Measuring biodiversity

The three levels of biodiversity

Biodiversity is described at three levels. Habitat diversity is the number of different habitats in an area: a farm with a wood, a pond, hedges and a stream has more than a farm with one enormous field. Species diversity is the number of species in a community and the abundance of each. Genetic diversity is the variety of alleles within a single species.

The three are not independent. Remove hedges and you lose habitat diversity, which takes species diversity with it, and a species reduced to a few isolated populations loses genetic diversity as well.

Species richness

The number of different species in a community.

Species evenness

How equally the individuals are shared out between the species in a community.

Species diversity

Richness and evenness together, usually expressed as an index.

Genetic diversity

The number of different alleles present in the gene pool of a population or species.

Endemism

Being found naturally in only one place, such as a single island or region, and nowhere else; a species like this is endemic to that place.

Richness on its own is a count. It treats a species represented by one individual in the same way as a species represented by a thousand, so it does not distinguish an evenly shared community from one dominated by a single species. An index of diversity combines richness with evenness in a single number.

An index of diversity does not weight species by their effect on the community. A keystone species is one whose effect on the structure of its community is far larger than its abundance would suggest, so that removing it changes the community out of all proportion. Sea otters are the standard case: they are never numerous, but they eat sea urchins, the urchins graze kelp, and where otters were hunted out the urchin population exploded and the kelp forest was stripped to bare rock, taking the fish and invertebrates that lived there with it. Returning the otters returned the forest. A diversity index calculated the year before the otters went would have given them almost no weight, because an index counts individuals rather than ecological effects. Conservation planning therefore considers which species a community depends on as well as how many species are present.

Describe the drawing

Two grids of a hundred coloured dots side by side, one dot per organism and one colour per plant species. In the grazed pasture eighty-eight dots share a single colour and the other three species are slivers; in the hay meadow the four colours are close to equal. Underneath, a small table gives species richness, the N times N minus one index, Simpson's index of diversity and the raw dominance value for each community, with the dominance row marked out because it moves in the opposite direction.

Simpson's index in its two forms

Simpson's index combines species richness with evenness. Two forms are common. Σ(n ÷ N)² estimates the probability that two individuals selected at random belong to the same species, so a larger value indicates lower diversity. 1 − Σ(n ÷ N)² is Simpson's index of diversity, so a larger value indicates higher diversity. Always state the formula used before interpreting the result.

Simpson's original quantity is the probability that two individuals picked at random from a community belong to the same species. It is called the dominance here and given no letter, because the boards use the letter D for other quantities:

dominance = Σ (n ÷ N)²n is the number of individuals of one species, N the total number of individuals of all species, and Σ means 'add this up across every species'. The squared form assumes sampling with replacement, or a sample large enough that replacement makes no difference; the finite-sample, no-replacement version uses n(n − 1) and N(N − 1) and appears below as the form AQA and Pearson Edexcel use.

That quantity measures dominance. If one species holds most of the individuals, two randomly chosen individuals are likely to be of the same species, so the dominance is close to 1. If the community is evenly shared between many species, it is close to 0. The dominance falls as diversity rises. Conventions vary: some texts call this quantity D and quote it directly, and others quote one of the transformed forms below, so an answer must state the formula used.

Two transformed forms appear on specifications.

Simpson's index of diversity:   D = 1 − Σ (n ÷ N)²Used by OCR A and by CAIE 9700. Runs between 0 and 1, and rises with diversity. These boards use the letter D for the subtracted version rather than for the raw sum.

Index of diversity:   d = N(N − 1) ÷ Σ n(n − 1)Used by AQA, which writes it d, and by Pearson Edexcel Biology A and B, which write the same formula as D. Has no upper limit, has a minimum value of 1 when every individual belongs to the same species, and rises with diversity.

Both of the second pair rise with diversity, so a bigger answer means a more diverse community in either. They are not on the same scale and cannot be compared with each other. The AQA form uses N(N − 1) and n(n − 1) rather than squares because it treats the sample as a finite population being sampled without replacement, since you cannot draw the same individual twice, and for a large sample its value is close to 1 ÷ Σ(n ÷ N)², the reciprocal of the dominance.

