Classification, biodiversity and conservation

Every objective in this topic is printed under "A Level subject content" in the 9700 syllabus, so all of it is A Level and none of it is AS. It is examined on Paper 4, and the sampling and statistics objectives feed Paper 5. Paper 1 is the AS multiple-choice paper and does not reach this topic, so no multiple-choice practice on this site is tagged to it.

Syllabus points

18.1 Classification

• Discuss the meaning of the term species, limited to the biological species concept, morphological species concept and ecological species concept.
• Describe the classification of organisms into three domains: Archaea, Bacteria and Eukarya.
• State that Archaea and Bacteria are prokaryotes and that there are differences between them, limited to differences in membrane lipids, ribosomal RNA and composition of cell walls.
• Describe the classification of organisms in the Eukarya domain into the taxonomic hierarchy of kingdom, phylum, class, order, family, genus and species.
• Outline the characteristic features of the kingdoms Protoctista, Fungi, Plantae and Animalia.
• Outline how viruses are classified, limited to the type of nucleic acid (RNA or DNA) and whether this is single stranded or double stranded.

18.2 Biodiversity

• Define the terms ecosystem and niche.
• Explain that biodiversity can be assessed at different levels, including: the number and range of different ecosystems and habitats; the number of species and their relative abundance; the genetic variation within each species.
• Explain the importance of random sampling in determining the biodiversity of an area.
• Describe and use suitable methods to assess the distribution and abundance of organisms in an area, limited to frame quadrats, line transects, belt transects and mark-release-recapture using the Lincoln index (the formula for the Lincoln index will be provided, as shown in the Mathematical requirements).
• Use Spearman's rank correlation and Pearson's linear correlation to analyse the relationships between two variables, including how biotic and abiotic factors affect the distribution and abundance of species (the formulae for these correlations will be provided, as shown in the Mathematical requirements).
• Use Simpson's index of diversity (D) to calculate the biodiversity of an area, and state the significance of different values of D (the formula for Simpson's index of diversity will be provided, as shown in the Mathematical requirements).

18.3 Conservation

• Explain why populations and species can become extinct as a result of: climate change; competition; hunting by humans; degradation and loss of habitats.
• Outline reasons for the need to maintain biodiversity.
• Outline the roles of zoos, botanic gardens, conserved areas (including national parks and marine parks), "frozen zoos" and seed banks, in the conservation of endangered species.
• Describe methods of assisted reproduction used in the conservation of endangered mammals, limited to IVF, embryo transfer and surrogacy.
• Explain reasons for controlling invasive alien species.
• Outline the role in conservation of the International Union for Conservation of Nature (IUCN) and the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES).

What is a species?

Three definitions are on the syllabus, and the marks are in knowing why none of them is sufficient on its own.

• The biological species concept: a group of organisms with similar morphology and physiology that can interbreed to produce fertile offspring, and that are reproductively isolated from other species. It is the strongest definition, but it cannot be applied to organisms that reproduce asexually, to extinct species known only from fossils, or to populations that never meet in the wild.
• The morphological species concept: a group of organisms sharing the same observable features. Easy to apply, including to fossils, but it fails on sexual dimorphism, where male and female look nothing alike, on species with several life stages, and on cryptic species that look identical yet do not interbreed.
• The ecological species concept: a group of organisms occupying the same niche. Useful for asexual organisms, but many species share parts of a niche and one species may occupy different niches in different places.

In practice taxonomists use all three, plus DNA sequence data, and the fact that the definition is contested is itself the discussion point the syllabus wants.

The three domains

All life is placed in three domains: Archaea, Bacteria and Eukarya. The split was made on the basis of ribosomal RNA sequences, and it replaced a simpler prokaryote and eukaryote division because it turned out that the two groups of prokaryotes differ from each other about as much as either differs from eukaryotes.

Archaea and Bacteria are both prokaryotes: no nucleus, no membrane-bound organelles, 70S ribosomes, circular DNA. Three differences are specified:

The peptidoglycan difference is the one to remember first, since it is also why antibiotics such as penicillin, which block peptidoglycan synthesis, affect bacteria and not archaea.

The taxonomic hierarchy

Within Eukarya, organisms are placed in a nested hierarchy:

kingdom → phylum → class → order → family → genus → species

Each level contains the ones below it, and each level down means a smaller group of more closely related organisms. Naming uses the binomial system: genus with a capital letter, species with a lower case letter, both in italics or underlined, as in Homo sapiens.

