Classification, biodiversity and populations

Classification: the hierarchy, the binomial and dichotomous keys

Classification is hierarchical: every group sits inside a larger group, and the further down you go the more features the members share. The eight groups in order, largest first, are domain, kingdom, phylum, class, order, family, genus, species. There are only a handful of domains but millions of species, so the domain is the broadest group and the species is the narrowest.

Every organism therefore has a full address in the hierarchy. The Peruvian anchoveta is in the domain Eukaryota, kingdom Animalia, phylum Chordata, class Actinopterygii, order Clupeiformes, family Engraulidae, genus Engraulis and species ringens. Any two organisms in the same species share the whole of that address; two organisms in the same phylum share only the top three groups, which is why a fish and a sea squirt are both chordates but nothing more specific than that.

The binomial is the two-word name made from the genus and the species: Engraulis ringens. The genus is written with a capital letter, the species with a lower-case letter, and the whole name is italicised in print or underlined when handwritten. It is universal because common names are not: 'anchovy' can mean different fish in different countries, but Engraulis ringens means the same animal to a biologist anywhere, and a name in Latin does not change with language.

A dichotomous key is a series of pairs of contrasting statements. At each pair you choose the one that fits the specimen, and that choice sends you to the next pair, until you arrive at a name. 'Dichotomous' simply means splitting into two at every step, so each decision is a yes or no rather than a judgement of degree.

The statements must be based on features you can actually see and that do not change between specimens, so presence or absence, number of legs, or whether the body is covered by a shell are all safe. Colour and 'large' or 'small' are not safe, because they depend on the individual, its age or the light. Each pair must also be genuinely opposite, with no specimen able to satisfy both statements or neither.

• Binomial: genus capitalised, species in lower case, both italicised in print or underlined by hand - never hyphenated, and the genus may be abbreviated after first use (P. glauca).
• The species word is a label, not a description, so it does not have to say anything about the animal.
• 1a Body with a hard shell -> go to 2; 1b body without a shell -> go to 3
• 2a Shell in two hinged halves -> bivalve mollusc; 2b shell a single coiled piece -> gastropod mollusc
• 3a Jointed legs and two pairs of antennae -> crustacean; 3b no jointed legs -> go to 4
• 4a Five arms arranged around a central mouth -> echinoderm; 4b soft sac-like body, no arms -> ascidian

Plankton: the drifters

Plankton is defined as a diverse collection of generally microscopic organisms that have limited motility and drift in water currents. Limited motility does not mean they cannot swim at all - many can move a few body lengths - but they cannot swim against a current, so where they are is decided by the water rather than by them. This is why plankton is a description of a way of life and not a taxonomic group: it contains algae, the larvae of animals that will later live on the bottom, and adult animals such as jellyfish.

Phytoplankton are the producers of the open water. They absorb dissolved nutrients from the water around them, just as all producers do, and they obtain their nutrition by photosynthesis, using light energy to build organic molecules and releasing oxygen.

The main examples you need are microscopic algae: diatoms and dinoflagellates. Because they depend on light they are confined to the sunlit surface layers, and because they need dissolved nutrients they are most abundant where mixing brings those nutrients up from below.

Zooplankton are consumers. The group includes the larvae of many animals - fish larvae, crab larvae, the larvae of bottom-living invertebrates - as well as adult copepods, which are small crustaceans, and much larger animals such as jellyfish. Some filter phytoplankton out of the water, some hunt smaller zooplankton, and a few are parasites of other plankton.

The ecological importance is straightforward: phytoplankton are the base of almost every marine food chain, zooplankton are the step that turns that production into animal tissue, and between them they support the fish, seabirds, whales and fisheries that come later. Plankton also matters beyond food, because phytoplankton take up carbon dioxide and release oxygen, which is why they are part of the climate-control service of the ocean.

Echinoderms and crustaceans

A typical adult echinoderm has pentaradial symmetry: the body is arranged in five parts around a central mouth, so there are five arms or five rows of structures. Echinoderms also have tube feet, small fleshy projections that work by water pressure and are used for very slow movement and for gripping rock or prey. Adults have no head and no brain, and the five-part plan is obvious in a starfish, a brittle star, a sea urchin and a sea cucumber.

