2. Genomes to Ecosystems

What are the levels of ecosystem organisation and why is 'population' more accurate than 'species'?

Individual, population, and differences between populations of the same species.

Populations refer to organisms of the same species at a specific time and place, which may not interbreed due to geographic or ecological separation.

What are key biological processes at the individual level and why is reproduction essential?

Growth, metabolism, activity, thermoregulation, and reproduction. Reproduction ensures survival and fitness by producing more individuals.

What is succession and how do primary and secondary succession differ?

Succession is the sequence of ecosystem development. Primary succession starts from a sterile surface (e.g., volcanic rock),

while secondary succession begins with existing soil after disturbance and is faster.

What are the roles of pioneer, intermediate, and climax species in succession?

Pioneer species (lichens, mosses) break down rock and create microhabitats. Intermediate species (grasses, shrubs) stabilize soil and outcompete pioneers. Climax communities are stable, biodiverse ecosystems.

Give examples of primary and secondary succession.

Primary: Surtsey Island, Iceland. Secondary: Children's Wood in Glasgow.

What are density-dependent factors in population growth?

Carrying capacity, predation, parasitism, disease, and competition. These factors intensify as population density increases.

What are density-independent factors and how do they affect populations?

Natural disasters, weather extremes, climate changes, and human activities. They impact population size regardless of density.

What is dispersal and migration, and what are their benefits and costs?

Dispersal is movement from one location to another; migration is regular, directional dispersal. Benefits include access to resources and reduced competition; costs include energy use, predation risk, and habitat uncertainty.

What is competition in ecological communities and what are its outcomes?

Organisms compete for limited resources. Outcomes include coexistence through niche differentiation or elimination when one species outcompetes another.

What traits define good competitors and what are the consequences?

Wide distribution, high abundance, and stress tolerance. Dominant species occupy preferred habitats; subordinate species are pushed to suboptimal areas.

What does the barnacle example illustrate about niches?

Chthamalus has a wide fundamental niche but is excluded by Balanus, reducing its realised niche.

What are fundamental and realised niches?

Fundamental niche: all conditions where a species could survive. Realised niche: where it actually survives due to competition and other pressures.

What is an assemblage in ecology?

A group of interacting populations in the same geographic area.

What is parasitism and how does it work?

A biotic interaction where a parasite benefits at the host's expense by using its body or resources, often causing harm.

What traits help parasites exploit their niche and what are examples?

Specialized mouthparts, immune evasion, and synchronized reproduction. Examples: tapeworms, mistletoe, ticks.

What is niche differentiation and why is it important?

A strategy where species access different resources to reduce competition. It enables coexistence and increases biodiversity.

How do Darwin's finches demonstrate adaptive radiation and character displacement?

They evolved from a single ancestor into multiple species with specialized beaks. In sympatry, divergent traits reduce competition by occupying distinct niches.

What is temporal variation and how does it expand niche availability?

Environmental changes over time (daily, seasonal, annual) allow species to share space at different times, reducing competition.

Give examples of temporal niche partitioning.

Hawks hunt by day, owls by night; plants flower in spring, insects emerge in summer.

What is mutualism and what are examples in marine and terrestrial ecosystems?

A symbiotic relationship where both species benefit. Examples: coral polyps and zooxanthellae; hippos and oxpeckers.

Why is individual fitness essential and how does succession affect resources?

Fitness maintains populations through survival and reproduction. Succession stages influence resource availability.

What affects population growth and how is biodiversity maintained?

Resource availability and density-dependent factors. Biodiversity is maintained through coexistence and niche diversity.

What happens when pressure increases in a community?

It triggers competition and forces species to find new ecological balances.

Why are coral reefs ecologically important?

They support 25% of marine species and provide coastal protection, food, tourism, medicine, and climate regulation.

What is coral bleaching and what causes it?

A stress response where corals expel zooxanthellae, losing color and energy. Causes include temperature changes, poor water quality, and ocean acidification.

Why are corals vulnerable and how does ocean acidification affect them?

Corals grow slowly and depend on specific conditions and species. Acidification lowers pH, reduces carbonate ions, weakens skeletons, and slows growth.

What is ecosystem interdependence in coral reefs?

Corals rely on species like herbivorous fish to control algae and maintain ecological balance.