The four eukaryotic kingdoms

• Protoctista. Eukaryotic, mostly unicellular or simple multicellular with no tissue differentiation. Very varied: some photosynthesise, some ingest food, some absorb it. Effectively the kingdom for eukaryotes that fit nowhere else. Amoeba, Plasmodium, Chlorella, seaweeds.
• Fungi. Eukaryotic, with cell walls of chitin. Body usually a mycelium of hyphae, often with many nuclei per cell. Never photosynthetic: they are saprotrophic or parasitic, secreting enzymes and absorbing the products. Store carbohydrate as glycogen.
• Plantae. Eukaryotic, multicellular, with cell walls of cellulose. Photosynthetic, with chlorophyll in chloroplasts. Store carbohydrate as starch. Cells have large permanent vacuoles.
• Animalia. Eukaryotic, multicellular, no cell walls. Heterotrophic, ingesting food and digesting it internally. Usually able to move about, with nervous coordination.

Two distinctions worth being precise about: fungi are not plants, and the reason is not just that they lack chlorophyll but that their walls are chitin and their food is absorbed after external digestion. And plants store starch while fungi store glycogen, like animals.

Viruses

Viruses are not placed in any of the three domains. They are not cells, they have no metabolism of their own and they can only replicate inside a host cell, so most classifications leave them outside the system entirely.

They are classified by nucleic acid type, on two questions:

• Is the genetic material DNA or RNA?
• Is it single stranded or double stranded?

That gives four main groups, and further subdivision uses the presence or absence of an envelope, the shape of the capsid and the host range. HIV is a single-stranded RNA virus, and the influenza virus is too; the Herpesviridae are double-stranded DNA viruses.

Ecosystem, niche and levels of biodiversity

An ecosystem is all the living organisms in an area together with the non-living components of the environment, and the interactions between them.

A niche is the role of an organism within its ecosystem: where it lives, what it feeds on, what feeds on it, when it is active, and how it interacts with everything else. Two species cannot occupy exactly the same niche in the same place indefinitely, because one will out-compete the other.

Biodiversity is assessed at three levels, and a question that asks about biodiversity without naming which level is asking you to distinguish them:

• Habitat or ecosystem diversity. The number and range of different ecosystems and habitats in an area. A region with woodland, marsh, dune and river has higher habitat diversity than one that is all arable field.
• Species diversity. Not just the number of species (species richness) but their relative abundance (species evenness). A wood with 10 species evenly represented is more diverse than one with 10 species where a single species makes up 95 per cent of the individuals.
• Genetic diversity. The genetic variation within each species, that is, the number of different alleles in the gene pool. This is what determines whether a species can adapt to change, and it is why a bottleneck matters even after the numbers recover.

Sampling

You cannot count everything, so you sample, and the sample must represent the whole area.

Random sampling matters because any other method carries bias. If you choose where to put the quadrat, you will unconsciously favour interesting patches, and the estimate will be wrong in a direction you cannot correct for. Random sampling makes the result statistically valid and lets you apply a significance test to it.

To sample randomly: lay out two tape measures at right angles as axes, use a random number generator to produce pairs of coordinates, and place the quadrat at each pair.

Frame quadrats

A frame quadrat is a square frame of known area, often divided into a grid. From it you can record:

• Species frequency: the proportion of quadrats in which a species occurs, useful for species that are hard to count individually.
• Species density: the mean number of individuals per quadrat, converted to number per square metre.
• Percentage cover: the proportion of the quadrat area covered by a species, estimated with the grid. Best for plants that grow as a mat, and note that percentage covers can total more than 100 where plants overlap.

Worked example. A student places 20 quadrats, each 0.25 m², at random and finds daisies in 13 of them, with 84 daisy plants in total.

frequency = 13 / 20 × 100 = 65%

total area sampled = 20 × 0.25 = 5

density = 84 / 5 = 16.8

so about 16.8 daisy plants per square metre.

Transects

Use a transect, not random sampling, when you are investigating how distribution changes along an environmental gradient, such as up a shore or from open ground into woodland shade. The sampling is deliberately not random because the gradient is the thing being studied.

