Introduction to the analysis of community data

Vojtech NovotnyCzech Academy of Science, University of South Bohemia & New Guinea Binatang Research Center

Ecological analysis of community samples

typical data format:

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?

Presence – absence characteristics: number of species and sites

5

7

9

11

13

15

17

19

21

1 2 3 4 5

No. of sites

No

. o

f sp

ecie

s .

Site accummulation 1-2-3-4-5 Randomised sites

Species accumulation curve

How many species?

Corrected estimate for missing species

Chao1 S + singletons2/(2*doubletons) S – number of species sampled

Courtesy Jonathan Coddington

..

Courtesy Jonathan Coddington

No. of species often depends on the number of individuals:samples with more individuals have also more species

0

5

10

15

20

25

0 100 200 300 400 500 600

No. of individuals

No

. o

f sp

ecie

s

observedrarefraction 36 ind.

Rarefraction:

Comparing the number of species in a random selection of the same number of individuals from each sample

Diversity measures: describing distribution of individuals among species

Simpson’s index: the probability that two individuals chosen from your sample will belong to the same speciesBerger-Parker’s index: share of the most common species

0

0.1

0.2

0.3

0.4

0.5

0.6

0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35

Simpson's index

Ber

ger

-Par

ker

ind

ex

Site 1

Site 5

Diversity estimate:Simpson’s diversity: 1- ∑[ni(ni-1)/N(N-1)] ni – number of individuals from species i, N – total number of individ.Berger-Parker’s Index: nmax/Nnmax = abundance of the most common species, N – total no. of individ.

alpha diversity

beta diversity

gamma diversity

αβ

γ

= avg +

= 20

avg = 16.6

= 20 - 16.6 = 3.4

Alpha, beta and gamma diversity

Community similarity estimate:Jaccard similarity: shared species/[total species X + Y]Jaccard similarity = A/(A+B+C)X, Y - samples

X Y

Koleff et al. 2003 J anim Ecol 72:367

Similarity indices

EstimateS data format, saved as TXT file

Chao1 S + singletons2/(2*doubletons) S = number of species sampled

Simpson's Index (D) measures the probability that two individuals randomly selected from a sample will belong to the same species

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)

SU 2

Present Absent

SU 1Present a b

Absent c d

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)

cba

aS

J

SU 2

Present Absent

SU 1Present a b

Absent c d

cba

aS

2

2BC

Sørenson Coefficient

• like Jaccard, ignores shared absences

Quantitative Version of Sørenson (Bray-Curtis) Similarity

s

iik

s

iij

s

iikij

XX

XX

11

1

,min2kj

jkjk TT

WS

2BC

• Morisita-Horn CmH

– Not influenced by sample size & richness– Highly sensitive to the abundance of common

spp.

– CmH = 2(ani * bni) / (da + db)(aN)(bN)• aN = total # of indiv in site A

• ani = # of individuals in ith species in site A

• da = ani2 / aN2