What are the abiotic components of an ecosystem?

Sunlight, temperature, precipitation, substrate type, and soil or water chemistry.

What are the biotic components of an ecosystem?

Primary producers, herbivores, carnivores, omnivores, and detritivores.

What are the four basic ecosystem functions?

Capturing, storing, and transferring energy, carbon dioxide, nutrients, and water.

What is ecosystem functioning?

The capacity of ecosystems to carry out primary processes like energy and nutrient transfer.

What is an ecosystem process?

A natural mechanism such as photosynthesis, decomposition, or nutrient cycling that supports ecosystem functioning.

How does energy flow through trophic levels?

From producers (10,000 kcal) → primary consumers (1,000 kcal) → secondary consumers (100 kcal) → tertiary consumers (10 kcal), with energy lost as heat at each level.

Name key ecological processes supporting energy transfer.

Photosynthesis, herbivory, carnivory, decomposition, nutrient uptake/release, pollination.

What are ecosystem goods and services?

Benefits humans derive from ecosystems, including food, water, climate regulation, and cultural enrichment.

What did the Millennium Ecosystem Assessment reveal?

Two-thirds of Earth's ecosystem services are in decline or threatened.

What are supporting services?

Services necessary for the production of all other ecosystem services, like nutrient cycling and primary production.

What are provisioning services?

Tangible goods obtained from ecosystems, such as food, water, minerals, and medicinal resources.

What are regulating services?

Benefits from ecosystem processes that regulate natural phenomena, like flood control and water purification.

What are cultural services?

Nonmaterial benefits like spiritual enrichment, recreation, aesthetic appreciation, and scientific discovery.

How do anthropogenic activities affect ecosystems?

They disrupt community structure, ecosystem processes, functions, and the delivery of goods and services.

Why is ecosystem accounting important?

It quantifies ecosystem services in monetary terms to inform policy and reward conservation efforts.

How does molecular genetics help us understand evolution?

By comparing DNA sequences across species, we can trace genetic changes over time and reconstruct evolutionary relationships.

What types of evidence support evolutionary theory?

Comparative anatomy, fossil records, and DNA evidence—all of which reveal patterns of similarity and divergence.

What does DNA evidence reveal about evolutionary history?

Differences in DNA sequences reflect how long ago species diverged, helping build phylogenetic trees.

Why do fossil, anatomical, and genetic data often produce similar evolutionary trees?

Because they all reflect shared ancestry and divergence over time, reinforcing each other's conclusions.

What is phylogeny?

The evolutionary history and relationships among species, often visualized as a branching tree.

What is a species?

A fundamental classification unit including organisms that share common characteristics and can interbreed naturally.

What is allopatric speciation?

Speciation due to geographic isolation; populations diverge genetically over time.

What is the founder effect in speciation?

A small isolated population evolves rapidly due to non-random gene sampling and environmental differences.

What is sympatric speciation?

Speciation without geographic isolation; occurs via assortative mating and genetic divergence within the same region.

What is random speciation?

Speciation driven by genetic drift and mutations, not by environmental pressures.

What is non-random speciation?

Speciation influenced by mate choice based on traits, behaviors, or preferences.

What is adaptive radiation?

Rapid diversification from an ancestral species into many forms due to new ecological opportunities.

What causes adaptive radiation?

Key innovations, environmental changes (e.g., new habitats), and ecological shifts.

How can radiation events be recognized in evolutionary trees?

By observing many branches stemming from a single node, indicating rapid speciation.

What innovation in bony fish contributed to adaptive radiation?

The swim bladder, enabling buoyancy control and access to diverse water depths.

What is the kinetic skull in bony fish?

A skull with multiple moving parts that enhances feeding versatility and supports adaptive radiation.

What is a mass extinction?

A widespread and rapid decrease in biodiversity due to catastrophic events.

What are common causes of mass extinction?

Asteroid impacts, volcanic activity, climate change, and human influence.

What is the Cambrian Explosion?

A period (~545-525 Mya) when most major animal phyla appeared suddenly in the fossil record.

What contributed to the Cambrian Explosion?

Environmental (oxygen increase), developmental (HOX genes), and ecological changes.

What is the Anthropocene?

A proposed epoch marked by significant human impact on Earth's ecosystems and geology.

