons (CFCs)	Refrigerants; aerosols (now largely banned)	Declining	~4,000--10,000

28.2 Biological Consequences of Climate Change

Consequence	Description	Biological Impact
Rising temperatures	Global average temperature has increased ~1.1$\degree\mathrm{C}$ since pre-industrial era	Species range shifts (moving poleward or to higher altitude); coral bleaching; changed phenology (timing of flowering, migration)
Ocean acidification	$\mathrm{CO_2}$ dissolves in seawater: $\mathrm{CO_2 + H_2O \rightleftharpoons H_2CO_3 \rightleftharpoons H^+ + HCO_3^-}$	Reduces carbonate ion concentration; impairs shell formation in molluscs, corals, and plankton (calcareous organisms)
Sea level rise	Thermal expansion of water + melting ice sheets	Coastal habitat loss; saltwater intrusion into freshwater ecosystems
Changed precipitation patterns	More intense rainfall in some areas; droughts in others	Altered species distributions; reduced agricultural productivity; increased wildfire risk
Extreme weather events	More frequent and severe storms, heatwaves, droughts	Direct mortality; habitat destruction; disruption of food webs

29. Measuring Biodiversity

29.1 Simpson's Index of Diversity

$D = 1 - \frac◆LB◆\sum n(n-1)◆RB◆◆LB◆N(N-1)◆RB◆$

Where:

• $n$ = number of individuals of each species
• $N$ = total number of individuals of all species

Simpson's Index Value	Interpretation
Close to 1	High diversity (many species, evenly distributed)
Close to 0	Low diversity (few species, or one species dominates)

29.2 Worked Example

A woodland contains 4 species of tree:

Species	Number of Individuals ($n$)	$n(n-1)$
Oak	40	$40 \times 39 = 1,560$
Birch	30	$30 \times 29 = 870$
Ash	20	$20 \times 19 = 380$
Hazel	10	$10 \times 9 = 90$
Total ($N$)	100	$\sum n(n-1) = 2,900$

$D = 1 - \frac◆LB◆2,900◆RB◆◆LB◆100 \times 99◆RB◆ = 1 - \frac{2,900}{9,900} = 1 - 0.293 = 0.707$

29.3 Species Richness vs Species Evenness

Concept	Definition	Example
Species richness	The number of different species in a habitat	A rainforest has high species richness; a monoculture wheat field has low species richness
Species evenness	How evenly individuals are distributed among species	If two habitats both have 4 species, the one where all 4 species have ~equal abundance has higher evenness (and higher Simpson's index)

30. Ecological Interactions

30.1 Types of Species Interactions

Interaction	Effect on Species A	Effect on Species B	Example
Mutualism (+/+)	Beneficial	Beneficial	Mycorrhizae (fungus + plant roots); nitrogen-fixing bacteria (Rhizobium) in legume root nodules; pollination (bee + flower); cleaner fish + client fish
Commensalism (+/0)	Beneficial	No effect	Epiphytes (orchids growing on tree branches); barnacles on whales
Parasitism (+/-)	Beneficial (parasite)	Harmful (host)	Tapeworm in human intestine; Plasmodium (malaria) in human RBCs; fleas on dogs; mistletoe on trees
Predation (+/-)	Beneficial (predator)	Harmful (prey)	Lion hunting zebra; owl catching mouse; hawk catching rabbit
Competition (-/-)	Harmful	Harmful	Two species competing for the same resource (light, water, nutrients, food)
Amensalism (-/0)	Harmful	No effect	A large tree shading out small plants beneath it; black walnut releasing juglone (inhibits growth of nearby plants)

30.2 Coevolution

Coevolution occurs when two species evolve in response to each other:

Example	Description
Predator-prey arms race	Predators evolve faster speed, better camouflage, sharper claws; prey evolve better camouflage, toxins, warning colouration, faster escape
Plant-herbivore coevolution	Plants evolve thorns, toxins, tough leaves; herbivores evolve resistance to toxins, specialised mouthparts
Flowering plants and pollinators	Flowers evolve specific shapes, colours, and nectar rewards; pollinators evolve specialised mouthparts and behaviours (e.g., hummingbird and long-tubed flowers; Darwin's moth with 30 cm proboscis and comet orchid)
Host-parasite coevolution	Hosts evolve immune defences; parasites evolve evasion mechanisms (antigenic variation in malaria, influenza)

