Methodology for Assessing Biodiversity
Prof. S. Ajmal Khan
Centre of Advanced Study in Marine Biology
Annamalai University
he biodiversity has remained as one of the central themes of ecology
T
since many years. However after the Rio s Earth Summit, it has
become the main theme for not only ecologists, but the whole biological
community, environmentalists, planners and administrators. As many
countries including India are party to the Convention on Biological
Diversity, each nation has the solemn and sincere responsibility to
record the species of plants and animals occurring in their respective
countries assess the biodiversity properly and evolve suitable
management strategies for conserving the biodiversity which is often
described as the Living Heritage of Man. The metholodology used for
biodiversity assessment is elaborated here.
Why to Study Biodiversity?
There are mainly three reasons why biodiversity should be studied.
First, the need has come as many countries are signatories to the
Convention on Biological Diversity. For various reasons the mangrove
forests have been ruthlessly exploited and cleared. Coral reefs have been
indiscriminately mined. The fishery resources have been overexploited.
Many other organisms have been exterminated for ornamental and
medicinal purposes. There has been widespread degradation of the
habitats. Due to industrial development and large scale use of pesticides
and insecticides in agriculture, the pollution load has increased in the
estuaries, mangroves backwaters and seas. Measures of diversity are
frequently seen as indicators of the wellbeing of ecological systems.
Secondly, despite changing fashions and preoccupations, diversity has
remained the central theme of ecology. The well documented patterns of
spatial and temporal variation in diversity which intrigued the early
investigators of the natural world continue to stimulate the minds of
ecologists today. Thirdly, considerable debate surrounds the
measurement of diversity. It is mainly due to the fact that ecologists
have devised a huge range of indices and models for measuring
diversity. So for the various environments, habitats and situations the
species abundance models and diversity indices should be used and the
suitability evaluated.
Biodiversity Indices
Given the large number of indices, it is often difficult to decide which
the best method of measuring diversity is. One good way to get a feel for
diversity measures is to test their performance with one s own data. A
rather more scientific method of selecting a diversity index is on the
basis of whether it fulfils certain functions criteria ability to discriminate
between sites, dependence on sample size, what component of diversity
is being measured, and whether the index is widely used and
understood. The various diversity measures are given below.
Species Richness Indices
Simpson s Index
Simpson gave the probability of any two individuals drawn at random
from an infinitely large community belonging to different species. The
Simpson index is therefore expressed as 1 D or 1/D. Simpson s index is
heavily weighed towards the most abundant species in the sample while
being less sensitive to species richness. It has been shown that once the
number of species exceeds 10 the underlying species abundance
distribution is important in determining whether the index has a high or
low value. The D value which is standing for the dominance index is
used in pollution monitoring studies. As D increases, diversity
decreases. That way it is effectively used in Environmental Impact
Assessment to identify perturbation.
Margalef Index
It is having a very good discriminating ability. However it is sensitive to
sample size. It is a measure of the number of species present for a given
number of individuals.
However it is weighed towards species richness. The advantage
of this index over the
Simpson index is that the values can come more than 1 unlike in
the other index where the values will be varying from 0 to 1. This way
comparing the species richness between different samples collected from
various habitats is easy.
Berger Parker Index
This simple intrinsic index expresses the proportional importance of the
most abundant species. As with the Simpson index, the reciprocal form
of the Berger Parker index is usually adopted so that an increase in the
value of the index accompanies an increase in diversity and a reduction
in dominance.
Rarefaction Index
Even though it is used for standardizing the sample size, it is also used
an index (Hsieh and Li, 1998). This index relates sample size (number of
organisms) with numbers of species. This is very much helpful in
comparing the diversity of organisms living in healthy and degraded
environments.
Species Diversity Indices
Shannon Wiener Index
Shannon and Wiener independently derived the function which has
become known as Shannon index of diversity. This indeed assumes that
individuals are randomly sampled from an independently large
population. The index also assumes that all the species are represented
in the sample. Log2 is often used for calculating this diversity index but
any log base may be used. It is of course essential to be consistent in the
choice of log base when comparing diversity between samples or
estimating evenness. The value of Shannon diversity is usually found to
fall between 1.5 and 3.5 and only rarely it surpasses 4.5. It has been
reported that under log normal distribution, 105 species will be needed to
produce a value of Shannon diversity more than 5. Expected Shannon
diversity is also used (Exp H ) as an alternative to H . Exp H is
equivalent to the number of equally common species required to
produce the value of H given by the sample. The observed diversity
(H ) is always compared with maximum Shannon diversity (Hmax) which
could possibly occur in a situation where all species were equally
abundant.
Shannon diversity is the very widely used index for comparing
diversity between various habitats (Clarke and Warwick, 2001).