Ecologically, echinoderms are grazers and predators that can change the structure of a whole community. The crown of thorns starfish (Acanthaster planci) feeds on coral polyps: when its numbers rise it kills large areas of living coral, which removes the habitat and food of reef fish and invertebrates and lowers reef diversity. Economically the same animal is costly, because a damaged reef supports fewer fish and fewer tourists, and reef managers spend money on control programmes in which divers remove the starfish by hand.

A typical adult crustacean has a hard carapace covering the front part of the body, a segmented abdomen, jointed legs and two pairs of antennae. The jointed legs and the segmented body allow movement at many points, and the carapace gives protection while still allowing the animal to grow by moulting. Crabs, lobsters, prawns, barnacles and krill are all crustaceans.

The named example is Antarctic krill (Euphausia superba), a small shrimp-like crustacean that swarms in the Southern Ocean. Ecologically it is the link between phytoplankton and almost everything larger: whales, seals, penguins and fish feed on it, so the whole food web depends on its abundance. Economically it supports a fishery, mainly for aquaculture feed and for oil sold as a dietary supplement, and the crustacean group as a whole is the basis of some of the most valuable seafood catches in the world.

Bony fish and cartilaginous fish

A typical adult bony fish has a bony skeleton, gills covering the gas exchange surface, an operculum - the bony flap that protects the gills and pumps water over them - and a swim bladder, a gas-filled sac that adjusts buoyancy so the fish can stay at a chosen depth without swimming. The body is covered in thin scales, the lateral line is visible as a line of pores along each side and detects vibration and pressure changes in the water, and there are five kinds of fin: pectoral, caudal, pelvic, anal and dorsal.

A typical adult cartilaginous fish has a cartilaginous skeleton, gills that open to the outside through several separate gill slits rather than under an operculum, and skin covered in denticles, which are small tooth-like scales that make the skin rough. It has a lateral line and the same five fins, but no operculum and no swim bladder, so it is denser than water and relies on a large oily liver and on continual swimming to stay up. Sharks, rays and skates are the familiar members of the group.

Both groups are chordates, in the phylum Chordata, and all chordates share four features at some point in their development: a notochord, a dorsal neural tube, pharyngeal slits and a post-anal tail. In adult fish the notochord is largely replaced by the backbone, but it was there in the embryo, and the gill slits are the adult version of the pharyngeal slits. That shared embryology is why a fish, a sea squirt and a human are placed in the same phylum.

The two named examples carry the ecological and economic importance. The Peruvian anchoveta (Engraulis ringens) is a small bony fish of the Humboldt Current, where upwelling supplies nutrients to phytoplankton; it turns that production into fish that seabirds, larger fish and marine mammals eat, and it supports one of the largest single-species fisheries in the world, landed mainly for fishmeal and fish oil. The blue shark (Prionace glauca) is a large cartilaginous predator that roams the open ocean and helps control the numbers of its prey; it is also caught in large numbers for its fins and meat, and it is worth more alive in some places, where divers pay to see it.

Macroalgae and marine plants

A typical macroalga, such as kelp, has a holdfast that anchors it to rock, a stipe that is the flexible stalk, blades that are the flat photosynthetic surfaces, and gas bladders that hold the blades up towards the light. A holdfast is not a root: it grips the rock but does not absorb nutrients, which the alga takes in through the whole surface of its blades. Macroalgae have no true roots, stems or leaves and no vascular tissue, which is the fundamental difference between them and the marine plants.

A typical marine plant, such as seagrass, has a rhizome - a horizontal stem that creeps through the sediment and anchors the plant - plus roots that absorb water and mineral ions from the sediment, leaves that photosynthesise, and flowers, because seagrass is a flowering plant and reproduces sexually, with the pollen carried by water. Seagrass is therefore in the kingdom Plantae, while kelp is a protist, and the flowers are the feature that settles the argument in an exam.

