Measurements of biodiversity
A variety of objective measures have been created in order to empirically measure biodiversity. The basic idea of a diversity index is to obtain a quantitative estimate of biological variability that can be used to compare biological entities, composed of direct components, in space or in time. It is important to distinguish ‘richness’ from ‘diversity’. Diversity usually implies a measure of both species number and ‘equitability’ (or ‘evenness’). Three types of indices can be distinguished:
1. Species richness indices: Species richness is a measure for the total number of the species in a community. However, complete inventories of all species present at a certain location, is an almost unattainable goal in practical applications.
2. Evenness indices: Evenness expresses how evenly the individuals in a community are distributed among the different species.
3. Taxonomic indices: These indices take into account the taxonomic relation between different organisms in a community. Taxonomic diversity, for example, reflects the average taxonomic distance between any two organisms, chosen at random from a sample. The distance can be seen as the length of the path connecting these two organisms along the branches of a phylogenetic tree.
These three types of indices can be used on different spatial 
- Alpha diversity refers to diversity within a particular area, community or ecosystem, and is usually measured by counting the number of taxa within the ecosystem (usually species level)
- Beta diversity is species diversity between ecosystems; this involves comparing the number of taxa that are unique to each of the ecosystems. For example, the diversity of mangroves versus the diversity of seagrass beds.
- Gamma diversity is a measure of the overall diversity for different ecosystems within a region. For example, the diversity of the coastal region of Gazi Bay in Kenia.
Diversity measurement is based on three assumptions
1. All species are equal: this means that richness measurement makes no distinctions amongst species and threat the species that are exceptionally abundant in the same way as those that are extremely rare species. The relative abundance of species in an assemblage is the only factor that determines its importance in a diversity measure.
2. All individuals are equal: this means that there is no distinction between the largest and the smallest individual, in practice however the smallest animals can often escape for example by sampling with nets.
Taxonomic and functional diversity measures, however, do not necessarily treat all species and individuals as equal.
3. Species abundance has been recorded in using appropriate and comparable units. It is clearly unwise to use different types of abundance measure, such as the number of individuals and the biomass, in the same investigation. Diversity estimates based on different units are not directly comparable.
Species richness indices
- Species richness S is the simplest measure of biodiversity and is simply a count of the number of different species in a given area. This measure is strongly dependent on sampling size and effort. Two species richness indices try to account for this problem:Margalef’s diversity index:
- Menhinick’s diversity index:
Where N = the total number of individuals in the sample and S = the number of species recorded.
Despite the attempt to correct for sample size, both measures remain strongly influenced by sampling effort. Nonetheless they are intuitively meaningful indices and can play a useful role in investigations of biological diversity.
Heterogeneity measures are those that combine the richness and the evenness component of diversity. Heterogeneity measures fall into two categories: parametric indices, which are based on a parameter of a species abundance model, and nonparametric indices, that make no assumptions about the underlying distributions of species abundances.
- The log series index (see also log-series distributions) is a parameter of the log series model. The parameter is independent of sample size. describes the way in which the individuals are divided among the species, which is a measure of diversity. The attractive properties of this diversity index are: it provides a good discrimination between sites, it is not very sensitive to density fluctuations and it is normally distributed, in this way confidence limits can be attached to .
The log series takes the form:
, , ,...,
is the number of species to have one individual, those with two individuals, and so on. Since 0<<1 and and are presumed to be constant, the expected number of species will be the highest in the first abundance class. is calculated interatively from:
And can be calculated from the equation:
The first two indices are based on information theory. These indices are based on the rationale that the diversity in a natural system can be measured in a similar way to the information contained in a code or message.
- The most widely used diversity index in the ecological literature is the Shannon-Wiener diversity index. 
It assumed that individuals are randomly sampled from an infinitely large community, and that all species are represented in the sample. The Shannon index is calculated from the equation:
is the proportion of individuals found in the ith species.
- Where the randomness cannot be guaranteed, for example when certain species are preferentially sampled, the Brillouin index  is the appropriated form of the information index. It is calculated as follows:
In which and the number of individuals in species i and N is the total number of individuals in the community.
- One of the best known and earliest evenness measures is the Simpson ’s index which is given by:
is the proportion of individuals found in the ith species This index is used for large, sampled communities. Simpson’s index expresses the probability that any two individuals drawn at random from an infinitely large community belong to the same species.
- The Hill numbers show the relation between the species-richness indices and the evenness-indices. Hill defined a set of diversity number of different order. The diversity number of order a is defined as:
where = the proportional abundance of species i in the sample and a = the order in which the index is dependent of rare species.
The most known are
(exponential of Shannon-Wiener diversity index)
(the reciprocal of Simpson’s )
If two data-sets have identical numbers of species and equivalent patterns of species abundance, but differ in the diversity of taxa to which the species belong, it seems intuitively appropriate that the most taxonomically varied data-set is the more diverse. As long as the phylogeny of the data-set of interest is reasonably well resolved, measures of taxonomic diversity are possible.