31. Adaptations to Extreme Environments

31.1 Xerophytes (Plants Adapted to Dry Conditions)

Adaptation	Description	How It Reduces Water Loss
Thick waxy cuticle	Thick layer of wax (cutin) on the upper surface of leaves	Waterproof barrier; reduces evaporation
Sunken stomata	Stomata located in pits or grooves on the lower leaf surface	Traps a layer of moist air; reduces the water vapour concentration gradient
Rolled leaves	Leaves curl inward; stomata are on the inside	Traps moist air; reduces transpiration
Hairy leaves	Dense layer of trichomes (hairs) on the leaf surface	Traps moist air; reflects some light (reduces heating)
Reduced leaf surface area	Needle-like leaves (conifers) or spines (cacti)	Smaller surface area = less evaporation
Succulent tissues	Thick, fleshy stems or leaves that store water	Stores water for dry periods; allows the plant to survive long droughts
Deep root system	Long taproot (e.g., cactus) or extensive lateral roots	Reaches deep groundwater
CAM photosynthesis	Stomata open at night; $\mathrm{CO_2}$ stored as malic acid; used during the day	Reduces water loss (stomata closed during the hottest part of the day)

31.2 Hydrophytes (Plants Adapted to Aquatic Environments)

Adaptation	Description	Why It Is Needed
No waxy cuticle (or very thin)	No barrier to water and gas exchange	No risk of water loss; easy gas exchange with water
Stomata only on upper surface	Stomata on the upper epidermis (exposed to air)	Lower surface is submerged; stomata on the upper surface can exchange gases with the air
Aerenchyma tissue	Large air spaces in the stems and leaves	Provides buoyancy; allows $\mathrm{O_2}$ to reach submerged tissues (supports aerobic respiration in roots)
Reduced xylem	Less vascular tissue needed	Water is abundant; no need for extensive water transport
Flexible stems	Stems bend with water currents	Prevents damage from water flow

32. Human Impact on Ecosystems

32.1 Deforestation

Effect	Description
Habitat loss	Species lose their habitat; biodiversity decreases
Soil erosion	Tree roots no longer hold soil together; topsoil is washed away by rain; nutrients are lost
Increased $\mathrm{CO_2}$	Trees store carbon; deforestation releases $\mathrm{CO_2}$ back into the atmosphere (contributing to climate change)
Altered water cycle	Reduced transpiration $\to$ less moisture in the atmosphere $\to$ reduced rainfall $\to$ drier climate
Flash flooding	Reduced interception of rain by trees $\to$ more surface runoff $\to$ flooding downstream

32.2 Overfishing

Impact	Description
Fish stock collapse	Populations of commercially important fish species have declined dramatically (e.g., Atlantic cod)
Disruption of food webs	Removal of top predators causes trophic cascades; prey species may increase, further destabilising the ecosystem
Bycatch	Non-target species (dolphins, turtles, seabirds) are caught and killed in fishing nets
Habitat destruction	Bottom trawling destroys seabed habitats (coral reefs, sponge beds)

32.3 Conservation Strategies for Fisheries

Strategy	Description
Fishing quotas	Legal limits on the amount of fish that can be caught
Minimum mesh sizes	Larger mesh allows smaller (juvenile) fish to escape; ensures they can reproduce before being caught
No-take zones (marine reserves)	Areas where all fishing is banned; fish populations recover and spill over into adjacent fishing areas
Seasonal closures	Fishing is banned during breeding seasons to protect spawning fish
MSC certification	Marine Stewardship Council certifies sustainable fisheries; consumers can choose sustainably sourced fish

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tip

tip Ready to test your understanding of Ecology? The diagnostic test contains the hardest questions within the A-Level specification for this topic, each with a full worked solution.