State the form used with the value. 'Index of diversity = 3.95' does not identify which index has been calculated; 'd = N(N − 1) ÷ Σn(n − 1) = 3.95' does.

A high index is not necessarily a desirable state and a low one is not necessarily an undesirable one. A raised bog and a saltmarsh are species-poor under their natural conditions, and the few species they hold are largely restricted to them; raising their index by adding common generalist species would be a conservation loss.

Sampling design and the validity of an index

An index is only as representative as the sample it is calculated from. The sampling design must match the inference the index is used to support.

Quadrats placed at random coordinates, generated before entering the site, support a claim about the site as a whole. Selecting locations by eye produces a sample biased towards whatever features drew the observer's attention. Describe randomisation as 'the site was divided into a numbered grid, coordinates were generated with a random number generator, and the quadrat was placed at those coordinates'.

Random placement is not the only method, and the alternatives have names OCR asks for. OCR groups them as non-random sampling, which comes in three recognised kinds. Opportunistic sampling uses whatever is conveniently available, such as the organisms along a path you can walk without trampling a crop. It is the quickest and the least trustworthy, because whatever made the sample convenient is very likely also to have made it unrepresentative. Stratified sampling divides the area into groups first, on the basis of something known about it, and then samples each group in proportion to its size: a heath that is one third bare sand and two thirds heather gets a third of its quadrats on the sand, so a small but real part of the site is not missed by chance. Systematic sampling places the samples in a regular pattern, which is what a belt transect or a line of quadrats at fixed intervals is doing, and it is the right choice wherever the question is about a gradient rather than about an average.

The sampling design must match the inference, so state which design was used and why. Random, stratified and systematic designs can all support statistical analysis when used appropriately. Random sampling supports a claim about the site as a whole. Stratified sampling supports the same claim on a site with known internal divisions, and reduces the chance of a small stratum being missed. Systematic sampling supports a claim about how a variable changes across a distance; it is less suitable for estimating a site average, because a regular sampling interval can coincide with a regular feature such as plough furrows. Opportunistic sampling gives no basis for generalisation and should be identified as a limitation in an evaluation.

The kit for small animals is examinable too, and each item exists because of how its animals move. A sweep net is swung through long grass or other vegetation in a figure of eight to collect the insects and spiders living among the stems. A pooter is a jar with two tubes, one to suck on and one to point at the animal, with gauze across the mouth of the sucking tube so nothing ends up in the collector; it lifts small invertebrates off a leaf or out of a tray without damaging them. A pitfall trap is a container sunk level with the soil surface, covered against rain, which catches ground-active animals such as beetles over a period of hours. A Tullgren funnel drives animals out of a soil or leaf litter sample by drying it from above with a lamp, so they move downwards and fall into a preservative. Beating a branch over a white tray collects what lives in a shrub. Each of these gives a biased sample of its own, since a sweep net catches what perches on vegetation and a pitfall trap catches what walks, so a survey of invertebrate diversity uses several methods rather than one.

The number of quadrats is determined from a species-accumulation curve. Plot the running total of species against the number of quadrats placed; the curve rises steeply and then flattens, and sampling stops once it has flattened, because further quadrats add little new information.

Describe the drawing

A square of grassland on the left, filling up with small square quadrats dropped at random positions, beside a graph on the right plotting the running total of species found against the number of quadrats placed. After one quadrat four species are known; after three, seven; after six, ten; after twelve, twelve; and the twenty-fourth quadrat turns up the thirteenth and last species. A dashed line across the graph marks the true total of thirteen, and the curve rises steeply at first and then flattens towards it.

The measure of abundance also affects the index. Percentage cover is the appropriate measure for plants that grow as mats or clumps where individuals cannot be distinguished, and frequency, the proportion of quadrats a species appears in, records presence rather than abundance. Define abundance consistently for an index: counts of individuals are the usual basis, while proportional cover can be used for sessile organisms provided the chosen form of the index and the method are stated. A transect answers a different question: it measures change along a gradient, from the top of a shore to the bottom or outwards from the shade of a wood, and it does not estimate a site average.

