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Agric Res J 54 (1) : 1-10, March 2017 Review Paper

DOI No. 10.5958/2395-146X.2017.00001.1

A REVIEW ON MEASUREMENT OF ALPHA DIVERSITY IN BIOLOGY


Ashwani K Thukral*
Department of Botanical and Environmental Sciences
Guru Nanak Dev University, Amritsar-143005, Punjab

ABSTRACT
Diversity studies make a central theme of study of biodiversity. Several measures of diversity have been proposed
by different authors, but Shannon’s, Simpson’s and Brillouin’s indices are the most widely used ones. At the same
time, these are the least understood indices. In the present review, some of the commonly used diversity indices
have been discussed with specific examples. Special emphasis has been laid to explain the derivation of diversity
indices from basic concepts.
Key words: Biodiversity, Brillouin’s index, Chao’s index, Shannon’s index, Simpson’s index

L oss of biodiversity is a global issue and an elusive


hazard. United Nations’ Earth Summit held at The Rio
de Janeiro in 1992, described biodiversity as “The variability
Hulbert (1969), Jost (2006a), Keylock (2005), McIntosh
(1967), Meffe et al. (2002), Magurran (1988), Parker (1979),
Ponce-Hernandez (2004), Routledge (1977), Smith (1986),
among living organisms from all sources, including interalia Southwood and Henderson (2000), Thukral (2010), Thukral
terrestrial, marine and aquatic systems and the ecological et al. (2006), Wilson and Mohler (1983) and many others.
complexes of which they are a part: this includes diversity Diversity indices are constrained by changes in species
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within species, between species and the ecosystems”. The composition, influx of new species with time, out flux of
totality of genes, species and ecosystems of an area constitutes species, immigration and emigration of species, dormant or
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the biodiversity. Biodiversity can be studied at three different hidden species, propagules of species etc. Model assumptions,
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levels of organization (Wikipedia, 2017a): variations in sampling techniques, time of sampling,


1. Diversity of genes within a species: Genetic diversity, experimental errors during sampling add to variations in
2. Diversity among the species: Species diversity, results. The present paper describes the indices commonly
used for the quantitative measurement of species diversity at
3. Diversity at ecosystem and landscape levels: Ecosystem the community and ecosystem levels.
diversity.
With respect to the habitat, measurement of diversity can Alpha diversity
be done at the three levels, Alpha, Beta and Gamma diversity Diversity at habitat level is the most widely used
(Whittaker, 1972). Alpha diversity is the within habitat or component in the characterization of communities. It has two
intra-community diversity. It has two components – species components viz. species richness and equitability indices.
richness and evenness. Beta diversity is the between habitat Heterogeneity indices combine both these components.
or inter community diversity. It measures change in species Species richness quantifies the number of individuals per
composition along a gradient. Gamma diversity encompasses unit area or per sample (e.g., quadrat), and species content of
diversity at the landscape level. the area. Species richness indices are also known as variety
Measurement of diversity of species is one of the most indices, are higher for species rich communities. Equitability
important characteristics of phytosociology. The quantitative indices give the relative abundance of different species
characterization of communities can be done using diversity of a community in terms of their evenness of distribution.
indices. A diversity index takes into consideration the number A community, in which the species have equal number of
of species, the number of individuals of different species in individuals of different species, will have a higher evenness
a sample, or habitat or a community. Change of diversity index. On the other hand, a community dominated by one or
from one community to another, or communities along an few species in terms of the number of individuals, will have
environmental gradient, or pooled communities or at the a lower evenness index.
landscape level constitutes beta and gamma diversities. Based
on certain assumptions, several indices have been proposed Species richness
by different authors for measurement of diversity. Some of As per Peet (1974), species richness is defined by the
the authors who have contributed to diversity studies are function:
Baumgartner (2005), Greig-Smith (1978), Henderson (2003),
E(S) = f (k, N)
*Corresponding author : akthukral.gndu@gmail.com where, E(S) = Expected value for number of species,
Date of receipt : 14.12.2016, Date of acceptance : 09.02.2017 N = Number of individuals,
1
k = Richness index. Whittaker’s second richness index is based on dividing the
Some of the commonly used richness indices are given number of species with 4 times of the geometric standard
below: deviation (σgm ) of the sample.

