Chapter Summary

• Taxonomy classifies organisms into a hierarchy: Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species (no overlap between groups).
• The three-domain system (Archaea, Eubacteria, Eukarya) replaced the old idea that all prokaryotes were one group, based on molecular phylogeny (RNA/DNA/protein comparisons).
• The five kingdoms (Prokaryotae, Protoctista, Fungi, Plantae, Animalia) sit under the domains — four of them (Protoctista, Fungi, Plantae, Animalia) are all Eukarya.
• Species are named using the binomial system (Genus species, italicised, genus capitalised).
• Human activity (habitat destruction, overexploitation, hunting, agriculture, climate change) is reducing global biodiversity.
• Biodiversity is assessed at three levels: ecosystem/habitat diversity, species diversity, and genetic diversity.
• Species richness (number of species) is simple but can be misleading — species abundance and an index of diversity give a fuller picture.
• Random sampling with quadrats, sweep nets, pitfall traps, and kick-sampling is used to estimate distribution and abundance.
• A niche is unique to one species; adaptations (anatomical, behavioural, physiological) let species fit their niche.
• The Hardy-Weinberg equation estimates allele/genotype frequencies in a population when no evolution is occurring.
• Allele frequencies change due to mutation, natural selection, genetic drift (bottlenecks, founder effect), which can lead to reproductive isolation and speciation.
• Seed banks and zoos play conservation roles, each with real advantages and limitations.

1. The Three Domains of Life

Why do we classify organisms at all?

Imagine trying to talk about biology without any grouping system — every single one of the ~8.7 million species on Earth would need its own totally separate conversation. Classification (called taxonomy) exists to make life easier to study, understand, and communicate about. It groups organisms based on evolutionary relationships — how closely related they are by descent from a common ancestor. This approach is called phylogenetic classification.

The system is hierarchical, meaning it's organised in nested levels called taxa (singular: taxon). Crucially: there is no overlap between groups at the same level — an organism belongs to exactly one species, one genus, one family, and so on. Smaller taxa nest inside bigger ones, like Russian dolls.

The pattern to understand, not just memorise: as you go from Domain down to Species, groups contain fewer organisms but those organisms are more similar to each other. A Domain contains billions of wildly different organisms; a Species contains only organisms that can interbreed to produce fertile offspring.

Why molecular evidence changed everything

Early classification relied purely on phenotype — what organisms look like on the outside. The problem? Looks can be deceiving. Whales and sharks look superficially similar (streamlined, fins, live in water) but are barely related — one's a mammal, one's a fish. This is called convergent evolution, and it fooled early taxonomists constantly.

Modern techniques like DNA sequencing let scientists compare genotypes directly. This is far more reliable because DNA carries the actual evolutionary history — the more similar two organisms' DNA/RNA/protein sequences are, the more recently they shared a common ancestor. This approach is called molecular phylogeny.

The three domains

Notice something interesting: Archaea share some features with Eukaryotes (histones, ribosome subunit) despite being prokaryotic like Eubacteria. This is exactly the kind of molecular evidence that justified splitting them into separate domains.

The Binomial System

Every species gets a unique two-part scientific name in Latin — its binomial. This solves a huge problem: common names vary by language and region (a "robin" in the UK is a totally different bird from a "robin" in the US), but a binomial is universal everywhere in the world.

2. The Five Kingdoms

Within the domain Eukarya sit four of the five kingdoms (Protoctista, Fungi, Plantae, Animalia). Prokaryotae (Monera) sits outside Eukarya entirely, split across Archaea and Eubacteria. Think of each kingdom as having a "signature combination" of features — learn the combinations, not just isolated facts.

3. The Variety of Life & Human Impact

Natural selection has increased life's variety over billions of years — but human population growth (exponential for the last 150 years, driven by better food technology raising birth rate and better medicine/hygiene lowering death rate) has put unprecedented pressure on natural resources, and therefore on biodiversity.

Five main threats to biodiversity

4. Biodiversity & Endemism

"Biodiversity" isn't a single number — it's assessed at three distinct levels, and you need to be able to explain each one separately with its own example.

Level 1: Ecosystem/habitat diversity

This is the range of different types of habitats within a region. A coral reef has huge habitat diversity (lots of microhabitats and niches) → high biodiversity. A sandy desert has almost uniform conditions everywhere → low biodiversity.