Mobile animals are counted differently again, by mark, release and recapture, and the estimate that comes out of it carries assumptions of its own. That belongs with the practical rather than here, but a diversity index built from recapture estimates inherits every one of those assumptions.

Genetic diversity within a species

Two populations of the same species can hold different amounts of genetic variation, and variation is what selection acts on. A population with little allelic variation has fewer variants available if a new disease arrives or conditions change.

The definition is about alleles. A gene locus is a position on a chromosome; a locus is polymorphic if more than one allele of that gene is present in the population. The standard measure at this level is the proportion of loci that are polymorphic.

proportion of polymorphic gene loci = number of polymorphic loci ÷ total number of loci examinedA proportion between 0 and 1, or a percentage. It depends on which loci were sampled, so two studies are only comparable if they looked at the same ones.

H = number of heterozygotes ÷ number of individuals in the populationThe heterozygosity index, the measure Pearson Edexcel Biology A names, taken at one locus. A population with many heterozygous individuals has a high H; a bottlenecked or inbred one, in which most individuals are homozygous, has a low H.

Describe the drawing

Two rows of ten columns, one column for each gene locus examined and one coloured disc for each different allele found at that locus. The upper row, a large continuous population, has stacks of two, three and four discs at most loci. The lower row, the same species after a population bottleneck, is almost all single discs. Under each row is the count of loci carrying more than one allele and that count expressed as a proportion.

Genetic diversity is measured directly, on molecules. Comparing the base sequence of DNA is the most complete method and is now cheap enough to be routine. Comparing the base sequence of mRNA looks at the genes actually being transcribed in a tissue. Comparing the amino acid sequence of a protein detects the differences that changed the product, and misses the ones the degenerate code absorbed.

Observable characteristics are a poor measure of genetic diversity, for three reasons. Most measurable characteristics are polygenic, so a single phenotype is the summed effect of many loci and cannot be read back to them. Many are strongly affected by the environment, so two genetically different plants raised in the same soil may look alike and two identical ones in different soils may not. And a large amount of allelic variation has no visible effect at all.

Two terms describe the loss of allelic variation through population history. A genetic bottleneck is a sharp reduction in population size that leaves the survivors carrying only a fraction of the original alleles; the northern elephant seal, hunted down to a few dozen animals in the 1890s, now numbers well over a hundred thousand and remains strikingly uniform genetically. The founder effect is the same loss produced by a small group establishing a new population. In both cases numbers can recover quickly and diversity does not, because lost alleles return only by mutation, which is slow, or by gene flow from another population, and an island population or a species reduced to one remnant has no other population to receive them from.

Agriculture and the three levels of diversity

Agriculture occupies most of the land surface of Britain and is a major influence on its biodiversity. Farming favours one crop or livestock species within a field and removes the species that compete with it, over large areas.

Monoculture is a single crop grown over a large area, often as the same crop year after year. The habitat it creates is uniform in structure, uniform in age and harvested at one time, so species requiring a nesting site, a different food plant or a sheltered overwintering place are not supported. Fewer plant species means fewer herbivores, which means fewer predators and parasites, so the loss propagates up the food web.

The last row concerns genetic diversity within the crop. Modern varieties are bred from a narrow set of parents and then planted over large areas, so the genetic diversity of a crop across a country can be very low. A pathogen able to overcome the resistance of one variety can affect the whole area planted with it. Resistance alleles are often found in a wild relative or a traditional landrace rather than in the commercial varieties.

Farming is also where most of the practical response happens, because most of the land is farmed. Hedgerows can be kept and replanted; field margins and beetle banks left uncropped give overwintering cover; sowing a crop in spring rather than autumn leaves winter stubble for seed-eating birds; grassland managed without heavy fertiliser keeps its wildflowers. In England these measures are funded through agri-environment schemes such as Countryside Stewardship. Each measure reduces the yield or the cropped area, and the payment compensates for that cost.

Whether to concentrate or spread production is contested. Land taken out of production has to be replaced elsewhere. One position holds that farming intensively on a smaller area and leaving more land uncultivated protects more species overall; the other holds that a landscape farmed less intensively throughout supports the species that depend on farmland itself. The evidence supports different conclusions for different groups of species.