Indicator%20Species%20Analysis

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CHAPTER 25 Indicator Species Analysis
Tables, Figures, and Equations
From McCune, B. J. B. Grace. 2002. Analysis
of Ecological Communities. MjM Software Design,
Gleneden Beach, Oregon http//www.pcord.com
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How it works 1. Calculate the proportional
abundance of a particular species in a particular
group relative to the abundance of that species
in all groups. Let A sample unit ? species
matrix aijk abundance of species j in sample
unit i of group k nk number of sample units in
group k g total number of groups First
calculate the mean abundance xkj of species j in
group k
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Then calculate the relative abundance RAkj of
species j in group k (this measures
exclusiveness, the concentration of abundance
into a particular group)
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Table 25.1. Relative abundance () of each
species in each group defined by topographic
position. The data matrix contains 54 plots and
85 species. Each group contains 18 items.
Sequence is the sequence of occurrence of the
group in the data Max is the maximum relative
abundance of the species.
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2. Calculate the proportional frequency of the
species in each group (the proportion of sample
units in each group that contain that species).
First transform A to a matrix of
presence-absence, B
Then calculate relative frequency RFkj of species
j in group k
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Table 25.2. Relative frequency () of each
species in each group defined by topographic
position. The data matrix contains 54 plots and
85 species. Max is the maximum relative
frequency of each species.
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3. Combine the two proportions calculated in
steps 1 and 2 by multiplying them. Express the
result as a percentage, yielding an indicator
value (IVkj) for each species j in each group k.
Because the component terms are multiplied, both
indicator criteria must be high for the overall
indicator value to be high. Conversely, if
either term is low, then the species is
considered a poor indicator.
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4. The highest indicator value (IVmax) for a
given species across groups is saved as a summary
of the overall indicator value of that species.
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Table 25.3. Indicator values ( of perfect
indication) of each species for each group,
rounded to the nearest whole percentage. These
values were obtained by combining the relative
abundances and relative frequencies in Tables
25.1 and 25.2. The data matrix contains 54 plots
and 85 species. Max is the maximum indicator
value of the species across the three groups.
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5. Evaluate statistical significance of IVmax by
randomly reassigning SUs to groups 1000 times.
Each time, calculate IVmax. H0 IVmax is no
larger than would be expected by chance (i.e.,
that the species has no indicator value). p
(type I error) proportion of times that the
IVmax from the randomized data set equals or
exceeds the IVmax from the actual data set.
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Table 25.4. Monte Carlo test of significance of
observed maximum indicator value (IV) for each
species, based on 1000 randomizations. The means
and standard deviations of the IV from the
randomizations are given along with p-values for
the hypothesis of no difference between groups.
The p-value is based on the proportion of
randomized trials with indicator value equal to
or exceeding the observed indicator value.
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Figure 25.1. Portion of an indicator species
hierarchy for freshwater zooplankton, based on
Warncke (1998). Only statistically significant
indicator species are shown. Groups and
subgroups were based on a hierarchical division
of sample units. The numbers for each species
represent the percentage of perfect indication
(IV) of that species in that subgroup.
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Figure 25.2. Dendrogram from cluster analysis of
the Bison Range data set. Is there an optimum
number of clusters?
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Figure 25.3. Use of indicator species analysis
as an objective criterion for pruning a
dendrogram. Left change in p-value from the
randomization tests, averaged across species at
each step in the clustering. Right number of
species with p ? 0.05 for each step of clustering.
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Figure 25.4. Ordination of species based on
indicator species analysis, contrasting
association with two mountain ranges, the
Cascades and the Coast Range (from Peterson
McCune 2001). See text for details.