Genomes to Ecosystems

What is an ecosystem?

An ecosystem is a biological community and the interactions between all the physical, climatological and chemical conditions that make up the environment

What are the three levels of organisation within an ecosystem

Individual - an individual organism 

• Key processes: Growth, Metabolism, Activit, Thermoregulation and reprooduction

Population - a group of the same species within one organisation e.g. a group of killer whales 

Community - Living organisms within the same habitat and the interactions they display 

Factors influencing population growth 

• Resource availability: Populations rely on food, water, and habitat space. The stage of succession (primary or secondary) affects how many resources are available.

• Carrying capacity (K): The maximum number of individuals an environment can support, based on resource limits.

• Density-dependent factors: Effects that intensify as population density increases (e.g. predation, parasitism, disease, competition).

• Density-independent factors: Abiotic stressors that impact populations regardless of size (e.g. flooding, storms, drought).

• Dispersal and migration: Movement helps individuals find new resources, reduce inbreeding, and avoid overcrowding, though it comes at energetic and survival costs.

• Individual fitness: Growth, reproduction, and survival strategies at the individual level are fundamental to population persistence.

What does population growth depend on

How many individuals can survive and reproduce, affected by biotic and abbiotic factors

What is competition

When two populations rely ont he same limited resource, one may outcompete and exclude the other . Strong competators = widely distributed, abundant, traits that let them monopolise resources

What is coexistence 

When populations persist together through ecological differentiation e.g. occupying different niches 

Why do some organisms prefer different strategies (competition or coexistnce)

• Organisms with broad ecological tolerance (generalists) may do better in competitive contexts.

• Organisms with specialised strategies (specialists) may avoid competition by occupying narrower, less contested niches.

• Environmental variation (spatial or temporal) can promote coexistence because resources are not constant in time or space, allowing multiple strategies to succeed.

Fundamental niche

The full range of environmental conditions and resources an organism could potentially use, in the absence of competition or other limiting factors.

Realised niche 

The actual set of conditions where the organism persists in reality, constrained by competition, predation, and other biotic interactions.

What are the four basic functions carried out by ecosystems

1. Energy Transfer

2. Nutrient Cycling

3. Water Cycling

4. CO2 Cycling

1. Energy Transfer

The movement of energy from one place to another, transfer instead of cycling because energy is coming from out with the earth (the sun)

Refers to the flow/transfer of energy as it is passed through a food chain from primary producers to top predators

Example: Sun (Energy) → Chloroplasts (In plants) → Energy (Through photosynthesis)

2. Nutrient Cycling

The continuous movement and recycling of essential nutrients between the Earths abiotic and biotic components within an ecosystem

• Elements such as C, N and P absorbed by producers and passed through the food chain then returned to the environment through waste (faeces)

• E.g. Decomposition of leaves in a deciduous forest. The leaves fall off the trees, die, go brown then the nutrients stored within them will return to the ground and new foliage will grow.

3. Water Cycling

Continuous process of water moving round the earths surface, atmosphere ad subsurface changing form and location

• E.g. plant use of transpiration - release water vapor from leaves to pull up water from soil through roots

4. CO2 Cycling

Movement of carbon between the atmosphere, land and ocean mainly as CO2

• e.g. The carbon cycle - plants absorb CO2 for photosynthesis and release it through respiration

What are different ecosystem processes?

• Nutrient Uptake/Release

• Decomposition

• Water uptake/evapotranspiration

• Photosynthesis

• Herbivory

• Pollination

• Predation/parasitism/pathogen attack

What are ecosystem goods and services?

Benefits to humanity provided by an ecosystem

• Goods: Things that are critical for human survival such as food, crops, water, minerals, energy, raw materials, medicine. genetic, etc

• Services: Things that play a role in the ecosystems survival e.g. processes

• There are 4 types: supporting, provisioning, regulating and cultural

Crucial for survival as they provide the means and resources for survival itself. They make life possible.

Supporting services

all ecosystem processes being carried out - necessary for production of all other services e.g. nutrient recycling

Provisioning services

raw materials (goods) obtained from ecosystems e.g. food and water

Regulating services

benefits obtained from ecosystem processes to help regulate natural phenomena e.g. CO2 being captured by rainforests reduces CO2 in atmosphere helping the environment

Cultural Services

• nonmaterial benefits e.g. aesthetic experience, spiritual enrichment, inspiration, tourism, recreation etc

  • Features within landscapes often historical objects etc

How can molecular genetic approach help us understand evolution and phylogeny

• DNA sequencing - direct comparison of genetic material 

• DNA differences - molecular clock showing how long ago species diverged

• Molecular genetics - complement fossil and anatomical evidence to build phylogenetic trees

• Modern sequencing technologies - quick and affordable to analyse genomes

What does DNA sequencing tell us about our ancesters

• DNA from fossils - genetic similarities and differences

• we share DNA with Neanderthals

• most human genetic variation = before humans left Africa

• Chimpanzees have greater genetic diversity than humans

• Preservation in dey or cold environments

What do isolated populations tell us about genetic basis of complex disease?