Species richness index S


E W2 =
Total number of species (S) present in the community 4σ gm
is called species richness index. Several indices have been
developed by different workers to determine diversity of S(In pi − In Pgm ) 2
species in a habitat. σ gm =
S
Biodiversity index: The ratio of number of species (S) to where, pi is the proportion of the species (ni / n), and pgm is the
number of individuals (N) in the sample is called biodiversity geometric mean of the pi values.
index. This index is commonly used for characterization of
forest communities (Woodwell, 1967). Estimation of total number of species
S The number of species present in a sample will depend
Rbiod =
N upon the size of the sample. Larger the sample size, higher
Menhinick’s index: Similar to biodiversity index, this index the species count. Maximum no. of species in a community
is defined as the ratio of number of species to square root of may be estimated using a species accumulation curve or
number of individuals in the sample. Chao’s method.
Species accumulation curve: Species accumulation curve
S
R MEN = is a curve plotted between the cumulative numbers of species
N against the sampling effort (Fig. 1). The sampling effort may
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Margalef’s index: It is defined as be expressed in terms of number of samples, sample size,


or the number of individuals in the sample. The slope of
S −1
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R MAR = the curve decreases with the sampling effort and tends to a
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In N limiting value.
Odum’s index: Odums’s index (Odum et al., 1960) is similar
to the Margalef’s index.
S
ROdum =
In N
Berger – Parker dominance index: Berger-Parker index is
the ratio of number of individuals of most abundant species
(Nmax) to the total number of individuals of all the species
(Ntot) in the sample.
N
DI BP = max
N tot Fig. 1. Species accumulation curve
Fisher’s a: This index is based upon the logarithmic The curve follows Michaelis–Menten’s equation and
distribution of number of individuals of different species. transcribes a hyperbola as per the following equation:
 N S max . n
S = a In  1+  S ( n) =
 a B+n
where, S is the total number of species and N is the total where S(n) = Number of species foe a sample size
number of individuals in the sample. The value of Fisher’s a
is computed by iteration. Smax = Maximum no. of species in the community,
n = number of samples or maximum sample size studied,
Average number of species per log cycle of B = Constant.
importance
The equation may be written in the form:
Whittaker (1972) defined log cycle of importance EWI as:
S 1 B 1
E W1 = = +
(In S1 − In Sn ) S (n) S max . n S max
where, S1 is the number of individuals of the most common The y-intercept of the double reciprocal plot between
species and Sn is the number of individuals of least common 1/S(n) and 1/n will provide the value of 1/Smax .
species, and S is the number of species.
2
Chao’s index Table 2. Decimal and binary systems
Chao’s index (Chao 1984, 1987) for estimation of Decimal number Binary number
species richness is given by the equation: 0 0
S(max) Chao = Sobs + (a² + b²) 1 1
where, Smax = Maximum no. of species, 2 1 0
Sobs = Number of species observed in different samples, 3 1 1
a = Singletons (Number of species represented by one 4 1 0 0
individual each), 5 1 0 1
b = Doubletons (Number of species represented by two 6 1 1 0
individuals each). 7 1 1 1
An example for computation of Smax by Chao’s method is 8 1 0 0 0
given in Table 1. Let there be 3 quadrats (Q1 through Q3) and 9 1 0 0 1
a total of 5 species observed (A through E). 10 1 0 1 0
Table 1. An example to calculate Smax by Chao’s method
prime sign on it, viz. H. It seen from the first two columns of
Sample Species
Table 2 that the message length (no. of alphabets) is related to
Sp1 Sp2 Sp3 Sp4 Sp5
the information content (H) as a power function, i.e., m = 2H.
I 1* 0 4 5 0 Vice-versa, H can be defined as a logarithmic function, viz., H
II 0 2** 3 1 1* = Log2 m, as given in column 3. Probability (pi) of each letter
III 0 0 3 4 0 in a message consisting m alphabets, each alphabet occurring
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Sobs = 5, a = 2 singletons ( marked by *), only once, will be 1/m. Information content, H, therefore can
b = 1 doubleton ( marked by **), Smax = 5+(4+2) = 11 be written as a function of probability (columns 5 and 6).
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It may be seen that the negative sign in column number 6