Level 2: Species diversity

This has two components that students often confuse:

• Species richness = simply the number of different species present.
• Species abundance = the relative number of individuals within each species.

Species diversity considers both together. This matters because richness alone can mislead you — two areas can have identical richness (same number of species) but wildly different diversity if one area is dominated by a single species.

Level 3: Genetic diversity

This is the diversity of alleles and genes within a species' genome — not between species, but within one species (or even within one population of that species). Individuals of the same species share the same genes but not necessarily the same alleles for each gene.

Genetic diversity matters because it's the raw material for adaptation: a population with more genetic diversity has a better chance that some individuals will survive a new biotic pressure (predator, pathogen, competitor) or abiotic pressure (temperature, humidity, rainfall change). Populations that are small or isolated suffer inbreeding, which increases the proportion of homozygous individuals — lowering genetic diversity and making recessive genetic diseases more common.

Endemism

A species is endemic to a region if it occurs naturally there and nowhere else on Earth (e.g. pygmy three-toed sloths only found on a small island off Panama). Endemic species are especially vulnerable to extinction because their entire population exists within one limited, easily-damaged range — there's no "backup population" elsewhere.

5. Species Richness, Sampling & Heterozygosity Index

Random sampling technique

You genuinely cannot count every organism in a large, complex ecosystem like a rainforest — it's simply impossible. So scientists take representative samples and use them to estimate the total picture. The key requirement is that sampling must be random, to avoid sampling bias (e.g. unconsciously picking the "nicest looking" patch of ground).

Method: convert the sampling area into a grid, number each square, then use a random number generator to select coordinates. Place a quadrat (a square frame, e.g. 0.25 m² or 1 m²) at each chosen point and record the abundance or percentage cover of species inside it.

Heterozygosity Index (H)

This measures genetic diversity at a specific gene locus within a population. A heterozygote is an organism with two different alleles at a given gene locus (e.g. Rr). The more heterozygotes there are in a population, the greater the genetic diversity.

6. Index of Diversity (Simpson's Index)

Because species richness alone can mislead (as shown above), conservationists calculate an index of diversity (D) that combines both richness AND abundance into a single number.

Step-by-step method

1. Step 1: Calculate N(N−1) → this is "value A"
2. Step 2: For each species, calculate n(n−1), then add all these values together → this is "value B"
3. Step 3: Divide value A by value B → this gives D

7. Ecological Niches & Adaptations

Habitat vs Niche — the classic confusion

These two terms get mixed up constantly, so let's be crystal clear:

• Habitat = the place where an organism lives (its "address").
• Niche = the role an organism plays within that habitat — including its biotic interactions (what it eats, what eats it) and abiotic interactions (how it exchanges gases with the environment, etc.) — essentially its "job".

Classic example — North American warblers: three warbler species share the exact same habitat (spruce/conifer trees), but each feeds at a different height within the tree — bay-breasted warbler in the middle, Cape May warbler near the top tips, yellow-rumped warbler in the lower branches. Same habitat, three different niches, zero competition, peaceful coexistence.

Three types of adaptation

Note some adaptations are combinations — e.g. hedgehog hibernation is both behavioural (choosing to hibernate) and physiological (lowering metabolic rate).

8. The Hardy-Weinberg Equation

The principle (not the equation — read this carefully)

This is one of the most misunderstood ideas in the whole chapter, so let's slow down. The Hardy-Weinberg principle states that if certain conditions are met, allele frequencies in a population will NOT change from one generation to the next. It describes a genetic "steady state" — a baseline of no evolution.

In reality, these conditions are almost never perfectly true — which is exactly the point. The Hardy-Weinberg equation gives you a baseline. If you measure real allele frequencies and they've shifted between generations, that tells you evolution IS happening (via mutation, selection, migration, or drift).

The equation itself

Why allele frequencies actually change

1. Mutation — the primary source of genetic variation. Mutations change the DNA base sequence, generating brand new alleles. A new allele might be advantageous, disadvantageous, or have no visible effect, and can stay "hidden" (unexpressed) in a population for generations before it matters.