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

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

33. Trophic Levels and Feeding Relationships

33.1 Food Chains and Food Webs

Feature	Food Chain	Food Web
Description	Linear sequence showing energy transfer from one organism to another	Network of interconnected food chains showing all feeding relationships in a community
Complexity	Simple	Complex
Example	Grass $\to$ rabbit $\to$ fox $\to$ flea	Multiple interconnected chains with shared organisms at different trophic levels

33.2 Trophic Levels

Trophic Level	Position	Organism Type	Energy Remaining (approximate)
1	Producer	Plants, algae, cyanobacteria	100%
2	Primary consumer	Herbivores (caterpillars, rabbits, zooplankton)	10%
3	Secondary consumer	Carnivores that eat herbivores (small birds, frogs, small fish)	1%
4	Tertiary consumer	Top carnivores (hawks, foxes, large fish, lions)	0.1%
5	Quaternary consumer	Apex predator (e.g., shark, eagle)	0.01%

33.3 Decomposers and Detritivores

Type	Organisms	Role
Decomposers	Fungi, bacteria	Secrete extracellular enzymes; break down dead organic matter; release inorganic nutrients ($\mathrm{NH_4^+}$, $\mathrm{PO_4^{3-}}$) back into the soil for producers to absorb
Detritivores	Earthworms, woodlice, maggots, dung beetles	Ingest dead organic matter; digest it internally; speed up decomposition by breaking material into smaller pieces (increasing surface area for decomposers)

34. Nitrogen Cycle

34.1 Key Processes

Process	Description	Organisms Involved
Nitrogen fixation	Atmospheric $\mathrm{N_2}$ ($\mathrm{N \equiv N}$ triple bond) is converted to $\mathrm{NH_3}$ (ammonia) / $\mathrm{NH_4^+}$ (ammonium)	Nitrogen-fixing bacteria: Rhizobium (symbiotic, in root nodules of legumes); Azotobacter (free-living in soil); Clostridium (anaerobic)
Nitrification	$\mathrm{NH_4^+}$ (ammonium) is converted to $\mathrm{NO_2^-}$ (nitrite) then $\mathrm{NO_3^-}$ (nitrate)	Nitrifying bacteria: Nitrosomonas ($\mathrm{NH_4^+} \to \mathrm{NO_2^-}$); Nitrobacter ($\mathrm{NO_2^-} \to \mathrm{NO_3^-}$)
Assimilation	Plants absorb $\mathrm{NO_3^-}$ (and some $\mathrm{NH_4^+}$) through their roots and incorporate nitrogen into amino acids, proteins, and nucleic acids	Plants; animals obtain nitrogen by eating plants or other animals
Ammonification	Decomposers break down proteins and urea in dead organic matter; release $\mathrm{NH_3}$ / $\mathrm{NH_4^+}$ back into the soil	Decomposers (bacteria and fungi)
Denitrification	$\mathrm{NO_3^-}$ is converted back to $\mathrm{N_2}$ and $\mathrm{N_2O}$ (nitrous oxide, a greenhouse gas); returns nitrogen to the atmosphere	Denitrifying bacteria: Pseudomonas denitrificans (anaerobic conditions in waterlogged soil)

35. Phosphorus Cycle

35.1 Key Processes

Process	Description
Weathering	Phosphorus is released from rocks (apatite) by weathering (rain, freezing/thawing, chemical breakdown)
Absorption by plants	Plants absorb phosphate ions ($\mathrm{PO_4^{3-}}$) through their roots
Transfer through food chains	Phosphorus passes from plants to herbivores to carnivores
Decomposition and mineralisation	Decomposers break down dead organic matter; release $\mathrm{PO_4^{3-}}$ back into the soil
Sedimentation	Phosphorus in dead marine organisms settles to the ocean floor; forms sedimentary rock over millions of years
Geological uplift	Tectonic activity lifts sedimentary rocks to the surface; weathering begins the cycle again