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Shannon – Wiener’s index appears as a result of conversion of log of reciprocal of a


One of the most widely used diversity indices is number and is not introduces to make the value of H positive,
Shannon – Wiener index proposed by Claude Shannon as is generally misunderstood by the students. Column 7
in 1948. Shannon’s index was originally developed for gives information content of each letter in the message.
communication systems and is based on information theory As for example, the total information content of a message
that any message can be transmitted using a binary code consisting 16 alphabets (one letter per alphabet) will be 4 bits
(Shannon, 1948). Most of the popular texts only mention the (column 2), and the information content per alphabet will
formula for Shannon’s index without explaining the logic be 4/16 = 0.25 bit. This will be the same that we get from
behind it. In this paper Shannon’s index is explained from its column 7 of Table 4.
basics for purpose of understanding by biologists. In actual practice, however, different letters in a text
Just like in decimal system consisting of 10 digits (viz., occur with different frequencies. Table (5) gives an example
0,1,2,3,…9), a number can be written as a combination of of a text consisting of five alphabets occurring with different
two binary digits called “bits”, a term derived from first two frequencies (colums 1-4). The probability of each letter in
and last two letters of the term “binary digits”, viz., 0 and the text will be reciprocal of total number of letters, 16 in
1 (Table 2). Similar to binary number system, a message in this case. Columns 7 and 8 give the information content of
a text can be converted to a binary code (Table 3). As for the message.
example, if a text contains only two letters, A and B, these can
be coded as 0 and 1. The binary coding of a text containing Units of information
4 letters, 8 letters or more is given in the table. It is seen Since the Shannon’s index as given above (generally
that the number of bits required for coding a text containing written as H’) uses binary numbers, the logarithmic function
2, 4, 8 or 16 letters will be 1, 2, 3 and 4 respectively, and uses 2 as the base. The units of information of H’are bits or
so on. The number of bits required to transmit a message is shannons. However, the logarithms to different bases are
called as the information content. It is generally represented inter-convertible. Information presented using log10 is given
by the Greek letter ‘H’ (‘Eta’, generally italicised), which is in hartleys or decits. The units of information content using
similar to the English alphabet H. If a message consists of 16 loge (log natural or ln) are nats (natural digits). Thus, we
alphabets, each occurring only once, the information content have,
per alphabet will be H/ number of alphabets.
H' (shannons or bits) = – Σ pi log2 pi
Table 4 describes the conversion of information content
H' (nats) = – Σ pi loge pi
of a message consisting of ‘m’ number of alphabets into
Shannon’s information measure, generally written with a H' (hartleys or decits) = – Σ pi log10 pi
3
Table 3. Information content of a message as the number of bits required to transmit a message

1 2 3 4 5
Message length Letters Binary code Information content Information
(m) (H) content per letter
No. of alphabets I bit II bit III bit IV bit No. of bits required No. of bits required
for message for each letter
2 A 0 1 ½
B 1 ½
4 A 0 0 2 2/4
B 0 1 2/4
C 1 0 2/4
D 1 1 2/4
8 A 0 0 0 3 3/8
B 0 0 1 3/8
C 0 1 0 3/8
D 0 1 1 3/8
E 1 0 0 3/8
F 1 0 1 3/8
G 1 1 0 3/8
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H 1 1 1 3/8
16 A 0 0 0 0 4 4/16
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B 0 0 0 1 4/16
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C 0 0 1 0 4/16
D 0 0 1 1 4/16
E 0 1 0 0 4/16
F 0 1 0 1 4/16
G 0 1 1 0 4/16
H 0 1 1 1 4/16
I 1 0 0 0 4/16
J 1 0 0 1 4/16
K 1 0 1 0 4/16
L 1 0 1 1 4/16
M 1 1 0 0 4/16
N 1 1 0 1 4/16
O 1 1 1 0 4/16
P 1 1 1 1 4/16