• Show founder effect - limited genetic diversity from a small number of ancestors

• This males it easier to link genetic variants to specific diseases or traits

• Shared ancestry means certain disease causing alleles are more common

Species

A group of organisms capable of interbreeding and producing fertile offspring, sharing genetic similarities and evolutionary history.

Speciation

The process by which new species arise due to evolutionary factors such as natural selection, genetic drift, and reproductive isolation.

What are the types of speciation?

Allopatric, sympatric, peripatric, and parapatric speciation.

Allopatric

Geographic barriers (e.g. mountains, rivers) separate populations → no gene flow → divergence.

Sympatric

New species evolve within the same area due to genetic or behavioral isolation.

Parapatric

Neighboring populations diverge while still having limited contact.

Peripatric

A small peripheral population becomes isolated and evolves rapidly (founder effect).

What is adaptive radiation?

• A single ancestral species diversifies into many new species, each adapted to different niches (e.g. Galápagos finches).

• Driven by key innovations, environmental changes, or ecological opportunities

Why do mass extinctions occur?

result from a large scale environmental or ecological shift that disrupt ecosystems globally 

Environmental Changes

Oxygen level shifts, global cooling/warming (e.g. Snowball Earth).

Ecological changes

New predators or prey (e.g. evolution of eyes → predator-prey arms race)

How many species are there?

estimated 8.7 ± 1.3 million species on Earth, though many remain undiscovered.

Species richness

not evenly distributed — biodiversity is highest in tropical regions and declines toward the poles.Historical records, museum specimens and global databases help map species distribution and diversity patterns

Bias on knowlenge of biodiversity

• Geographical bias: Some areas (e.g. Europe, North America) are well-sampled, while tropics and deep oceans are under-studied.

• Taxonomic bias: Large, charismatic animals (e.g. tigers, elephants) are overrepresented, whereas insects and microbes dominate global diversity but are under-documented.

• Institutional bias: Biodiversity data often depend on contributions from wealthier nations, leading to gaps for developing regions.

Role of citizen science in measuring biodiversity 

• Citizen science platforms (e.g. iNaturalist) allow the public to record and share species sightings.

• These observations supplement professional research, fill geographic gaps, and increase data collection globally.

• Crowdsourced data helps track species distributions and detect changes over time.

Undiscovered biodiversity

A vast portion of Earth’s biodiversity — especially microbes and small invertebrates — remains undiscovered or undescribed.

DNA barcoding

• uses short genetic sequences (unique to each species) to rapidly identify and classify organisms, even from small samples.

• It helps reveal cryptic species and accelerates biodiversity assessment on a global scale.

What is migration?

Migration refers to the regular, seasonal movement of species from one location to another, often driven by changes in climate, food availability, or reproductive needs.

Advantages of migrations

• Access to new or seasonal resources (food, breeding sites).

• Protection for young or vulnerable individuals.

• Avoid inbreeding by mixing with new populations.

• Reduce competition within overcrowded areas.

Disadvantages of migration

• Weather hazards, predation, and exhaustion.

• Navigation errors (e.g. artificial lights disrupting cues).

• Limited resting or feeding sites along migration routes.

Energy storage and migratory birds

• Carbohydrates (glycogen) for short-term, high-intensity energy.

• Fats (lipids) for long-term, high-yield energy during sustained travel.

• Migratory birds use fatty acids as their main fuel source, storing large fat reserves before migration.

Biomechanical adaptations for migrations

• Streamlined bodies and efficient muscle use to minimize energy cost.

• Example: Semi-palmated sandpipers consume shrimp rich in EPA & DHA, enhancing membrane fluidity, oxygen diffusion, and endurance — effectively boosting long-distance performance.

cellular processes influencing ecology

• PUFAs (EPA & DHA) incorporated into cell and mitochondrial membranes improve oxidative phosphorylation and energy metabolism.

• These molecular adaptations enhance aerobic efficiency and fat metabolism, allowing sustained flight or movement.

• Gene expression shifts toward pathways favoring fatty acid oxidation, optimizing endurance.