Kelp is ecologically a forest. The holdfasts and stipes create three-dimensional habitat and shelter for fish and invertebrates, the blades feed grazers such as sea urchins, and the whole bed calms water movement and traps sediment, which stabilises the shore. Economically kelp is harvested and farmed for alginate, a thickener used in foods and medicines, for fertiliser and animal feed, and as a food in its own right, and kelp beds support fisheries and tourism.

Seagrass meadows are nurseries: young fish and invertebrates shelter among the leaves, which raises the survival of the juveniles that later stock nearby fisheries. The rhizomes and roots bind the sediment, which keeps the water clear and protects the shore from erosion, the leaves are food for animals such as dugongs and green turtles, and the sediment beneath a meadow stores carbon. That combination of nursery, coastal protection and carbon storage is why seagrass is one of the most valuable shallow-water habitats, and why its loss is costly.

Biodiversity at three levels

Biodiversity is a measure of the range of different species and ecosystems, as well as the genetic diversity within a species. The syllabus splits it into three levels, and a question that says 'explain the three levels' wants all three named and distinguished, not a list of species.

Genetic diversity is the variation in the genes within a single species. It is the raw material for natural selection: a population with high genetic diversity is more likely to contain individuals that can survive a change such as warmer water or a new disease, while a uniform population can be wiped out by one threat.

Species diversity is the number of species in a habitat and their relative abundance, so a reef with many species but one species covering most of the surface is less diverse than one with fewer species more evenly spread. Ecological diversity is the variation in ecosystems at a regional and global level - the range of habitats such as mangrove, seagrass, reef and deep sea across a coastline or across the planet.

High biodiversity tends to be linked to stability, at both small and large scales. A community with many species has many links between organisms and between organisms and the physical environment, so if one species is lost others can take over its role and the community keeps working. A community with few species has few alternatives, and one change can run through the whole system.

The services that marine biodiversity provides are a standard exam answer, and each one needs a mechanism and an example rather than a slogan.

Populations, communities and the factors that affect them

Six terms carry the marks here, and each has to be defined separately. A species is a group of organisms with similar features that can interbreed to produce fertile offspring. A population is all the individuals of one species in a defined area at a given time.

A community is all the populations of different species living and interacting in the same place. A habitat is the place where an organism lives. An ecosystem is the community together with the non-living environment, interacting as a unit.

A niche is the role a species plays: what it eats, where it lives, when it is active, and the range of conditions it can tolerate. A habitat is an address and a niche is a job, and in a stable community no two species occupy exactly the same niche, because they would compete for the same resources until one was excluded.

In a named ecosystem you should be able to give all of these - a rocky shore as the habitat, the population of limpets on one boulder, the community of barnacles, limpets, winkles and seaweed on that shore, and the limpet's niche as a nocturnal grazer of the algal film on the rock surface.

Biotic factors are the effects of other living organisms. Intra-specific competition is competition between members of the same species, for space, food or mates, and it is usually the most intense because they need exactly the same resources. Inter-specific competition is competition between different species with overlapping needs.

Symbioses are close, long-term relationships between species, including mutualism where both benefit, commensalism where one benefits and the other is unaffected, and parasitism where one benefits at the other's expense. Predation is one organism eating another, and disease is caused by pathogens that spread more easily where density is high.

Sampling: quadrats, transects and mark-release-recapture

You cannot count every organism, so you sample and then estimate. Random sampling means every point in the area has an equal chance of being chosen: you lay a grid over the shore or the map, use a random number generator to pick coordinates, and place the quadrat there. Systematic sampling means samples are taken at regular intervals along a line, which is the right choice when the habitat changes in one direction, such as the zonation up a shore or the change in sediment with depth.

A frame quadrat is a square frame laid on the bottom; you record the number of individuals, the frequency of a species in a number of quadrats, or the percentage cover, which is estimated by counting the squares of a gridded frame. Line transects record which species touch the line at intervals and show how the community changes along it. Belt transects place quadrats at regular intervals along the line, so they give abundance as well as presence, and they are the standard tool for studying zonation on a rocky shore.