35.2 Key Difference from the Carbon and Nitrogen Cycles

Feature	Carbon and Nitrogen	Phosphorus
Atmospheric component	Significant ($\mathrm{CO_2}$, $\mathrm{N_2}$)	Negligible (no major gaseous phase)
Main reservoir	Atmosphere (N); atmosphere and oceans (C)	Rocks and sediments
Rate of cycling	Fast (days to years)	Slow (millions of years for the sedimentary component)
Bottleneck	Recycling through decomposers is efficient	Phosphorus is often a limiting factor in ecosystems because it cycles slowly

37. Water Pollution

37.1 Types and Sources

Pollutant	Sources	Effects
Sewage	Untreated or partially treated domestic wastewater; agricultural runoff	Eutrophication; disease (cholera, typhoid); BOD increases; DO decreases
Fertiliser runoff	Agricultural land (nitrates and phosphates)	Eutrophication; algal blooms
Heavy metals	Industrial discharge; mining; old paints (lead, mercury, cadmium)	Bioaccumulation in food chains; toxic to aquatic organisms; Minamata disease (mercury)
Oil spills	Tanker accidents; offshore drilling	Coats feathers of seabirds (loss of insulation $\to$ hypothermia); coats gills of fish; blocks light penetration; toxic components
Pesticides	Agricultural runoff (herbicides, insecticides)	Bioaccumulation (DDT in birds of prey $\to$ eggshell thinning); kills non-target species; water contamination
Plastics	Litter; microplastics from clothing and cosmetics	Ingested by marine organisms; entangles wildlife; microplastics enter food chain; persists for hundreds of years
Thermal pollution	Power station cooling water discharged into rivers	Reduces DO (warm water holds less dissolved oxygen); affects metabolic rate and distribution of aquatic species

37.2 Indicator Species for Water Quality

Species	Tolerance to Pollution	What Their Presence/Absence Indicates
Stonefly larvae (Plecoptera)	Very sensitive	Clean water (high DO, low pollution)
Mayfly nymphs (Ephemeroptera)	Sensitive	Clean water
Freshwater shrimp (Gammarus)	Moderately sensitive	Moderate water quality
Bloodworms (Chironomus)	Tolerant	Polluted water (low DO)
Sludgeworms (Tubifex)	Very tolerant	Heavily polluted water (very low DO, high organic matter)

38. Conservation Case Studies

38.1 Yellowstone National Park: Wolf Reintroduction

Feature	Details
Background	Grey wolves were extirpated from Yellowstone by 1926 (hunting and predator control)
Reintroduction	41 wolves from western Canada released in 1995--1996
Ecological effects	Wolves reduced elk populations in valleys; this allowed willow and aspen to regenerate along riverbanks; more willows stabilised riverbanks and increased habitat for beavers; beaver dams created wetland habitats; fish populations increased; songbirds returned (more habitat); scavenger species (ravens, bears) benefited from wolf kills
Economic effects	Increased ecotourism revenue (~$35 million/year)
Social conflict	Wolves occasionally preyed on livestock outside the park; conflict with ranchers
Lesson	Reintroducing a top predator had cascading effects throughout the ecosystem (trophic cascade)

38.2 Galapagos Islands: Conservation Challenges

Challenge	Description
Invasive species	Goats, rats, cats, and introduced plants threaten endemic species
Tourism	Large numbers of visitors can disturb wildlife and introduce pathogens
Climate change	El Nino events cause food shortages for marine species (e.g., iguanas, sea lions)
Fishing	Overfishing depletes marine food webs
Conservation measures	Strict quarantine on islands; removal of invasive species; visitor limits; marine reserves

40. Molecular Ecology

40.1 Using DNA in Ecology

Molecular techniques are increasingly used in ecology to answer questions that are difficult or impossible to address with traditional field methods alone.

