A2 18 Classification, biodiversity and conservation | A Level Biology 9700

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🎯What you need to be able to do

Discuss the biological, morphological and ecological species concepts.
Describe classification into the three domains Archaea, Bacteria and Eukarya, and the differences between Archaea and Bacteria.
Describe the taxonomic hierarchy and the characteristic features of the kingdoms Protoctista, Fungi, Plantae and Animalia.
Outline how viruses are classified.
Define ecosystem and niche, and explain the levels at which biodiversity can be assessed.
Explain the importance of random sampling and use quadrats, transects and mark–release–recapture with the Lincoln index.
Use Spearman’s rank and Pearson’s linear correlation, and calculate Simpson’s index of diversity.
Explain the causes of extinction, reasons for maintaining biodiversity, and the roles of zoos, botanic gardens, conserved areas, frozen zoos, seed banks, assisted reproduction, the IUCN and CITES.

📚The biology

What is a species?

Three concepts, each useful in different circumstances, and each with a weakness:

Biological species concept — a group of organisms with similar characteristics that can interbreed to produce fertile offspring. Clear in principle, but it cannot be applied to organisms that reproduce asexually, to extinct species known only from fossils, or to populations that never meet.
Morphological species concept — a group sharing the same observable features. Practical, and the only option for fossils, but it fails where species look alike, or where males, females and juveniles of one species look very different.
Ecological species concept — a group occupying the same niche. Useful for asexual organisms, but niches overlap and are hard to define precisely.

Three domains and the hierarchy

Organisms are classified into three domains: Archaea, Bacteria and Eukarya. Archaea and Bacteria are both prokaryotes, but they differ in three respects the syllabus names: their membrane lipids, their ribosomal RNA, and the composition of their cell walls (bacterial walls contain peptidoglycan; archaeal walls do not).

Within Eukarya, the taxonomic hierarchy runs:

\[ \text{kingdom} \rightarrow \text{phylum} \rightarrow \text{class} \rightarrow \text{order} \rightarrow \text{family} \rightarrow \text{genus} \rightarrow \text{species} \]

Four kingdoms are named:

Protoctista — eukaryotic, mostly unicellular or simple multicellular; some photosynthetic, some not; a very varied group defined largely by exclusion from the other three.
Fungi — eukaryotic, cell walls of chitin, body of hyphae forming a mycelium, heterotrophic by saprotrophic (extracellular) digestion, store glycogen, reproduce by spores, no chlorophyll.
Plantae — eukaryotic, multicellular, cell walls of cellulose, autotrophic by photosynthesis using chlorophyll in chloroplasts, store starch.
Animalia — eukaryotic, multicellular, no cell wall, heterotrophic by ingestion, store glycogen, usually have nervous coordination and move.

Viruses sit outside this system, because they are non-cellular. They are classified by the type of nucleic acid (RNA or DNA) and whether it is single stranded or double stranded.

Biodiversity

An ecosystem is a community of organisms together with the non-living components of their environment, interacting as a unit. A niche is the role an organism plays within its ecosystem — where it lives, what it feeds on, what feeds on it, and how it interacts with everything else. No two species occupy exactly the same niche indefinitely.

Biodiversity can be assessed at three levels: the number and range of ecosystems and habitats; the number of species and their relative abundance; and the genetic variation within each species.

Sampling

Random sampling matters because organisms are not evenly distributed and human choice is biased — we place quadrats where things look interesting. Randomise by laying out two tape measures at right angles as axes and using random numbers to generate coordinates. This makes the sample representative, so results can be applied to the whole area, and it allows valid statistical treatment.

Frame quadrats — for estimating abundance of non-motile organisms, by species frequency (the proportion of quadrats a species occurs in) or percentage cover.
Line transect — record the species touching a line at fixed intervals.
Belt transect — place quadrats along a line and record abundance in each. Both transects are used where there is a gradient in conditions, such as up a shore or from a path into a wood — and they are the one case where systematic rather than random placement is correct.
Mark–release–recapture — for motile animals, using the Lincoln index:
\[ N = \frac{n_1 \times n_2}{m_2} \]
where \( n_1 \) is the number caught and marked in the first sample, \( n_2 \) the total number caught in the second sample, and \( m_2 \) the number of marked individuals in the second sample. Assumptions: the marked animals mix randomly back into the population; the mark does not affect survival or make the animal more visible to predators, and does not rub off; there is no significant birth, death, immigration or emigration between the two samples; and enough time is allowed for mixing but not so much that the population changes.