Brillouin Index
The Brillouin index is used instead of the Shannon index when diversity
of non random samples or collections is being estimated. For instance,
fishes collected using the light produce biased samples since not all the
fishes are attracted by the light. The Brillouin index is used here to
calculate the diversity of fishes collected by gears which use light for
fishing.
Log series Index
This popular method is very widely used because of its good
discriminant ability and the fact that, it is not unduly influenced by
sample size. It is reported to be a satisfactory measure of diversity, even
when the underlying species abundances do not follow a log series
distribution and it is less affected by the abundances of the commonest
species.
Log Normal Diversity
It is reported to be independent of the sample size and that way very
efficient for comparing the biodiversity of one habitat from another.
However it can not be accurately estimated when the sample size is
small. Therefore it can be used when the sample size is large. It is also
used as a measure of evenness.
McIntosh s Measure of Diversity
Mcintosh proposed that a community could be envisaged as a point in
an S dimensional hyper volume and that the Euclidian distance of the
assemblage from the origin could be used as a measure of diversity.
Jackknife Index
It is a technique which allows the estimate of virtually any statistic to be
improved. The beauty of this method is that it makes no assumption
about the underlying distribution. Instead a series of Jack knife
estimates and pseudo values are produced. The pseudo values are
normally distributed and their mean forms the best estimate of the
statistic. Confidence limits can also be attached to the estimate.
Q Statistic
An interesting approach to the measurements of diversity which takes
into account the distribution of species abundances but does not actually
entail fitting a model is the Q statistic. This index is the measure of the
inter quartile slope of the cumulative species abundance curve and
provides an indication of the diversity of the community with no
weighting either towards very abundant or very rare species.
Species Evenness Indices
Evenness index is also an important component of the diversity indices.
This expresses how evenly the individuals are distributed among the
different species. Pielou s evenness index is commonly used. Heip
evenness index is also there but comparatively less used.
Hill Numbers
Hill (1973b) proposed a unification of several diversity measures in a
single statistic. While N1 is the equivalent of Shannon diversity, N2 the
reciprocal of Simpson s Ä„ë and NÄ„Ä is the evenness index. The advantage
is that instead of calculating various indices for diversity, richness and
evenness, it can be used to calculate all these measures. That is its
advantage.
Caswell Neutral Model / V Statistics
This is helpful in comparing the observed diversity with the diversity
provided by the neutral model (Caswell, 1976). This model constructs an
ecologically neutral community with the same number of species and
individuals as the observed community assuming certain community
assembly rules (random birth/deaths and random
immigration/emigrations and no interactions between species). The
deviation statistics V is then determined which compares the observed
diversity (H ) with that predicted from the neutral model [E(H)]. While
the V value of zero indicates neutrality, positive values indicate greater
diversity than predicted and negative values lower diversity. Values >
+2 or < 2 indicate significant departure from neutrality. This is helpful in
comparing the coral associated organisms inhabiting healthy corals and
degraded or mined corals.
Newly Introduced Indices
Taking into consideration the demerits of the routinely used
conventional indices, new indices have been recently introduced.
Conventional indices are heavily dependent on sample size/ effort.
Indices with similar effort only can be compared. But with respect to the
conventional indices, the effort is not mentioned. Also the old indices
do not reflect the phylogenetic diversity. There is also no statistical
framework for testing the departure from expectation and the response
of species richness to environmental degradation is not monotonic.
Lastly there is no way of distinguishing natural variation to
anthropogenic disturbance. The newly introduced diversity measures
(Warwick and Clarke, 1995) do not have these demerits.
Taxonomic Diversity Index
It is defined as the average taxonomic distance between any two
individuals (conditional that they must belong to two different species)
chosen at random along the taxonomic tree drawn following the
Linnaean classification. When the sample has many species, the values
are on the higher side reflecting the taxonomic breadth.
Taxonomic Distinctness Index
It is defined as the average path length between any two individuals
(conditional that these must belong to two different species) chosen at
random along the taxonomic tree drawn using the Linnaean
classification. Here also the higher values reflect the higher diversity of
samples. Another advantage of this index is that making use of the
average taxonomic distinctness and variation in taxonomic distinctness
index, biodiversity between healthy, moderately degraded and heavily
degraded habitats could be compared using the 95% histogram, 95%
funnel and ellipse plot. Another feature of this index is that in the
absence of quantitative data, the above could be accomplished based on
qualitative data.
Phylogenetic Diversity Index
The total phylogenetic diversity index denotes the taxonomic breadth/
total taxonomic path length and the average phylogenetic index is
obtained by dividing the total phylogenetic diversity index by the
number of species. In healthy environment due to rich faunal
assemblages, (taxonomic breadth) the total phylogenetic diversity and
average phylogenetic diversity are always more.