Because log2 tables or software are generally not a species, and number of letters of an alphabet with the
available, Shannon’s index is calculated either in nats or in frequency of the species. The Shannon’s index thus obtained
decits. Different units of diversity may be inter-converted as will be the diversity of the community as represented in the
follows: sample. This index presumes that all the species in the sample
Bits = 1.4427 x Nats (or the quadrat) are represented in the proportions in a larger
Bits = 3.3219 x Decits community (Poole, 1974). Larger the information content
Nats = 2.3026 x Decits (H’), more heterogeneous the sample will be. For the analysis
of biological communities, Shannon’s index may be written
The units of the diversity index must be mentioned in the as
calculations. Shannon’s information as explained above can
ni ni
be used to define the biological diversity of the communities. H' (nats) = – Σ loge
In the text given above, message length can be equated with N N
the number of species in a community, an alphabet with ni = Number of individuals of the i th species,

4
Table 4. Information content (H) of a message if each alphabet occurs only once
1 2 3 4 5 6 7
Message Infor- Information Probability Information as log Information as Shannon’s
length mation as log of (pi) of each of reciprocal of negative log of information of each
content message letter in probability probability letter in message (bits)
length message
No. of (H bits) 1
alphabets H = log2 m pi 1 H = log2 p H = – log2 p1 Hi = – p1 log2 p1
(m) m 1

1 1 1 1
2 1 H = log2 2 1/2 H = log2 H = – log2 Hi = – log2
1/2 2 2 2

1 1 1 1
4 2 H = log2 4 1/4 H = log2 H = – log2 Hi = – log2
1/4 4 4 4

1 1 1 1
8 3 H = log2 8 1/8 H = log2 H = – log2 Hi = – log2
1/8 8 8 8

1 1 1 1
16 4 H = log2 16 1/16 H = log2 H = – log2 Hi = – log2
1/6 16 16 16
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Table 5. Example of Shannon’s information content of a message if different letters occur with different frequencies

1 2 3 4 5 6 7 8
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Message Alphabets Frequency Letters Probability of Probability of Shannon’s information H


length (m) each letter each alphabet content of each alphabet

No. of ni 1/m bits


Alphabets
5 A 8 A 1/16
A 1/16
A 1/16
1 1
A 1/16 8/16 = 1/2 Hi = – log2 1/2
2 2
A 1/16
A 1/16
A 1/16
A 1/16
B 4 B 1/16
1 1
B 1/16 4/16 = 1/4 Hi = – log2 1/2
4 4
B 1/16
B 1/16
C 2 C 1/16
C 1/16 2/16 = 1/8 Hi = – 1 log2 1 3/8
16 16

D 1 D 1/16 1/4
1/16 Hi = – 1 log2 1
16 16

E 1 E 1/16 1/4
1/16

Total 16 Probability 1 H' = – Σ pi log2 pi 1.875


Frequency

5
N = Total number of individuals of all the species in the The minimum value of H’ is 0 for one species community,
sample. that is, when all the individuals in the sample belong to the
Table 6 gives the computation of Shannon’s information same species. The information content will be maximum (H’
measure for plotting a graph. For a probability equal to 0, = H’max = ln S), if all the species in the sample are represented
since the limit of (0 log 0) is zero, the Shannon’s index at this by equal number of individuals. More the heterogeneous a
point will be zero. A typical graph for Shannon’s diversity sample is, larger the information content will be.
index diversity will be a concave curve (downward). A graph It would be pertinent to mention here that Shannon’s
of the Shannon’s information measure is plotted by taking index is variously refered to as Shannon-Weaver index
the probability values on the X-axis, and the H’ values on the or Shannon-Wiener index. Spellerberg and Fedor (2003)
Y-axis (Fig. 2). studied the historical perspective of the development of the
Table 6. Shannon-Wiener’s index for 2 species communities Shannon’s index. Shannon’s expression for entropy (H) was
having different probabilities first published independently by Shannon in 1948. Shannon
and Weaver jointly authored a book 1949 “The Mathematical
pi 1-pi H’
Theory of Communication” published by the University of
0 1 0 (Limit) Illinois. In the second part of the book Weaver developed
0.05 0.95 0.198515 on the concept. Shannon had built the concept on the work
0.1 0.9 0.325083 already done by Wiener (1939, 1948, 1949). The name
0.2 0.8 0.500402 Shannon-Weaver came from the jointly written book and
the name Shannon-Wiener came from the several references
0.3 0.7 0.610864
cited by Shannon in his work and the idea developed after
0.4 0.6 0.673012 Wiener.
0.5 0.5 0.693147
Simpson’s index
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0.6 0.4 0.673012


Another widely used index for community analysis is
0.7 0.3 0.610864
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Simpson’s index proposed by Edward Hugh Simpson (1949).