Simpson’s index of diversity

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

where \( n \) is the number of individuals of each type and \( N \) the total number of all individuals. \( D \) ranges from 0 to 1: a value near 0 indicates low diversity (few species, or one species dominating), and a value near 1 indicates high diversity. High diversity generally indicates a stable, mature ecosystem that is better able to withstand change, because a species lost is more likely to be replaced in its role by another.

The index accounts for both the number of species and their relative abundance, which is its advantage over simply counting species: ten species with one dominating and nine rare is less diverse than ten species evenly represented, and only an index of this kind detects that.

Correlation

Two tests, and choosing between them is what is examined:

Pearson’s linear correlation — use when the data are continuous, drawn from a normally distributed population, and a scatter diagram suggests a linear relationship. At least five paired observations, ideally ten or more.
Spearman’s rank correlation — use when the data are not normally distributed, or are ordinal or can be ranked, and a scatter diagram suggests an increasing or decreasing but not necessarily linear relationship. More than five paired observations, ideally 10–30.

Both give values from −1 (perfect negative correlation) through 0 (no correlation) to +1 (perfect positive correlation). Always plot a scatter diagram first to see whether a correlation is plausible and of what kind.

Correlation is not causation. A significant correlation between an abiotic factor and a species’ abundance shows only that the two vary together. A third factor may be responsible for both, or the causation may run the other way. Establishing cause requires a controlled experiment. Examiners ask this every year and reward the candidate who says it explicitly.

Conservation

Why species become extinct: climate change, altering conditions faster than species can adapt or migrate; competition, particularly from introduced species; hunting by humans, for food, trade or sport; and degradation and loss of habitats, which is generally the largest cause.

Why maintain biodiversity: ethical, that species have a right to exist; ecological, that species are interdependent and removing one destabilises an ecosystem; economic, that wild species provide food, medicines, timber and tourism income; agricultural, that wild relatives of crops are a reservoir of alleles — for disease resistance, for example — needed for future breeding; scientific, that undiscovered species may have unknown uses; and aesthetic.

Methods:

Zoos — captive breeding programmes with studbooks to avoid inbreeding, research, education, and reintroduction to the wild.
Botanic gardens — the same for plants, plus propagation and research into germination requirements.
Conserved areas — national parks and marine parks, protecting whole habitats in situ, which conserves the interactions as well as the species.
Frozen zoos — cryogenic storage of sperm, eggs, embryos and tissue, preserving genetic material indefinitely in a small space at low cost.
Seed banks — seeds dried and stored at low temperature; enormous genetic diversity in a small space, though seeds must be periodically germinated and replaced, and some species do not survive drying.

Assisted reproduction in endangered mammals is limited to three named techniques: IVF, embryo transfer, and surrogacy — often using a related, more common species as the surrogate mother.

Invasive alien species are controlled because, arriving without their natural predators, parasites and competitors, they may out-compete native species for resources, prey on them directly, or introduce new diseases — and native species have not evolved defences against them.

The IUCN assesses species and publishes the Red List, categorising extinction risk, which directs conservation effort and informs governments. CITES is an international agreement regulating trade in endangered species and their products, banning it for the most threatened and licensing it for others.

✏️Worked example

A student sampled invertebrates in a stream using ten randomly placed samples and counted: mayfly nymphs 20, caddis larvae 12, freshwater shrimps 8, blackfly larvae 4. (a) Calculate Simpson’s index of diversity. (b) A second stream gave D = 0.31. Compare the two sites and suggest what the difference might indicate. (c) In the same stream the student caught 60 shrimps, marked and released them. Two days later a second sample of 75 shrimps contained 15 marked individuals. Estimate the population, and state two assumptions.