The following hypothetical data of mangroves explain the
efficiency of the newly used diversity indices which capture the higher
level diversity also efficiently (genera and families). In island 1 there are
12 species of mangroves, belonging to 12 genera and 12 families. But in
island 2, the same number of species are there but belonging only to 5
genera and 4 families (Tables 1 4).
Table 1. Species composition of mangroves present in island 1
Name of the Species No. of the
trees
Acanthus ilicifolius 30
Nypa fruticans 30
Avicennia officinalis 30
Lumnitzera racemosa 30
Excoecaria agallocha 30
Pemphis acidula 30
Xylocarpus granatum 30
Aegiceras corniculatum 30
Bruguiera cylindrica 30
Scyphiphora hydrophyllacea 30
Sonneratia alba 30
Heritiera fomes 30
12 360
Table 2. Aggregation of mangrove species in island 1
Species Genus Family
Acanthus ilicifolius Acanthus Acanthaceae
Nypa fruticans Nypa Arecaceae
Avicennia officinalis Avicennia Avicenniaceae
Lumnitzera racemosa Lumnitzera Combretaceae
Excoecaria agallocha Excoecaria Euphorbiaceae
Pemphis acidula Pemphis Lythraceae
Xylocarpus granatum Xylocarpus Meliaceae
Aegiceras corniculatum Aegiceras Myrsinaceae
Bruguiera cylindrica Bruguiera Rhizophoraceae
Scyphiphora hydrophyllacea Scyphiphora Rubiaceae
Sonneratia alba Sonneratia Sonneratiaceae
Heritiera fomes Heritiera Sterculiaceae
No. of species 12 No. of genera 12 No. of families 12
Table 3. Species composition of mangroves present in island 2.
Name of the species No. of trees
Acanthus ilicifolius 30
Avicennia officinalis 30
A. alba 30
A. marina 30
Xylocarpus granatum 30
X. mekongensis 30
Bruguiera cylindrica 30
B. gymnorrhiza 30
B. parviflora 30
B. sexangula 30
Ceriops decandra 30
C. tagal 30
12 360
Table 4. Aggregation of species in island 2
Species Genus Family
Acanthus ilicifolius Acanthus Acanthaceae
Avicennia officinalis Avicennia Avicenniaceae
A. alba Avicennia Avicenniaceae
A. marina Avicennia Avicenniaceae
Xylocarpus granatum Xylocarpus Meliaceae
X. mekongensis Xylocarpus Meliaceae
Bruguiera cylindrica Bruguiera Rhizophoraceae
B. gymnorrhiza Bruguiera Rhizophoraceae
B. parviflora Bruguiera Rhizophoraceae
B. sexangula Bruguiera Rhizophoraceae
Ceriops decandra Ceriops Rhizophoraceae
C. tagal Ceriops Rhizophoraceae
No. of species 12 No. of genera 5 No. of families 4
While the conventional indices fail to distinguish the two reefs,
the newly introduced indices efficiently make out the differences (Table
5).
Table 5. Biodiversity indices of mangroves in islands 1 and 2
Stations S N d J H 1 Delta Delta* Delta+ Lambda+ Phi+ Sphi+
Lambda
Island 1 12 360 1.868 1 3.585 0.919 91.922 100 100 0 100 1200
Island 2 12 360 1.868 1 3.585 0.919 77.998 84.843 84.843 645.852 58.333 700
Abundance/Biomass Comparison (ABC) Plots
The advantage of distribution plots such as k dominance curves is that
the distribution of species abundances among individuals and the
distribution of species biomasses among individuals can be compared
on the same terms. Since the two have different units of measurement,
this is not possible with diversity indices. This is the basis of the
Abundance/Biomass Comparision (ABC) method of determining levels
of disturbance (pollution induced or otherwise) on benthic communities.
Under stable conditions of infrequent disturbance the competitive
dominants in benthic communities are k selected or conservative
species, with the attributes of large body size and long life span: these
are rarely dominant numerically but are dominant in terms of biomass.
Also present in these communities are smaller r selected or
opportunistic species with a short life span, which are usually
numerically dominant but do not represent a large proportion of the
community biomass. When pollution perturbs a community,
conservative species are less favoured and opportunistic species often
become the biomass dominants as well as the numerical dominants.