What caused the extinction of megafauna like the woolly mammoth?

Human hunting, climate change, disease, and second-order predation.

What is de-extinction?

The process of reviving extinct species using genetic technologies.

What are ethical concerns around de-extinction?

Ecosystem disruption, resource allocation, and the risk of repeating extinction causes.

How have humans influenced ecosystems?

Through habitat destruction, climate change, pollution, and species extinction.

What is the Teleost Genome Duplication (TGD)?

A third whole genome duplication in bony fish ~300 Mya, enabling evolutionary innovation.

How did TGD affect bony fish evolution?

It led to diverse body plans, sensory systems, and reproductive strategies.

Did TGD cause a burst in transposable elements?

No; TE evolution was shaped more by lineage-specific shifts.

What model describes gene loss after TGD?

A two-phase model: rapid initial loss followed by slower selective retention.

How many species are estimated to exist globally?

Around 8.7 million species, with a margin of ±1-3 million.

What is the difference between known and unknown species?

Only a fraction are formally described; many, especially microbes and invertebrates, remain undiscovered.

What does the "Species Scape" illustrate?

It visually represents species richness across groups, showing insects dominate global biodiversity.

Where is biodiversity highest globally?

In tropical regions, due to climate, habitat complexity, and evolutionary history.

How do marine and terrestrial ecosystems differ in species richness?

They vary significantly, with distribution influenced by environmental and evolutionary factors.

What is taxonomic bias in biodiversity studies?

Vertebrates are overrepresented, while microbes, fungi, and invertebrates are underrepresented.

What is geographic bias in biodiversity data?

Most data comes from wealthier countries, despite higher biodiversity in tropical regions.

What is an example of geographic bias in data collection?

Biodiversity data for Kenya is mostly collected by non-Kenyan researchers.

What is charisma bias?

Charismatic species like pandas and whales receive more attention and funding than less appealing organisms.

What is technological bias in biodiversity research?

Imaging and sequencing advances benefit some groups, but microbial diversity remains vastly under-sampled.

How much of Earth's DNA has been sequenced?

Only about 1 × 10⁻²²%, meaning microbial diversity is almost entirely unexplored.

What is iNaturalist and how does it work?

A platform where users upload species photos; AI and community help identify them.

What does the Seek App do?

Uses phone sensors and AI to identify species in real time.

What is LifeScanner?

A DNA-based identification tool for citizen scientists (limited uptake).

What is DiversityScanner?

A robotic tool using machine learning to discover small invertebrates.

What are the benefits of citizen science in biodiversity?

Expands data collection, engages the public, and improves AI models.

What are challenges of citizen science?

Data quality, tourist vs local uploads, phone access, and bias toward visible species.

Why is microbial diversity largely unknown?

Because only a minuscule fraction of microbial DNA has been sequenced.

What is DNA barcoding?

A method using short genetic sequences (e.g., COI gene) to identify species.

What is the Barcode Index Number (BIN) system?

A DNA-based registry that assigns unique identifiers to species.

What is an example of DNA barcoding in action?

Australian rays show clear genetic divergence between species using barcoding.

What are the impacts of DNA barcoding?

Accelerates species discovery, reduces reliance on morphology, and supports global biodiversity databases like BOLD.

What did DNA sequencing reveal about Neanderthals and modern humans?

They co-existed in Europe around 30,000 years ago and interbred, leaving traces of Neanderthal DNA in modern humans.

What does human migration tell us about genetic variation?

Over 90% of human genetic variation predates migration out of Africa; migrating groups carried only a subset of this variation.

Why are humans less genetically variable than chimpanzees?

Humans are more inbred due to population bottlenecks and founder effects during migration.

What is shared DNA by descent?

DNA inherited from common ancestors, used by companies like 23andMe to identify relatives.

Why is finding distant relatives via DNA less accurate?

It requires those relatives to be in the database and relies on smaller shared segments that are harder to detect.

What does Iceland's genetic data reveal about its founders?

Y-chromosomes are Scandinavian, while mitochondrial DNA is Celtic—suggesting male Norse settlers and Celtic women.

Who is Svante Pääbo and what was his contribution?

He developed methods to sequence ancient, damaged DNA, enabling insights into extinct human relatives.