Introduction%20to%20the%20analysis%20of%20community%20data

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Introduction to the analysis of community data
Vojtech Novotny Czech Academy of Science,
University of South Bohemia New Guinea Binatang
Research Center
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Ecological analysis of community samples
typical data format
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Some of the questions you can ask about the
samples How many species? How many
individuals? What species are common /
rare? How different are the sites in their
species composition? How different are the
species in their distribution?
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Presence absence characteristics number of
species and sites
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Species accumulation curve
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How many species? Corrected estimate for
missing species
Chao1 S singletons2/(2doubletons) S number
of species sampled
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Courtesy Jonathan Coddington
. .
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Courtesy Jonathan Coddington
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No. of species often depends on the number of
individuals samples with more individuals have
also more species
Rarefraction Comparing the number of species in
a random selection of the same number of
individuals from each sample
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Diversity measures describing distribution of
individuals among species
Simpsons index the probability that two
individuals chosen from your sample will belong
to the same species Berger-Parkers index share
of the most common species
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Diversity estimate Simpsons diversity 1-
?ni(ni-1)/N(N-1) ni number of individuals
from species i, N total number of
individ. Berger-Parkers Index nmax/N nmax
abundance of the most common species, N total
no. of individ.
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Alpha, beta and gamma diversity
alpha diversity beta diversity gamma diversity
? ?avg ?
?avg 16.6
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• 20 - 16.6 3.4

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Community similarity estimate Jaccard
similarity shared species/total species X
Y Jaccard similarity A/(ABC) X, Y -
samples
X Y
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Similarity indices
Koleff et al. 2003 J anim Ecol 72367
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"Broad sense" measures incorporate differences in
species richness as well as differences in
composition
Lennon et al.
"Narrow sense" measures independent of
differences in species richness
Example 1 a 10, b 10, c 100 Jaccard
10/120 0.08 Sorensen 20/130 0.15 Lennon
1- 10/20 0.5
Example 2 a 10, b 10, c 1000 Jaccard
10/1020 0.010 Sorensen 20/1030 0.019 Lennon
1- 10/20 0.5
Koleff et al. 2003 J anim Ecol 72367
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EstimateS data format, saved as TXT file
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Chao1 S singletons2/(2doubletons) S number
of species sampled
Jaccard CJ CJ a / (a b c) a richness in
first site, b richness in second site, j
shared species Sorenson CS CS 2a / (2a b c)
Simpson's Index (D) measures the probability that
two individuals randomly selected from a sample
will belong to the same species
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Jaccard Coefficient

• number of shared species as proportion of total
  number of species in the two SUs
• ranges from 0 (no species in common) to 1 (the
  SUs have identical species lists)

SU 2 SU 2
Present Absent
SU 1 Present a b
SU 1 Absent c d
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Sørenson Coefficient

• like Jaccard, ignores shared absences

SU 2 SU 2
Present Absent
SU 1 Present a b
SU 1 Absent c d
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Quantitative Version of Sørenson (Bray-Curtis)
Similarity
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• Morisita-Horn CmH
• Not influenced by sample size richness
• Highly sensitive to the abundance of common spp.
• CmH 2S(ani bni) / (da db)(aN)(bN)
• aN total of indiv in site A
• ani of individuals in ith species in site A
• da Sani2 / aN2