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Section: Diversity analysis

Diversity indices

Theory R functions Examples

This section will overview commonly used indices measuring diversity of ecological community (species
richness, Shannon index, Simpson index). We will also introduce the measures of evenness, concept of effective
number of species and general framework of Hill numbers.

As already mentioned in the general section, diversity consists of two components – species richness, i.e. the
number of species in the community, and evenness, i.e. the fact that some species in community are common
and other are rare. All diversity measures suffer from the same problem – they depend on the sampling effort,
i.e. energy spent by researcher to discover all species present in a community. Rare species, i.e. those
represented by few individuals, small biomass or low cover, are those most easily undetected, requiring
disproportionately larger sampling effort than common species.

Diversity indices reviewed below differ from each other in the weight they put on either species richness or
evenness.

Species richness

(denoted as S here) is the most intuitive and natural index of diversity, and I bet that it is used the most
frequently in studies dealing with diversity. However, it is also the most sensitive to the difference in sampling
effort, since it weights all species equally independent from their relative abundances, i.e. rare species count
equally to common species although they are more likely to be undetected.

Shannon index

(or Shannon entropy2), Shannon-Wiener or (incorrectly) Shannon-

Wiever; denoted as H, H’ or HSh) considers both species richness and
Shannon index
evenness. The index is derived from information theory and
represents the uncertainty with which we can predict of which
species will be one randomly selected individual in the community.
1)
If community contains only one species, the uncertainty is zero,
since we are sure that randomly chosen individual will belong to that
one only species. The more species the community contains, the where
more uncertainty increases; in a diverse community, we are unlikely S = species richness,
to guess of which species will be the randomly chosen individual. pi = relative abundance of species i,
However, if community has many species, but only one (or few) log = usually natural logarithm (i.e.
prevails (many individuals of one or few species), uncertainty will loge or ln)
not be so high, since we have high probability that randomly
selected individual will be the most abundant species. This is why
Shannon index increases with richness and evenness, and it puts
more weight on the richness than on evenness.

In real ecological data, values of H are usually between 1.5-3.5 (the units are bits of information); note that
absolute value of the H depends on the base of the logarithm used for the calculation (usually loge, where e =
2.718). The maximum value of H index (Hmax) for community of given richness occurs at situation that it is
perfectly even (all species have the same relative proportion).

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Simpson index

(also Simpson concentration index, denoted as D, HS or λ) is also

considering both richness and evenness, but compared to Shannon
Simpson index
it is more influenced by evenness than richness. It represents the
probability that two randomly selected individuals will be of the
same species. Since this probability decreases with increasing
species richness, the Simpson index also decreases with richness, 3)
which is not too intuitive. For that reason, more meaningful is to use
Gini-Simpson index, which is simply 1-Simpson index, and which
Gini-Simpson index
with increasing richness increases (it is identical with Hurlbert’s
probability of interspecific encounter, PIE).

The values of D are in the range between 0 and 1 and the units is a where
probability. When the species richness of community exceeds 10, S = species richness,
the values of Simpson index are mostly influenced by evenness. pi = relative abundance of species i,

Comparison of species richness, Shannon index and Simpson index

In case of perfectly even communities, the Shannon and Gini-Simpson index increases non-linearly with number
of species in the community; Gini-Simpson index increases faster. This relationship also illustrates that Gini-
Simpson index changes very fast in low species richness values (0.5 for S = 2, 0.67 for S = 3, 0.75 for S = 4, ...
0.9 for S = 10), and with richness over 10 it changes much slower (0.95 for S = 20 and 0.99 for S = 100).

Dependence of the three diversity indices (richness, Shannon and Simpson) on the (un)evenness and diversity
of the community is illustrated below.

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The A, B and C labels within the figures note three example communities, each with 12 species (species
richness = 12). Community A is perfectly even, B is moderately uneven, and C is highly uneven. See the species
abundance distribution barplots below.

Evenness

is a synthetic measure describing pattern of relative species abundances in a community. There are many ways
how evenness can be calculated, here I mention just two common ones, one derived from Shannon and the
other from Simpson index.

Shannon’s evenness

(called also Pielou’s J) is calculated as a ratio of Shannon index

calculated from real community (with S species and p1, p2i, p3....pi

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relative species abundances), and maximum Shannon index for the Shannon's evenness
community with the same richness (i.e. with S species all having p1
= p2 = pi = 1/S). The value is 1 in case that all species have the
same relative abundances.