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0.8 0.2 0.500402 If there are k species consisting of n individuals, distributed


0.9 0.1 0.325083 among different species as n1, n2, n3, …nk, then the
0.95 0.05 0.198515 probability (p1) of the first individual belonging to a species
1 0 0 (Limit) will be
n1
p1 =
n

Fig. 2. Graph for Shannon’s information Fig. 3. Simpson’s index for concentration Fig. 4. Simpson’s index for diversity
measure (abundance)

Fig. 5. Relation between Simpson’s Fig. 6. Inverse Simpson’s index for diversity
concentration and diversity indices.
6
Probability (p1,2) that the second individual drawn from the of 10 individuals is 1/10. The probability of drawing second
sample without replacement also belongs to the same species individual of species A, out of remaining 9 individuals will
will be be (1/10)(2/9). Given in the table are the steps to understand
 n n − 1 the derivation of Brillouin’s index.
p1,2 =  1 . 1  The negative logarithm of the equation thus derived (or
 n n −1
the logarithm of reciprocal of probability) may be used as
The sum of such probabilities for all the species is a measure Brillouin’s information measure.
of the concentration (or abundance) (C) of the species.
 ∑ n1 (ni − 1)  Good’s Series of Indices
CSimpson =  
 n(n − 1)  Following generalized equation can be used to derive
If the sample size is quite large, then the probability (p1,2) some important indices:
that the second individual drawn from the sample with
HGood = ∑ pi ( − In pi ) n
m
replacement also belongs to the same species (C’) will be
where different values of m and n (0, 1, 2, 3) give different
∑n
2

CSimpson = ∑ pi
2 i
= indices. For example,
n2 For species richness index (S), (m, n) = (0, 0)
Simpson’s index for abundance (concentration) is a typical For Simpson’s index (S pi2 ), (m, n) = (2, 0)
convex curve as shown in Fig. 3. The maximum value of For Shannon’s index (H’), (m, n) = (1, 1)
Simpson’s concentration is one when all the individuals in
the sample belong to the same species. Gini-Simpson’s index Variance as a measure of diversity
of diversity (D) is defined as
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Generally diversity is measured for discrete variables


DGini − Simpson = 1 − ∑ pi
2 which give the numbers of individuals of different species
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in the community. Diversity indices can also be obtained


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for all discrete data including non-living objects. Parkash


The graph for Gini-Simpson index of diversity is a
and Thukral (2010) proved that sample statistics such as
typical concave curve (Fig. 4). Simpson’s concentration and
standard deviation, variance, standard error, coefficient of
diversity indices are inversely related to each other as shown
variation, quadratic mean, geometric mean, harmonic mean,
in Fig. 5. Another index of diversity is inverse Simpson’s
quadratic mean, power mean, exponential mean, log mean,
diversity index (D’) (Fig. 6):
moments etc. may be used to derive information measures
1 which can be used as measures of concentration or diversity.
D' Inverse Simpson = Two of the statistics frequently used to characterize a sample
∑p
2
1 are arithmetic mean and standard deviation. Given these
statistics we can define the species abundance or diversity of
Brillouin’s index a community. Variance (σ2) of a discrete variable (X) with n
Let ni be the number of individuals of the ith species, number of observations is defined as
N be the total number of individuals of all the species (k) n n
1 n
present in the sample, then the Brillouin’s index (H), will be: ∑ ( x1 − x ) 2 ∑ xi
2

n
( ∑ xi ) 2
N! σ2 = i =1
= i =1 i =1
H Brillouin (nats) = In n n
n1!n 2 ! n3 !... nk !
In terms of community analysis, let the community
1 N! consist of n species, with the numbers individuals of each
H Brillouin (nats / individual ) = In species represented as xi. We can convert this equation into a
N n1!n 2 ! n3 !... nk !
probability equation. We know that
The units of information for Brillouin’s index will be xi
the same as those for Shannon-Wiener’s index. Minimum pi = n
value of H will be 0 for communities consisting of a single ∑x i
species. This index is also widely computed for diversity i =1
studies. Brillouin’s index is derived from the probability that Squaring both sides,
all the individuals drawn from a sample will belong to the xi
2
2
same species. Computation of Brillouin’s index is given in pi = n
Table 7. Let there be 3 species consisting of 10 individuals. ( ∑ xi ) 2
The probability of drawing an individual of species A, out i =1