Challanges in long term migrations 

• Tracking difficulties: Animals often cross inaccessible or vast regions (oceans, deserts).

What are methods for tracking in migratory animals

• Methods used:

  • Point counts and natural markings for population estimates.

  • Radar and satellite/GPS tracking for real-time movement.

  • Tagging (colored rings, collars) for individual identification.

• Technological improvements now allow detailed movement data, but human impacts (habitat loss, light pollution, hunting) still disrupt migration routes.

What is tragedy of the commons

• occurs when individuals act in self-interest to exploit a shared resource, leading to its depletion and harming everyone long-term.

• Example: Four villagers overfishing from a shared pond — short-term gain causes fish population collapse and starvation.

• Highlights the need for management strategies to regulate use of shared, finite resources.

What are the flow of events leading to a change in UK law to protect the environment

1. Issue identified → often through research or public concern.

2. International agreement or directive proposed.

3. Government consultation with public, conservationists, and industry.

4. National policy developed, including enforcement procedures and penalties.

5. Legislation enacted, making policies legally binding and enforceable.

Legislative approaches

Strong and evidence-based but slow to implement.

Non-legislative approaches

Quick and flexible (e.g., education, campaigns) but lack enforcement or longevity.

Limitations for legislative 

• Time-consuming and bureaucratic.

• Difficult to adapt quickly to new data.

Limitations for non-legislative

• Rely on voluntary compliance and public motivation.

• May lack scientific backing or continuity.

Protected area designation

Legally or formally recognized space set aside for long-term conservation of nature

Marine protected area (MPA)

A designated part of the ocean or coast managed to protect biodiversity, habitats, and cultural resources.

Marine boundary

Defines the jurisdictional limits of a country’s marine territory

Exclusive Economic Zone (EEZ)

Extends up to 200 nautical miles from a nation’s coast — the state controls resource use and management.

• 0–12 nm: Territorial waters (full sovereignty).

• 12–200 nm: EEZ (economic rights only).

• Beyond 200 nm: High seas (international waters).

What is the criteria needed to designate a marine protected area 

• Identification: Area contains unique or important ecological, biological, or geographic features.

• Prioritisation: Features must be viable and capable of recovery.

• Scale assessment: Must be large enough to maintain ecological integrity but still manageable.

• Management feasibility: Clear enforcement and monitoring plan required.

• Network contribution: Area should enhance the wider MPA network through connectivity and ecological value

Biological effects of plastics in marine environments

Plastics are durable, synthetic polymers that persist for decades without degrading.

Secondary effects: Disruption of ecosystems, transport of invasive species, and introduction of harmful chemicals.

Macroplastics (>5mm)

Cause entanglement and ingestion by marine animals, leading to injury, suffocation, or death.

Microplastics (<5mm)

Enter food webs through ingestion by small organisms → bioaccumulation and biomagnification of toxins up the chain.

What are other human pollutants

• Sewage: Introduces pathogens.

• Toxic metals & chemicals: Poison aquatic life.

• Oil spills: Smother organisms and habitats.

• Agricultural runoff: Causes eutrophication and dead zones.

• Noise, light, and thermal pollution: Disrupt animal behavior and physiology.

• Plastics stand out as long-term, widespread, and nearly irreversible compared to most other pollutants.

What is Good Environmental Status (GES)

means keeping ecosystems healthy, resilient, and sustainable.

How do humans maintain GES

• Reduce waste inputs (especially from land, where ~80% of marine pollution originates).

• Improve waste management and filtration systems.

• Support circular economies (reuse, recycle, repurpose).

• Adopt biodegradable materials and sustainable industry practices.

• Public awareness and responsible consumption are essential to maintaining GES.

Solutions to reduce human impacts

• Circular economy models: Design products for reuse, repair, and recycling.

• Technological innovations: Better wastewater treatment, efficient washing machines, and biodegradable plastics.

• Policy and regulation: Enforce waste reduction and pollution control.

• Behavioral change: Education and awareness to shift consumer habits

Environmental cost of Gen AI

• AI systems require vast computational power and cooling resources, consuming large amounts of water and energy.

• A single AI prompt (e.g. ChatGPT query) ≈ 10 web searches in energy use.

• Contributes to carbon emissions and resource competition (water, electricity, rare materials).

Methods to manage AI usage 

• Context and control: Use AI only when necessary and justified.

• Critical use: Focus on high-impact, beneficial applications (education, science, sustainability).

• Efficiency: Scale systems to reduce wasteful processing; optimize infrastructure for renewable energy.

• Aim for a balanced approach—meeting societal needs while minimizing environmental costs and aligning with sustainability principles.