- Clarke and Warwick’s taxonomic distinctness indexwhich describes the average taxonomic distance – simply the “path length” between two randomly chosen organisms through the phylogeny of all the species in a data-set – has different forms: taxonomic diversity and taxonomic distinctness.
• Taxonomic diversity (Δ) reflects the average taxonomic distance between any two organisms, chosen at random from a sample. The distance can be seen as the length of the path connecting these two organisms through a phylogenetic tree or a Linnean classification. This index includes aspects of taxonomic relatedness and evenness.
• Taxonomic distinctness (Δ*) is the average path length between two randomly chosen but taxonomically different organisms. This measure is measure of pure taxonomic relatedness.
• When only presence/absence data is considered both Δ and Δ* converge to the same statistic Δ+, which can be seen as the average taxonomic path length between any two randomly chosen species.
The positive relationship between ecosystem functioning and species richness is often attributed to the greater number of functional groups found in richer assemblages. Petchey and Gaston  proposed a method for quantifying functional diversity. It is based on total branch length of a dendrogram, which is constructed from species trait values. One important consideration is that only those traits linked to the ecosystem process of interest are used. Thus a study focusing on bird-mediated seed dispersal would exclude traits such as plumage color that are not related to this function, but traits such as beak size and shape should be included With standard clustering algorithms a dendrogram is then constructed. The method makes sense. For example a community with five species with different traits will have a higher functional diversity than a community of equal richness but where the species are functional similar.
Nearly all diversity and evenness indices are based on the relative abundance of species, thus on estimates of pi in which:
with Ni the abundance of the i-th species in the sample and
with S the total number of species in the sample.
If one records the abundance of different species in a sample, it is invariably found that some species are rare, whereas others are more abundant. This feature of ecological communities is found independent of the taxonomic group or the area investigated. An important goal of ecology is to describe these consistent patterns in different communities, and explain them in terms of interactions with the biotic and abiotic environment.
Different investigators have visualized the species-abundance distribution in different ways.
1. The rank/abundance plot is one of the best known and most informative method. In this species are ranked in sequence from most to least abundant along the horizontal (or x) axis. Their abundances are typically displayed in a log10 format on the y axis, so that species whose abundances span several orders of magnitude can be easily accommodated on the same graph. In addition proportional and or percentage abundances are often used.
2. The k-dominance plot shows the cumulative percentage (the percentage of the k-th most dominant plus all more dominant species) in relation to species (k) rank or log species (k) rank.
3. The Lorenzen curve is based on the k-dominance plot but the species rank k is transformed to (k/S) x 100 to facilitate comparison between communities with different numbers of species.
4. The collector’s curve addresses a different problem. When one increases the sampling effort, and thus the number of the animals N caught, new species will appear in the collection. A collector’s curve expresses the number of species as a function of the number of specimens caught. As more specimens are caught, a collector’s curve can reach an asymptotic value but they often don’t due to the vague boundaries of ecological communities: as sampling effort increases, also the number of different patches increases.
5. The species-abundance distribution plots the number of species that are represented by r = 0,1,2,… individuals against the abundance r. This can only be drawn if the collection is large and contains many species. More often than not the species are grouped in logarithmic densities classes.
A diverse range of models has also been developed to describe species abundance data. The fitting of a model to field data is meaningful if the parameter estimates are to be used in further analysis.
1. The niche preemption model or the geometric model.
It assumes that a species preempts a fraction k of a limiting resource, a second species the same fraction k of the remainder and so on. If the abundances are proportional to their share of the resource, the ranked abundances list is given by geometric series:
k, k(1-k), …, k(1-k)(S-2), k(1-k)(S-1)
where S is the number of the species in the community.
The geometric model gives a straight line on a plot of log abundance against rank (species sequence). It is not very often found in nature, only in early successional stages or in species poor environments.
2. The broken stick model or the negative exponential distribution.
In this model a limiting resource is compared with a stick, broken in S parts at S-1 randomly located points. The length of the parts is taken as representative for the density of the S species subdividing the limiting resource. If the species are ranked according to abundance, the expected abundance of species i, Ni is given by:
The negative exponential distribution is not often found in nature. It describes a too even distribution of individuals over species to be a good representation of natural communities.
3. The log-series distribution.
Fisher’s logarithmic series model (see also the log series index ) describes the relationship between the number of species and the number of individuals in those species.
4. The log-normal distribution.
Preston first suggested to use a log-normal distribution for the description of species-abundances distributions. The distribution is traditionally written in the form:
With S(R) = the number of the species in the Rth octave to the right, and to the left of the symmetric curve; S0 = the number of the species in the modal octave; and = the inverse width of the distribution
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