(a) Total \( N = 20 + 12 + 8 + 4 = 44 \). Compute \( (n/N)^{2} \) for each species:

\( (20/44)^{2} = 0.4545^{2} = 0.2066 \)

\( (12/44)^{2} = 0.2727^{2} = 0.0744 \)

\( (8/44)^{2} = 0.1818^{2} = 0.0331 \)

\( (4/44)^{2} = 0.0909^{2} = 0.0083 \)

Summing gives \( 0.3223 \), so

\[ D = 1 - 0.3223 = \mathbf{0.68} \]

(b) The first stream, at D = 0.68, has the higher diversity; 0.31 is much closer to 0, indicating low diversity — either few species, or one species heavily dominating the community.

Higher diversity generally indicates a more stable and mature ecosystem, better able to withstand change, because a species lost is more likely to be functionally replaced by another. Low diversity may indicate pollution or another environmental stress: many invertebrates are pollution-sensitive, and organic pollution typically leaves a community dominated by a few tolerant species. It could also indicate a recently disturbed or newly colonised habitat.

(c) Using the Lincoln index, with \( n_1 = 60 \), \( n_2 = 75 \), \( m_2 = 15 \):

\[ N = \frac{n_1 \times n_2}{m_2} = \frac{60 \times 75}{15} = \mathbf{300} \]

Assumptions, any two: the marked shrimps mixed randomly back into the population before the second sample; the marking did not affect survival or behaviour, for instance by making them more visible to predators, and did not wear off; there was no significant birth, death, immigration or emigration between the two samples; and marked and unmarked individuals were equally likely to be caught.

Check it. Simpson's D must lie between 0 and 1 — a value outside that range means the subtraction from 1 was omitted or the squares were mishandled. Check also that the dominant species contributes most to the sum: mayflies at 0.2066 dwarf blackflies at 0.0083, which is the index doing its job of weighting by abundance. For the Lincoln index, the estimate must be larger than either sample — 300 exceeds both 60 and 75 ✓ — and if it came out smaller than \( n_2 \) you have inverted the formula.

Forgetting to subtract from 1, and squaring after summing. The quantity \( \sum (n/N)^{2} \) on its own is a measure of dominance, and reporting 0.32 as the diversity index inverts the meaning entirely — you would call the diverse site the poor one. Each proportion must be squared individually and then summed, not summed and then squared, which would always give 1. Keep the intermediate values to four decimal places: rounding to two before summing loses enough precision to change the second decimal place of D.

📝Practise

Work through these, then reveal the answer. Each question targets a different objective from the list above.

1. State the three domains and describe three ways in which Archaea differ from Bacteria.

The three domains are Archaea, Bacteria and Eukarya. Archaea and Bacteria are both prokaryotes — no nucleus, no membrane-bound organelles, circular DNA — but they differ in: (i) the composition of their membrane lipids, which are chemically distinct in the two groups; (ii) their ribosomal RNA sequences, which is the evidence on which the three-domain system was originally built; and (iii) the composition of their cell walls — bacterial walls contain peptidoglycan, archaeal walls do not. These molecular differences are large enough that Archaea are in some respects more closely related to Eukarya than to Bacteria, which is why they are given their own domain despite looking like bacteria under a microscope.

2. Explain why random sampling is important and describe how you would sample the plants in a field randomly.

Organisms are not evenly distributed, and if a person chooses where to place quadrats they will unconsciously select interesting or convenient areas, introducing bias. Random sampling makes the sample representative of the whole area, so that estimates of abundance can be validly applied to it, and it allows the results to be treated statistically, since statistical tests assume random sampling. Method: lay two long tape measures at right angles along two edges of the area to form x and y axes. Use a random number generator or table to produce pairs of coordinates, and place a quadrat at each. Record the species present and estimate abundance as percentage cover or species frequency in each. Take enough samples for the running mean to stabilise, and calculate a mean for the area. Note the exception: where there is an environmental gradient, a systematic belt or line transect is used instead, because random placement would obscure the very pattern being investigated.