Technique	Application	Example
DNA barcoding	Identifying species from short DNA sequences (e.g., COI gene for animals, rbcL for plants)	Identifying cryptic species that look identical but are genetically distinct
Environmental DNA (eDNA)	Detecting species from DNA shed into water, soil, or air	Monitoring endangered or invasive species in lakes without needing to catch them
Microsatellites	Highly variable repetitive DNA used to measure genetic diversity within populations	Assessing genetic bottleneck in cheetah populations
Mitochondrial DNA sequencing	Tracing maternal lineages and historical population sizes	Reconstructing human migration routes out of Africa
Genome-wide SNP analysis	Identifying genes under selection in wild populations	Detecting genes for pesticide resistance in mosquito populations

40.2 eDNA Methodology

Step	Description
1. Sample collection	Collect water or soil from the study site; filter to capture DNA fragments
2. DNA extraction	Extract DNA from the filter using commercial kits
3. PCR amplification	Amplify species-specific or universal barcode regions using primers
4. Sequencing	Sequence the PCR products (Sanger for known species; NGS metabarcoding for whole communities)
5. Bioinformatics	Compare sequences to reference databases (e.g., GenBank, BOLD) to identify species present

41. Carbon Cycle

41.1 Key Processes

Process	Description	Carbon Flux
Photosynthesis	Plants and algae convert $\mathrm{CO_2}$ to organic compounds (glucose) using light energy	$\mathrm{CO_2}$ from atmosphere $\to$ biomass
Respiration	All living organisms break down organic compounds, releasing $\mathrm{CO_2}$	Biomass $\to$ $\mathrm{CO_2}$ to atmosphere
Combustion	Burning fossil fuels and biomass releases stored carbon as $\mathrm{CO_2}$	Fossil fuel/biomass $\to$ $\mathrm{CO_2}$ to atmosphere
Decomposition	Decomposers break down dead organic matter, releasing $\mathrm{CO_2}$	Dead matter $\to$ $\mathrm{CO_2}$ to atmosphere
Fossilisation	Organic matter is buried under sediment and slowly converted to fossil fuels over millions of years	Biomass $\to$ fossil fuels (long-term carbon sink)
Ocean absorption	$\mathrm{CO_2}$ dissolves in ocean water; marine organisms use it for photosynthesis and shell formation	Atmosphere $\to$ ocean (carbon sink)
Volcanic activity	Volcanoes release $\mathrm{CO_2}$ from subducted carbonate rocks	Geological carbon $\to$ atmosphere

41.2 Human Impact on the Carbon Cycle

Impact	Description
Deforestation	Reduces photosynthesis (less $\mathrm{CO_2}$ removed); burning releases stored carbon
Fossil fuel combustion	Releases carbon that has been locked away for millions of years; major driver of increased atmospheric $\mathrm{CO_2}$
Ocean acidification	Increased $\mathrm{CO_2}$ dissolves in oceans $\to$ forms carbonic acid $\to$ lowers pH $\to$ damages coral reefs and shellfish

42. Primary and Secondary Succession

42.1 Primary Succession

Stage	Description
Bare rock	No soil; no organisms (e.g., after a volcanic eruption or glacial retreat)
Pioneer species	Lichens and mosses colonise the rock; lichens secrete acids that begin to break down the rock into mineral particles (start of soil formation)
Soil development	Dead organic matter from lichens/mosses accumulates; simple plants (ferns, grasses) can grow in the thin soil
Intermediate species	Grasses, herbs, and small shrubs replace the pioneer species; soil deepens and becomes more nutrient-rich
Climax community	Trees dominate; the community is stable and self-sustaining; the species composition does not change significantly over time (in the UK climate, this is typically oak/ash woodland)

42.2 Secondary Succession

Feature	Description
What it is	Succession that occurs on previously colonised land after a disturbance has removed the existing community
Starting point	Soil is already present (unlike primary succession)
Examples	After a forest fire; after a field is abandoned (old field succession); after logging
Speed	Faster than primary succession (soil and seeds are already present)
Stages	Herbaceous plants $\to$ shrubs $\to$ fast-growing trees (e.g., birch) $\to$ slow-growing climax trees (e.g., oak)

42.3 Deflected Succession

Feature	Description
What it is	Succession is prevented from reaching the natural climax community by human activity or other factors
Example	Regular mowing of grassland prevents the growth of shrubs and trees; the grassland is a plagioclimax (a stable community maintained by human intervention)
Other examples	Grazing by sheep on hillsides; burning of heather moorland; rice paddy fields

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