Simpson’s evenness

(called also equitability) is calculated from Simpson’s effective

number of species divided by observed number of species. Effective
Simpson's evenness
number of species (ENS) is the number of equally abundant species
which would need to be in a community so as it has the same
Simpson’s index as the one really calculated (more about the
concept of effective number of species below). In case of Simpson’s
D, effective number of species is simply 1/D.

Effective numbers of species (ENS)

Lou Jost (2002) argued that to call Shannon and Simpson (or Ginni-
Simpson, respectively) indices as diversity is misleading, since
Effective number of species
diversity should be measured in intuitive units of species, while each
of the two indices have different units (Shannon bits and Simpson
for species richness = S
probability)4). This problem can be overcome by introducing concept
for Shannon index = eH
of effective number of species (ENS, MacArthur 1965), i.e.
(exponential of Shannon entropy
number of species in equivalent community (i.e. the one which has
index)
the same value of diversity index as the community in question)
for Simpson index = 1/D
composed of equally-abundant species. In cace of perfectly even
(reciprocal of Simpson
community, ENS is equal to species richness; for unevenn
concentration index)
communities, ENS is always smaller than S. Each of the indices
above can be converted into effective number of species following a
simple formulas.

Hill numbers

Mark Hill (British scientist, known also for introducing Detrended

correspondence analysis (DCA), Twinspan, and recallibrating
Ellenberg species indicator values for Britain) realized that species
richness, Shannon entropy and Simpson's concentration index are
all members of the same family of diversity indices, later called as
Hill numbers. Individual Hill numbers differ by the parameter q, Hill numbers
which quantifies how much the measure discounts rare species
when calculating diversity. Hill number for q = 0 is simply species For q = 0, 1 and 2 (also noted as N0, N1
richness, for q = 15) it is Shannon diversity, i.e. effective number and N2):
of species derived from Shannon entropy, and for q = 2 it is (species richness)
Simpson diversity, i.e. ENS for Simpson concentration index. For q
(exponential of Shannon entropy)
> 0, indices discount rare species, while for q < 0 the indices
discount common species and focus on number of rare species
(reciprocal of Simpson index)
(usually not meaningful).

Dependence of species richness, Shannon diversity (effective

number of species based on Shannon entropy index) and Simpson's
diversity (effective number of species based on Simpson's index) on
(un)evenness and diversity is illustrated below.

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Diversity profiles

It is possible to draw the effective number of species as a function of coefficient q - increasing q decreases the
impact of rare species on the measure of diversity. The value for q = 0 equals to species richness (in the
diagram displayed by squares), for q = 1 equals to Shannon diversity (circles) and for q = 2 Simpson diversity
(triangles). The shape of the diversity profile considers the differences in evenness between the three
communities; the more is the community species abundance uneven, the faster the curve declines with
increasing coefficient q. The future will see what exactly can this form of diversity visualization bring new.

Summary of values for diversity measures discussed in this chapter

Community A Community B Community C

(perfectly even) (moderately uneven) (highly uneven)
Species richness 12 12 12
Shannon entropy 2.48 1.81 0.87

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Community A Community B Community C

(perfectly even) (moderately uneven) (highly uneven)
Simpson index 0.92 0.79 0.46
Shannon evenness 1 0.73 0.35
Simpson evenness 1 0.38 0.15
Shannon diversity (1D, N1) 12 6.14 2.39
2
Simpson diversity ( D, N2) 12 4.66 1.86
1)

Why log (S)? H = -∑ pi log pi. In case of S equally abundant species, each pi = 1/S. Then, H = -∑ 1/S log 1/S = - S
* 1/S * log (1/S) = - log (1/S) = - log S-1 = - (- log S) = log S.
2)

Entropy of the system represents the uncertainty, expected measure of surprise.

3)

Why 1/S? D = ∑pi2. In case of S equally abundant species, each pi = 1/S. Then D = ∑1/S2 = S*1/S2 = S/S2 = 1/S.
4)

Jost (2002) argues: “The radius of a sphere is an index of its volume but is not itself the volume, and using the
radius in place of the volume in engineering equations will give dangerously misleading results. This is what
biologists have done with diversity indices. The most common diversity measure, the Shannon-Wiener index, is
an entropy, giving the uncertainty in the outcome of a sampling process.... Entropies are reasonable indices of
diversity, but this is no reason to claim that entropy is diversity.”
5)

In fact the Hill's formula is not defined for q = 1, but it can be shown that when q approaches 1 from below or
above, the index gets equal to exponential Shannon.

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