7
Table 7. Calculation of probability of drawing an individual from a community consisting 3 species and 10 individuals

Sp. No. of ind. Names of No. of ind. No. of ind. of sp. drawn Probability of drawing individuals upto the
(ni) ind. left i th individual
A 5 A1 10 1  1
 
(1st)  10 

A2 9 2  1 2
 . 
(1st, 2nd)  10 9 
A3 8 3  1 2 3
 . . 
(1st, 2nd, 3rd)  10 9 8 

A4 7 4  1 2 3 4
 . . . 
(1st, 2nd, 3rd, 4th)  10 9 8 7 
A5 6 5  1 2 3 4 5
 . . . . 
(1st, 2nd, 3rd, 4th, 5th)  10 9 8 7 6 

B 3 B1 5 1  1 2 3 4 5   1
 . . . .  
 10 9 8 7 6   5

B2 4 2  1 2 3 4 5  1 2 
 . . . .  . 
 10 9 8 7 6   5 4 

B3 3 3  1 2 3 4 5   1 2 3
 . . . .  . . 
(5 ind of A and 3 of B)  10 9 8 7 6   5 4 3
C 2 C1 2 1  1 2 3 4 5   1 2 3  1 
 . . . .  . .  
 10 9 8 7 6   5 4 3  2 
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C2 1 2  1 2 3 4 5   1 2 3  1 2 
 . . . .  . .  . 
(5 ind of A, 3 of B and 2 of C)  10 9 8 7 6   5 4 3  2 1 
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Total 10 All 10 5! 3! 2 ! n1 ! n2 ! n3 !
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=
10! N!

The authors proved that for a population or for a large a column vector ƒ1 (p1) with a row vector ƒ2 (p2). Either
sample, the sum of squares of probabilities, i.e., Gini- diagonal or non-diagonal elements, or both of these elements
Simpson’s concentration (C’) will be given as of the probability matrix can be used to derive the information
measures which can be used as measures of diversity.
n
σ2 + M2
∑p i
2
= n
i =1 nM 2 I = ∑ f 1 ( p1i ) f 2 ( p2i )
where M is the mean of the sample. Thus variance can be i =1
used as a measure of heterogeneity of data for a continuous The probability matrix generated will be
variable such as length, height, weight, concentration etc.
The relation between the variance of a small sample (S2) and
a population or large sample (σ2) is,
S 2 (n − 1)
σ2 =
n
Therefore, for a small sample, the Simpson’s index will be
In the above matrix if both the row and column matrices
S 2 (n − 1) comprise of pi elements, the sum of diagonal elements will be
n + M2
n

i =1
2
pi =
nM 2
produce Simpson’s concentration, which is Simpson’s index
of diversity.
Same way Simpson’s index can be found for standard error n n
C ' Simpson = ∑ pi pi = ∑ pi
2
(SE) and coefficient of variation (CV).
i =1 i =1
n
SE 2 (n − 1) + M 2

i =1
pi =
2

nM 2
Similarly, non-diagonal elements of this probability
matrix can also be used to derive new information measures
(I),
Information Measures via Matrix Methods
Sarangal et al. (2012) proved that in several cases a
probability matrix can be produced by multiplication of

8
which gives Gini-Simpson’s index LITERATURE CITED
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purpose? University of Heidelberg. Germany. http://www.bio-
nica.info/biblioteca/Baumgartner2005Biodiversity.pdf)
Bronikowski A and Webb C 1996. Appendix: A critical examination
Similarly, in the matrix given above, if either the row of rainfall variability measures used in behavioral ecology. Beh
or the column vectors comprises of pi and the other vector Ecol Sociobiol 39: 27 – 30.
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