3. Describe how you would use mark–release–recapture to estimate a woodlouse population, and state three assumptions.

Collect a sample of woodlice, count them (\( n_1 \)) and mark each one in a way that is not harmful and not conspicuous to predators — a small dot of non-toxic paint on the underside. Release them at the point of capture and allow enough time for them to mix randomly with the rest of the population, but not so long that the population changes. Take a second sample, count the total caught (\( n_2 \)) and the number of marked individuals among them (\( m_2 \)). Estimate the population as \( N = (n_1 \times n_2) / m_2 \), the Lincoln index. Assumptions: (i) marked individuals mix randomly back into the population; (ii) the mark does not affect survival, behaviour or the chance of being recaptured, and does not rub off; (iii) there is no significant birth, death, immigration or emigration between the two samples. A fourth: marked and unmarked individuals are equally likely to be caught, so the sampling method must not be biased.

4. Two habitats each contain five species. Habitat A has 96, 1, 1, 1, 1 individuals; habitat B has 20, 20, 20, 20, 20. Without full calculation, predict which has the higher Simpson’s index and explain why.

Habitat B has the higher index. Both habitats have the same number of species, so a simple species count would rate them identically. Simpson’s index also takes account of relative abundance. In habitat A one species is overwhelmingly dominant at 96 of 100 individuals, so \( (n/N)^{2} \) for that species alone is \( 0.96^{2} = 0.92 \); the sum of squares is close to 1 and D is close to 0. In habitat B the individuals are evenly distributed, so each proportion is 0.2 and each square is 0.04; the sum is 5 × 0.04 = 0.2, giving D = 0.8. Habitat A is effectively a monoculture with four rare species clinging on, and the index correctly reflects that it is less diverse. This is exactly why an index is preferred to a species count: evenness matters as well as richness.

5. Compare the advantages and limitations of seed banks and zoos as conservation methods.

Seed banks: store enormous genetic diversity — many varieties of many species — in a small space at low cost; seeds remain viable for decades when dried and frozen; no risk from disease, predation or habitat loss; and stored material can be used for reintroduction or plant breeding. Limitations: some species have seeds that do not survive drying or freezing; stored seeds must be periodically germinated and replaced, which is labour-intensive; the species is not evolving with its environment, so stored material may be poorly adapted when reintroduced; and only plants can be conserved this way. Zoos: allow captive breeding of animals too rare to survive in the wild, with studbooks to minimise inbreeding; permit research on behaviour, nutrition and reproduction, and the use of IVF, embryo transfer and surrogacy; and provide public education and funding. Limitations: very expensive per individual, so only a few species can be kept; populations are small so inbreeding and loss of diversity are hard to avoid; animals may fail to breed or lose behaviours needed for survival, so reintroduction often fails; and neither method conserves the habitat or the ecological interactions. Both are ex situ methods, and both are a supplement to, not a substitute for, protecting habitat in situ.

6. A study finds a significant positive correlation between soil nitrate concentration and the abundance of a plant species. Explain what may and may not be concluded, and state which correlation test you would use and why.

May be concluded: that soil nitrate concentration and the abundance of the species vary together — where nitrate is higher, abundance tends to be higher — and that this association is unlikely (p less than 0.05) to have arisen by chance. May not be concluded: that nitrate causes the increased abundance. Correlation does not establish causation. A third factor may influence both — for example, wetter or more sheltered areas may accumulate nitrate and favour the plant independently. The causation could also run the other way: a dense stand of the plant may alter the soil. Establishing cause requires a controlled experiment in which nitrate is varied and everything else held constant. Choice of test: if both sets of data are continuous, drawn from normally distributed populations, and the scatter diagram suggests a linear relationship, use Pearson’s linear correlation. If the data are not normally distributed, or abundance was recorded on an ordinal scale such as an abundance rating, or the relationship is monotonic but not linear, use Spearman’s rank correlation. Plot a scatter diagram first to decide.

🔗Go deeper — other people’s work

These are external resources, not mine. If one stops working, tell me and everything above it on this page still stands.

IUCN Red List — searchable by species, with the assessment criteria explained; excellent for concrete conservation examples
CITES appendices — useful for seeing exactly what ‘regulating trade’ means in practice
The Field Studies Council — practical guidance on quadrats, transects and the calculation of diversity indices, written for exactly this syllabus level