• A line transect records only the organisms that touch the line, at set intervals along it.
• A belt transect places quadrats along the line, either touching one another (a continuous belt) or at regular intervals (an interrupted belt), and gives abundance data as well as presence.

Mark-release-recapture

For mobile animals, use the Lincoln index. Capture a sample, mark them harmlessly, release them, allow time for mixing, then capture a second sample.

population estimate = (number in first sample × number in second sample) / number marked in the second sample

Worked example. 60 woodlice are caught and marked. In a second sample of 80, 15 are marked.

population = 60 × 80 / 15 = 320

The estimate is only valid if several assumptions hold, and questions almost always ask for them:

• The marking does not harm the animal or make it more visible to predators, and the mark does not rub off.
• The marked animals mix randomly back into the population before the second sample.
• There is no significant migration, birth or death between the two samples.
• Marked and unmarked animals are equally likely to be caught, so the first capture does not teach them to avoid the trap.

Correlation

Two tests, and choosing between them is examinable.

• Pearson's linear correlation is used when both sets of data are on a continuous, interval scale, are approximately normally distributed, and a scatter graph suggests a linear relationship.
• Spearman's rank correlation is used when the data are ranked, are not normally distributed, or the relationship is not linear. It works on the order of the values rather than the values themselves.

Both give a coefficient between -1 and +1. A value near +1 means a strong positive correlation, near -1 a strong negative correlation, and near 0 no correlation. The calculated value is compared with a critical value at p = 0.05 for the number of pairs, and a value above the critical value means the correlation is significant.

The point to make in any conclusion: a correlation does not establish cause. Two variables may both depend on a third. An abiotic factor correlating with the abundance of a species is a reason to investigate further, not a demonstration that it controls the distribution.

Simpson's index of diversity

The formula is provided. In the form the syllabus uses:

D = 1 - Σ (n / N)²

where n is the number of individuals of one species and N the total number of individuals of all species.

Worked example. A quadrat contains three species: 8, 5 and 2 individuals.

N = 8 + 5 + 2 = 15

Σ (n / N)² = 0.284 + 0.111 + 0.018 = 0.413

D = 1 - 0.413 = 0.587

What the value means. D runs from 0 to 1. A value near 1 means high diversity: many species with fairly even numbers. A value near 0 means low diversity: few species, or one species dominating.

Because the index uses both the number of species and their relative abundance, it separates two communities that species richness alone would call identical. A high value also implies a more stable ecosystem, because a food web with many links is less disturbed by the loss of any one species, and it usually implies a less hostile environment.

Extinction

Four causes are named, and each works through the same underlying mechanism: the population falls below the level at which it can sustain itself.

• Climate change. Temperature and rainfall patterns shift faster than a species can adapt or migrate, and habitats such as sea ice or cloud forest disappear. Species with narrow tolerance ranges or nowhere to move to, such as those on mountain tops, go first.
• Competition. An introduced or newly arrived species out-competes a native one for the same resource, so the native population declines. The red squirrel and the grey squirrel in Britain is the standard case.
• Hunting by humans. Direct killing for food, for materials such as ivory or horn, for sport, or to protect livestock. The passenger pigeon and the dodo are extinct through hunting.
• Degradation and loss of habitat. Deforestation, drainage of wetland, ploughing of grassland, pollution and urban development. This is the largest cause overall. Fragmentation matters as much as outright loss, because small isolated populations suffer inbreeding and drift.

Why maintain biodiversity

• Ecological. Species are interdependent through food webs, pollination, seed dispersal, decomposition and nutrient cycling. Removing one species has effects on others that are hard to predict, and diverse ecosystems are more stable.
• Economic and agricultural. Wild relatives of crop plants hold the allele pool that plant breeders draw on for disease resistance and drought tolerance. Once a wild population is gone, those alleles are gone.
• Medical. A large proportion of drugs originate in compounds found in wild organisms, and most species have never been screened.
• Environmental services. Forests and peatlands store carbon, wetlands purify water, vegetation prevents soil erosion.
• Aesthetic and ethical. Landscapes and wildlife have value for recreation and tourism, and there is an argument that other species have a right to exist independent of their usefulness.

Methods of conservation

In situ, meaning in the organism's own habitat, is preferred because the species continues to live and evolve in its niche, and the whole ecosystem is protected with it.

