Roeland Kindt senior ecologist World Agroforestry Centre (ICRAF) R.Kindt@CGIAR.org

Tree Diversity Analysis: Application to sentinel landscape data Introduction to BiodiversityR

How to measure diversity?

• Richness: species number • Diversity: richness and evenness • Sample size effects (hierarchical

structure) • Differences in species composition:

ordination and cluster analysis

Diversity: richness and evenness Less diverse More diverse

richness

evenness

Rényi diversity profiles • One of several methods for

diversity ordering • Considers richness and evenness • Based on proportional abundance

for each species

α

α

α −=

∑=

1

)ln(1

S

iip

H

Rényi diversity profiles

S1 S2

Site A

Site D

S1 S2 S2

Site C

Site B

S3

S1 S2

S3S4

S5

S3

S1

S1

S1

S1 S1

S2

S3 S3

0 0.25 0.5 1 2 4 8 Inf

scale

0.0

0.5

1.0

1.5

Ren

yi d

iver

sity

Community ACommunity BCommunity CCommunity D

Scale parameter changes influence of richness and evenness on diversity measurement

Diversity profile ranks communities according to differences in diversity

B

A = D

C

EVENNESS RICHNESS

DIV

ERSITY

Rényi diversity profiles

S1 S2

Site A

Site D

S1 S2 S2

Site C

Site B

S3

S1 S2

S3S4

S5

S3

S1

S1

S1

S1 S1

S2

S3 S3

0 0.25 0.5 1 2 4 8 Inf

scale

0.0

0.5

1.0

1.5

Ren

yi d

iver

sity

Community ACommunity BCommunity CCommunity D

ln(richness)

Shannon ln(1/Simpson) ln(1/BergerParker)

B

A = D

C

Rényi diversity profiles

0 0.25 0.5 1 2 4 8 Inf

scale

0.8

1.0

1.2

1.4

1.6

1.8

2.0

Ren

yi d

iver

sity

Community ACommunity BCommunity C

1 2 3 4 50

5

10

15

20

25

30

35 33

29

5

28

5

Community A

1 2 3 4 5 60

5

10

15

20

25

30

35

40

45 42

Community B30

810

55

1 2 3 4 5 6 70

5

10

15

20

25

30

35 32

Community C21

12

16

4

96

Partial ordering: one community is richer but with lower evenness than a second community

Rényi diversity profiles

1 2 3 40

5

1010

Community A

6

1

4

1 2 3 4 5 6 7 80

5

1010

Community B

10

66

1

4 4

1

1 2 3 4 5 6 7 80

5

10

15

17

Community C

1 11 11 1 1

1 2 3 40

5

10

15

10

Community D

10 1010

1 2 3 4 5 6 7 80

5

10

15

20

25

30

3535

Community E

1 11 11 1 1

0 0.25 0.5 1 2 4 8 Inf

scale

0.0

0.5

1.0

1.5

2.0

Ren

yi d

iver

sity

Community ACommunity BCommunity CCommunity DCommunity E

0 0.1 0.25 0.5 0.75 1 1.25 1.5 1.75 2 2.5 3 10 100 inf.

alpha

0

1

2

3

4

5

6

H

boundaryfruitfirewoodmedicinetimberconstructionshadesoil fertilitybeveragecharcoalfodderornamentalall

1.0

1.6

2.7

4.5

7.4

12.2

20.1

33.1

54.6

90.0

148.4

244.7

403.4

EXP(

H)

Kindt R, Van Damme P, Simons AJ. 2006. Tree diversity in western Kenya: using profiles to characterise richness and evenness. Biodiversity and Conservation 15: 1253-1270.

0 0.1 0.25 0.5 0.75 1 1.25 1.5 1.75 2 2.5 3 10 100 inf.

alpha

0

1

2

3

4

5H

1.0

1.6

2.7

4.5

7.4

12.2

20.1

33.1

54.6

90.0

148.4

EXP(

H)

spicesfruitfirewoodmedicinestimuliconstructionshadesoil fertilitytoolsgumsfodderdrugsvegetablesall

0 0.1 0.25 0.5 0.75 1 1.25 1.5 1.75 2 2.5 3 10 100 inf.

alpha

0

1

2

3

4

5

6

H

boundaryfruitfirewoodmedicinetimberconstructionshadesoil fertilitybeveragecharcoalfodderornamentalall

1.0

1.6

2.7

4.5

7.4

12.2

20.1

33.1

54.6

90.0

148.4

244.7

403.4

EXP(

H)

0 0.1 0.25 0.5 0.75 1 1.25 1.5 1.75 2 2.5 3 10 100 inf.