Thus under pollution stress, the distribution of numbers of individuals
among species behaves differently from the distribution of biomass
among species. The ABC method, involves the plotting of separate k
dominance curves for species abundances and species biomasses on the
same graph and making a comparison of the forms of these curves. The
species are ranked in order of importance in terms of abundance or
biomass on the x axis (logarithmic scale) with percentage dominance on
the y axis (cumulative scale). In undisturbed communities the biomass is
dominated by one or few large species, each represented by rather few
individuals, whilst the numerical dominants are small species with a
strong stochastic element in the determination of their abundance. The
distribution of number of individuals among species is more even than
the distribution of biomass, the latter showing strong dominance. Thus,
the k dominance curve of biomass lies above the curve of abundance for
its entire length. Under moderate pollution, the large competitive
dominants are eliminated and the inequality in size between the
numerical and biomass dominants is reduced so that the biomass and
abundance curves are closely coincident and may cross each other one
or more times. As pollution becomes more severe, benthic communities
become increasingly dominated by one or a few very small species and
the abundance curve lies above biomass curve throughout its length.
These three conditions (unpolluted, moderately polluted and grossly
polluted) can be easily recognized in a community without reference to
the control samples. That is the advantage of this ABC plot (Clark and
Warwick, 2001)
Dominance Plot
Dominance plot is also called as the ranked species abundance plot. This
can be computed for abundance, biomass, %cover or other biotic
measure representing quantity of each taxon (Clarke and Warwick,
2001). For each sample, or pooled set of samples, species are ranked in
decreasing order of abundance. Relative abundance is then defined as
their abundance expressed as a percentage of the total abundance in the
sample, and this is plotted across the species, against the increasing rank
as the x axis, the latter on a log scale. On the y axis either the relative
abundance itself or the cumulative relative abundance is plotted, the
former therefore always decreasing and the latter always increasing. The
cumulative plot is often referred to as a k dominance plot. The
cumulative curve is used for comparing the biodiversity. When k
dominance curve is used for comparing the biodiversity between many
habitats, it is called as multiple k dominance curves. Here the sample
representing the lower line has the higher diversity. In the relative
dominance curve, the curves representing samples from polluted sites
will be J shaped, showing high dominance of abundant species, whereas
the curves for less polluted habitats will be flatter. In the cumulative
dominance plot, the curves for the unpolluted sites will be sigma shaped
and the curves for the polluted habitats will be elevated (rises very
quickly).
Geometric Class Plots
These are essentially frequency polygons, plotted for each sample, of the
number of species that fall in to a set of geometric (x2) abundance
classes. That is, it plots the number of species represented in the sample
by a single individual (class 1), 2 or 3 individuals (class 2), 4 7
individuals (class 3), 8 15 individuals (class 4) etc. It has been suggested
that impact on assemblages tends to change the form of this distribution,
lengthening the right tail (some species become very abundant and
many rare species disappear) and giving a jagged curve.
Species Area Plot
It is a curvilinear curve, plotting the cumulative number of different
species observed as each new sample is added (Clarke and Warwick,
2001). The curve which rises further and further with addition of sample
is more diverse than the one which has attained the plateau .It is also
used for deciding the number of samples to be collected in a particular
habitat to get all the species.
Conclusion
The variety of diversity measures, species abundance models and
graphical tools available help ably in assessing the biodiversity of all the
habitats. The advancement in computer technology has made
biodiversity studies more easy and interesting. However this
development should be made good use of in protecting the very rich
biodiversity our country is blessed with.
References
Caswell, H. (1976). Community structure: a natural model analysis. Ecol.
Monogr., 46: 327 354.
Clarke, K.R. and Warwick, R.M. (2001). Changes in marine communities: an
approach to statistical analysis and interpretation, 2nd edition, PRIMER E:
Plymouth.
Dawson Shepherd, A., Warwick, R.M., Clark, K.R. and Brown, B.E. (1992). An
analysis of fish community response to coral mining in the Maldives.
Environ. Biol. Fish., 33 : 367 380.
Hsieh, H.L. and Li, L.A. (1998). Rarefaction diversity: a case study of
polychaetes communities using an amended FORTRAN program.
Zoological Studies, 37(1): 13 21.
Hill, M.O. (1973). Diversity and evenness: a unifying notation and its
consequences. Ecology, 54 : 427 432.
Mackie, A.S.Y., Oliver, P.G. and Kingston, P.F. (1990). The macro benthic
infauna of Hoi Ha Wan and Tolo channel, Hong Kong. In: Morton, B.
(Ed.). The Marine Biology of the South China Sea. Hong Kong University
Press, Hong Kong, 657 674.
Warwick, R.M. and Clarke, K.R. (1993). Increased variability as a symptom of
stress in marine communities. J. exp. Mar. Biol. Ecol., 172 : 215 226.
Warwick, R.M. and Clarke, K.R. (1995). New biodiversity measures reveal a
decrease in taxonomic distinctness with increasing stress. Mar. Ecol. Prog.
Ser., 129 : 301 305.
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