• Conserved areas, including national parks and marine parks. Legal protection, restrictions on hunting, fishing, building and access, habitat management, and control of introduced species. Marine parks may include no-take zones from which fish spill over into surrounding waters.

Ex situ, meaning away from the habitat, is a last resort or a support.

• Zoos. Captive breeding programmes, with studbooks to record ancestry so that mating pairs are chosen to keep genetic diversity high and avoid inbreeding. Also research, public education and, in some cases, reintroduction to the wild.
• Botanic gardens. Growing and propagating rare plants, storing them, and supplying material for reintroduction.
• Seed banks. Seeds are dried and stored at about -20 °C, where they remain viable for decades. Cheap, compact, and able to hold enormous genetic diversity, since thousands of seeds from many populations can be stored. Samples are germinated periodically to test viability and to renew the stock. Not all species can be stored this way: some seeds do not survive drying.
• Frozen zoos. Storage in liquid nitrogen of gametes, embryos and tissue or cells from endangered animals, preserving genetic material even from individuals that have died.

Assisted reproduction

Three techniques are named, and they matter because a captive population is often small, scattered between institutions, and unwilling to breed.

• IVF. Eggs are collected after hormone treatment to stimulate ovulation and are fertilised with collected sperm outside the body. This allows a female to produce more offspring than she would naturally, and allows sperm to be used from a male on a different continent, or from a male that is already dead.
• Embryo transfer. The embryo produced is implanted into the uterus of a female, which frees the genetic mother to produce further eggs rather than carrying one pregnancy to term.
• Surrogacy. The embryo is carried by a female of a closely related but more common species, so that the rare females are not used up in pregnancies. It also allows more offspring per year from the same small number of endangered adults.

Invasive alien species

An invasive alien species is one introduced, deliberately or accidentally, outside its natural range, which then spreads and damages the new ecosystem. Control is needed because such a species typically:

• out-competes native species for food, light, space or nesting sites, since it arrives without the predators, parasites and diseases that limited it at home,
• preys on native species that have no evolved defences against it,
• introduces new diseases or parasites to which natives have no resistance,
• hybridises with a native species, so the native gene pool is diluted, and
• damages crops, forestry or infrastructure, which is an economic cost as well as a biological one.

The result is a fall in native populations, sometimes to extinction, and a fall in overall biodiversity.

IUCN and CITES

The International Union for Conservation of Nature (IUCN) is an organisation of governments and non-governmental bodies. It:

• publishes the Red List, which assesses species against set criteria and places them in categories from Least Concern up to Critically Endangered, Extinct in the Wild and Extinct,
• provides the evidence base that governments and conservation bodies use to set priorities, and
• advises on and helps to run conservation programmes and protected areas.

CITES is the Convention on International Trade in Endangered Species of Wild Fauna and Flora, an agreement between governments. It:

• regulates and, for the most endangered species, bans international trade in listed species and in products made from them, such as ivory, rhino horn, tortoiseshell and certain timbers,
• works through a system of permits and appendices, with the level of protection depending on how threatened the species is, and
• depends on member countries passing and enforcing their own laws, which is also its main weakness, since enforcement varies and illegal trade continues.

Note the division of labour, because questions test it: the IUCN assesses and advises; CITES regulates trade. Neither owns land or runs reserves.

Common mistakes

• Defining a species as organisms that can interbreed, leaving out that the offspring must be fertile.
• Saying the biological species concept works for all organisms. It fails for asexual species and for fossils.
• Placing Archaea and Bacteria together as one group because both are prokaryotes. The domain system separates them.
• Saying fungi are plants that cannot photosynthesise, rather than giving chitin walls, saprotrophic nutrition and glycogen storage.
• Treating viruses as members of a kingdom or domain.
• Describing biodiversity as the number of species only, and leaving out relative abundance and genetic diversity.
• Using a transect where the question requires random sampling, or randomly sampling across a gradient that the transect exists to reveal.
• Forgetting the assumptions of mark-release-recapture, particularly that the marked animals must mix back in.
• Reading a Simpson's index near 0 as high diversity. A value near 1 is high.
• Concluding cause from a significant correlation.
• Saying seed banks preserve animals, or that a frozen zoo holds live animals.
• Saying surrogacy uses a female of the same endangered species, which would defeat the purpose.
• Confusing the roles of the IUCN and CITES.