alpha

0

1

2

3

4

5

6

H

1.0

1.6

2.7

4.5

7.4

12.2

20.1

33.1

54.6

90.0

148.4

244.7

403.4

EXP(

H)

boundaryfruitfirewoodmedicinetimberconstructionshadesoil fertilityleavescharcoalfodderornamentalstakesall

0 0.1 0.25 0.5 0.75 1 1.25 1.5 1.75 2 2.5 3 10 100 inf.

alpha

0

1

2

3

4

5

6

H

boundaryfruit/nutfirewoodmedicinetimberconstructionshadecashplant supportcharcoalfodderanimal trapsornamentalstool handlesall

1.0

1.6

2.7

4.5

7.4

12.2

20.1

33.1

54.6

90.0

148.4

244.7

403.4

EXP(

H)

Cameroon Mabira

Meru W-Kenya

Rényi evenness profiles

• Based on shape of diversity profiles: when richness is equal then differences in diversity reflect differences in evenness

• Expansion of measurement of evenness of Shannon index

• Transforms evenness defined for Hill diversity series

0ln HHE −= αα

Rényi evenness profiles

1 2 3 40

5

1010

Community A

6

1

4

1 2 3 4 5 6 7 80

5

1010

Community B

10

66

1

4 4

1

1 2 3 4 5 6 7 80

5

10

15

17

Community C

1 11 11 1 1

1 2 3 40

5

10

15

10

Community D

10 1010

1 2 3 4 5 6 7 80

5

10

15

20

25

30

3535

Community E

1 11 11 1 1

0 0.25 0.5 1 2 4 8 Inf

scale

-2.0

-1.5

-1.0

-0.5

0.0

Ren

yi e

venn

ess

Community ACommunity BCommunity CCommunity DCommunity E

0 0.25 0.5 1 2 4 8 Inf

scale

0.0

0.5

1.0

1.5

2.0

Ren

yi d

iver

sity

Community ACommunity BCommunity CCommunity DCommunity E

A = B

1 10 100

Number of farms

1

10

100

Num

ber o

f spe

cies

boundaryfruitfirewoodmedicinetimberconstructionshadesoil fertilitybeveragecharcoalfodderornamentalall

W-Kenya

Species accumulation curves

Kindt R, Van Damme P, Simons AJ. 2006. Patterns of Species Richness at Varying Scales in western Kenya: Planning for Agroecosystem Diversification. Biodiversity and Conservation 15: 3235-3249.

n = 35 n = 35

n = 35

Cameroon Mabira

W-Kenya Meru

Diversity accumulation surfaces

Analysis of differences in species composition

• Diversity only depends on frequencies, not on identities of the species

• Various ecological distance measures for pairwise differences in species composition

• Various ordination and cluster methods to summarize or analyze distances

Kindt R, Van Damme P, Simons AJ, Beeckman H. 2006. Planning tree species diversification in Kenya based on differences in tree species composition between farms. I. Study of Tree Uses. Agroforestry Systems 67: 215-228.

A B

C

Euclidean distance often problematic for species composition

A B C

BiodiversityR A free manual

and software for biodiversity and community ecology analysis

http://cran.r-project.org/web/packages/BiodiversityR/

http://cran.r-project.org/web/packages/vegan/

𝐵𝐵𝐵𝐵𝐵𝐵𝐵𝐵𝐵𝐵.𝐵𝐵𝐴𝐴𝐴𝐴𝐵𝐵 = 𝜋𝜋 𝑟𝑟2

𝐶𝐶𝐴𝐴𝐶𝐶𝐶𝐶𝐶𝐶.𝐵𝐵𝐴𝐴𝐴𝐴𝐵𝐵

= 𝜋𝜋 𝐴𝐴1 +𝐴𝐴2

2

2

All trees, basal area

CA = DD: NO TREES

All trees, crown area

FIREWOOD

Frequencies calculated from basal area

CHARCOAL TIMBER

FODDER SHADE LIFE FENCE

FIREWOOD

Frequencies calculated from crown area

CHARCOAL TIMBER

FODDER SHADE LIFE FENCE

… short commercial break

AUC = 0.8775

Ensemble suitability modelling

∑∑=

mod

modmod )(w

PwPensemble

Ensemble = (weighted) average of different Modeling algorithms such as random forests (RF), Maximum Entropy (MAXENT) or Support Vector Machines (SVM, SVME)

VECEA: A higher resolution map for 7 countries in eastern Africa (Ethiopia, Kenya, Malawi, Rwanda, Uganda, Tanzania and Zambia)

http://www.vegetationmap4africa.org

Application domains: • Climate change modelling • Species selection • Seed source selection • (agro)ecological zonation • Protected area evaluation • Species distribution

mapping

http://www.vegetationmap4africa.org

Seed sources and seed zones http://www.vegetationmap4africa.org

Agroforestry Species Switchboard http://www.worldagroforestry.org/our_products/databases/switchboard