2. Natural selection — environmental factors act as a selection pressure. Individuals with the "fitter" phenotype (better suited/adapted) survive and reproduce more successfully, passing their alleles on more often. Over generations, advantageous alleles increase in frequency; disadvantageous ones decrease.

3. Reproductive isolation — when changes prevent successful breeding between subgroups of a population:

• Seasonal changes — different mating/flowering times
• Mechanical changes — genitalia no longer physically compatible
• Behavioural changes — courtship behaviours no longer attract mates

4. Speciation — occurs when reproductive isolation persists long enough (with enough selection pressure and mutation acting independently on each isolated group) that the populations diverge into genuinely separate species.

Population bottlenecks & the founder effect

A population bottleneck occurs when a dramatic event (disease, natural disaster) sharply reduces population size, drastically shrinking the gene pool and skewing allele frequencies. The survivors are more vulnerable to further loss of alleles and mutations become "magnified" in effect (because there are so few individuals to dilute them). Cheetahs are the textbook example — a past near-extinction event left them with extremely low genetic diversity today, making them highly vulnerable to disease.

The founder effect is a related but distinct idea: it happens when a small number of individuals leave the main population to start a new population elsewhere. Because the founding gene pool is small, it's unlikely to represent the full genetic diversity of the original population — and any unusual mutations the founders happen to carry become disproportionately common in the new population.

9. Conservation: Seed Banks & Zoos

The best conservation strategy is keeping species in their natural habitat (national/marine parks), since all the support systems for life already exist there. When that's not possible, species can be conserved in captivity.

Seed banks

A facility that conserves plant diversity by drying and storing seeds in a temperature-controlled environment. Seeds of the same species are collected from different sites specifically to maintain genetic diversity — not just to preserve the species, but to preserve its full range of genetic variation.

The Svalbard Global Seed Vault in Norway (Arctic Circle) stores almost 1 million plant species' seeds, largely from crop plants sent by organisations worldwide. Not all seeds can survive freezing though — coffee and cocoa seeds can't be frozen, so successive generations of these must be grown, or tissue cultures taken, to preserve their genetic diversity.

Zoos

Captive breeding programmes can breed endangered species so offspring can eventually be released into the wild. Zoos also provide invaluable resources for scientific research (studying genetics, behaviour, habitat needs closely) and public education/engagement.

Reintroduction back into the wild

Benefits: prevents extinction in the wild; helps organisms that depend on the reintroduced species; restores degraded habitats.

Risks: reintroduced organisms may carry new diseases harmful to the existing ecosystem; captive-raised animals may lack the ability to find food or communicate effectively with wild members of their own species.

What to Memorise

Concepts Checklist

Tick off each concept once you can explain it out loud, without looking at your notes.

• I can list the full taxonomic hierarchy from Domain to Species, in order.
• I can explain why the three-domain system replaced the old two-kingdom prokaryote model, using molecular phylogeny.
• I can compare Archaea, Eubacteria, and Eukaryotes across at least 4 features (cell wall, ribosomes, histones, etc.).
• I can correctly write a binomial name, including capitalisation and italics rules.
• I can describe the key distinguishing features of each of the five kingdoms.
• I can list and explain the 5 main human threats to biodiversity with a specific example for each.
• I can explain the three levels at which biodiversity is assessed (habitat, species, genetic).
• I understand why species richness alone can be misleading, and can explain the role of abundance.
• I can describe random sampling using quadrats and explain why randomness matters.
• I know when to use sweep nets, pitfall traps, and kick-sampling.
• I can calculate the Heterozygosity Index from given data.
• I can calculate the Index of Diversity (D) using the 3-step method.
• I can distinguish between habitat and niche, and explain why one niche = one species.
• I can classify adaptations as anatomical, behavioural, or physiological.
• I understand what the Hardy-Weinberg principle states and the conditions required for it to hold.
• I can solve Hardy-Weinberg problems starting from q², including finding p, p², and 2pq.
• I can explain how mutation and natural selection change allele frequencies over generations.
• I can distinguish allopatric from sympatric speciation.
• I can distinguish a population bottleneck from the founder effect, with an example of each.
• I can evaluate the advantages and disadvantages of seed banks and zoos in conservation.

Exam Tips & Common Mistakes