Mark-release-recapture is used for animals that move around. You catch a sample, mark them harmlessly, release them, allow time to mix, then catch a second sample and record how many of them are marked. The proportion marked in the second sample is assumed to equal the proportion marked in the whole population, which gives the Lincoln index: N = (n1 × n2) / m2, where N is the estimate of population size, n1 is the number caught and marked in the first sample, n2 is the number caught in the second sample, and m2 is the number of marked individuals recaptured.

Worked example. On a rocky shore, 40 flat periwinkles are collected, marked with a small spot of nail varnish on the shell, and released. The next day, 50 periwinkles are collected from the same area and 8 of them carry the mark.

N = (40 × 50) / 8 = 2000 / 8 = 250. The estimate is that about 250 periwinkles live in that area, and because it is an estimate it should be given as a whole number, with the reasoning shown rather than only the answer.

The method rests on assumptions, and each assumption is a limitation when it is broken: the population must be closed, with no births, deaths, immigration or emigration between the two samples, and marks must not be lost or change the animal's chance of survival. Marked animals must mix at random with the rest, and every individual must be equally catchable, which fails for trap-shy animals or animals living deep in crevices. A small second sample, and therefore a small m2, makes the estimate very imprecise.

• Ethically: mark harmlessly, handle briefly, keep animals cool and wet, and return them to exactly where they were found.
• Safely: check the tide table, work in pairs, wear non-slip footwear and never turn your back on the sea.
• Choose random sampling where the habitat is uniform and you want an unbiased estimate; choose a systematic belt transect where there is a gradient such as zonation up a shore.
• State the area sampled with any abundance figure, because a count without an area cannot be compared with anything.

Measuring diversity and correlation: Simpson's index and Spearman's rank

Simpson's index of diversity combines species richness with evenness in a single number: D = 1 - Σ(n/N)^2, where n is the number of individuals of each species, N is the total number of individuals of all species, and Σ means add up the values for every species. Because each fraction is squared, a species that dominates the sample contributes most of the total, so a habitat with one very common species scores low even if several rare species are present.

Worked example. A 0.25 m2 quadrat in a seagrass bed contains 20 individuals of species A, 10 of B, 6 of C and 4 of D, so N = 40. The fractions are 0.500, 0.250, 0.150 and 0.100, and their squares are 0.2500, 0.0625, 0.0225 and 0.0100, which add to 0.3450, so D = 1 - 0.345 = 0.655, or 0.66 to two decimal places.

A quadrat from a muddy, disturbed site nearby contains 34, 3, 2 and 1 individuals of the same four species: the squares are 0.7225, 0.0056, 0.0025 and 0.0006, adding to 0.7312, so D = 0.27. The seagrass bed is the more diverse habitat even though both quadrats contain four species, because its individuals are spread more evenly.

The value of D runs from 0, where every individual belongs to the same species, towards 1, where all species are equally abundant, and it has no units. It is only comparable between samples of the same size and the same area, so always say what area was sampled, and it cannot tell you which species are present or whether any are rare and important.

Spearman's rank correlation tests whether two variables change together: rs = 1 - (6ΣD^2) / (n(n^2 - 1)), where D is the difference between the two ranks for each item and n is the number of pairs. You rank each variable separately from 1 (lowest or highest, as long as you are consistent), subtract one rank from the other for each pair, square the differences, add them up and substitute.

Worked example. Eight quadrats in a seagrass bed were ranked for sediment organic content (x) and for the density of a burrowing worm (y). The rank differences are -1, +1, -1, +1, -1, +1, -1 and +1, so ΣD^2 = 8 and n = 8. Then rs = 1 - (6 × 8) / (8 × 63) = 1 - 48/504 = 1 - 0.095 = +0.905, a strong positive correlation: worm density rises with organic content.

rs always lies between -1 and +1. A value of +1 is a perfect positive correlation, where the ranks are in exactly the same order; 0 means no correlation, with the ranks in no consistent order; -1 is a perfect negative correlation, where one variable rises exactly as the other falls.

The sign gives the direction and the size gives the strength, and a value near zero is weak in either direction. Crucially, a correlation does not prove causation: organic content and worm density may both be controlled by something else, such as the amount of fine sediment or the current speed, and only an experiment can separate the two.