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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 – PowerPoint PPT presentation

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


1
Introduction to the analysis of community data
Vojtech Novotny Czech Academy of Science,
University of South Bohemia New Guinea Binatang
Research Center
2
Ecological analysis of community samples
typical data format
3
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?
4
Presence absence characteristics number of
species and sites
5
Species accumulation curve
6
How many species? Corrected estimate for
missing species
Chao1 S singletons2/(2doubletons) S number
of species sampled
7


Courtesy Jonathan Coddington
. .
8
Courtesy Jonathan Coddington
9
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
10
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
11
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.
12
Alpha, beta and gamma diversity
alpha diversity beta diversity gamma diversity
? ?avg ?
?avg 16.6
? 20
  • 20 - 16.6 3.4

a
ß
?
13
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14
Community similarity estimate Jaccard
similarity shared species/total species X
Y Jaccard similarity A/(ABC) X, Y -
samples
X Y
15
Similarity indices
Koleff et al. 2003 J anim Ecol 72367
16
"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
17
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18
EstimateS data format, saved as TXT file
19
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
20
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
21
Sørenson Coefficient
  • like Jaccard, ignores shared absences

SU 2 SU 2
Present Absent
SU 1 Present a b
SU 1 Absent c d
22
Quantitative Version of Sørenson (Bray-Curtis)
Similarity
23
  • 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
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