Local and regional species richness

y = 0.54x - 1.2R2 = 0.56

0

5

10

15

20

0 10 20 30

Species of regional pool

Spe

cies

of l

ocal

poo

l

• Species richness on bracken is higher at richer sites

• At species poorer sites there seem to be many empty niches

• Local habitats are not saturated with species

Bracken occurs whole over the worldSpecies numbers of phytophages on bracken differIs this difference an effect of competitive exlusion or do empty niches exist?

John H.Lawton

The common brushtail Possum Trichosurus vulpecula is at its

introduced sites often free of natural parasites. There are empty niches

Cynipid gall wasps in Norh America (Cornell 1985) Lacutrine fish in North America (Gaston 2000)

Relationship between local species richness and the regional species pool size for 14 vegetation types in Estonia (Pärtel et al. 1996)

Dry grasslands Moist grasslands

y = 0.49x + 0.51

R2 = 0.73

0

5

10

15

20

25

0 10 20 30 40

Number of species regionally

Num

ber o

f spe

cies

lo

cally

y = 0.36x + 0.41R2 = 0.83

00.5

11.5

22.5

33.5

4

0 2 4 6 8 10

Regional number of species

Loca

l num

ber o

f spe

cies

y = 0.27x - 6.9R2 = 0.93

0

20

40

60

80

100

120

0 100 200 300 400

Number of species regionally

Num

ber o

f spe

cies

loca

lly

y = 16Ln(x) - 49R2 = 0.86

0

20

40

60

80

100

120

0 100 200 300 400

Number of species regionally

Num

ber o

f spe

cies

loca

lly

Local and regional species richness

Four possible relations between local and regional species numbers

05

10152025303540

0 10 20 30 40

Regional number of species

Loca

l num

ber o

f spe

cies

Abundance – range size relationshipsFreshwater gyrinid beetles in temporary pools (Svensson 1992) Regional distribution of 21 Bombus species in northern Spain (Obeso 1992)

Local abundance in relation to regional distribution of soil mites (Karppinen 1958)

D: Local abundance in relation to regional distribution of bumblebees in Poland (Anasiewicz 1971)

Diptera colonising dead snails in a beech forest (Ulrich 2001) Parasitic Hymenoptera of these Diptera (Ulrich 2001)

y = 0.95e2.58x

R2 = 0.83

0

2

4

6

8

0 0.2 0.4 0.6 0.8

Fraction of pools occupied

Mea

n ab

unda

nce

y = 0.067e6.97x

R2 = 0.5472

0%5%

10%15%20%25%30%

0 0.05 0.1 0.15 0.2

Fraction of sites occupied

Per

cent

age

of to

tal

Abu

ndan

ce

y = 3.06e0.11x

R2 = 0.90

0

200

400

600

800

1000

0 10 20 30 40 50

Number of sites occupied

log

rel.

abun

danc

e

y = 1.0e0.33x

R2 = 0.82

0

20

40

60

80

0 2 4 6 8 10

Number of sites occupied

log

rel.

abun

danc

ey = 1.35e3.674x

R2 = 0.59

0

20

40

60

80

0% 20% 40% 60% 80% 100%

Percentage of site occupied

Mea

n de

nsity

per

oc

cupi

ed p

atch

y = 1.57e2.97x

R2 = 0.78

02468

10

0% 20% 40% 60%

Percentage of site occupied

Mea

n de

nsity

per

oc

cupi

ed p

atch

Patch occupancy models

204

3

2

1 8

5

121713

1

4

5

44

4

• A matrix of cells refers to a metacommunity scale

• Each cell represents one local community• Cells might have different sizes • Individuals of different species of the meta-

community are now placed at random or according to certain predefined rules into the cells

• A random placement is called a passive sampling model

• The spatial distribution patterns are then compared to observed ones.

y = 6e 1.61x

R2 = 0.60

0

10

20

30

40

0.01 0.1 1

Fraction of cells occupied

Mea

n de

nsity

per

oc

cupi

ed c

ell

Individuals of 100 species were placed at random into a 100x100 matrix.

Species had different individual numbers

Matrix cells had different capacities

• The model produces an abundance - range size relationship

• This relationship follows an exponential model as observed in reality

• Abundance - range size relationships are most parsimonous explained from passive sampling in heterogeneous environments

Core and satellite species

Insects on small mangrove islands (Simberloff 1976)

Plant species in Russian Karelia (Linkola 1916)

In an assemblage of species distributed over many sites we can often differentiate a group of core species, which occur in most or even all of the

sites, and a group of satellite species, which occur only in a few or even only in one site.

020406080

100

1 2 3 4 5 6 7 8 9

Number of sites occupied

Num

ber o

f spe

cies

0

20

40

60

80

0 1 2 3 4 5 6 7 8 9 10 11 12

Number of sites occupied

Num

ber o

f spe

cies

Core and satellite species

05

1015202530

1 2 4 8 17S

peci

es

Sites occupied

Ground beetles species on Mazuran lake island

Satellite (infrequent, tourist) species Core (frequent, permanent) species

• Random pattern of temporal or spatial occurrence

• High dispersal ability• Log-series rank abundance

distributions• Weak species interactions• Forming random assemblages

• Non-random pattern of temporal or spatial occurrence

• Lower dispersal ability• Log-normal rank abundance

distributions• Importance of species interactions• Forming true ecological

communities

Importance of ecological interactions

Nestedness

Species gil ful lip sos kor guc 3pog hel dab wron mil wil 2pog ter wros swi 1pog Occurren-ces

Carabus granulatus 110 12 113 59 154 25 52 11 11 18 0 77 11 11 19 1 0 15Pterostichus melanarius 345 187 704 428 1199 60 13 169 17 26 394 29 36 4 0 13 0 15Pterostichus strennus (Panzer) 30 13 24 14 28 5 3 6 47 3 22 7 5 0 5 4 0 15Oxypselaphus obscurus (Herbst) 166 27 7 278 96 80 27 0 96 85 48 25 0 13 37 0 1 14Pterostichus diligens (Sturm) 18 1 1 5 4 11 0 1 12 5 0 4 1 1 0 3 0 13Synuchus vivalis (Illiger) 24 19 5 1 4 1 2 10 51 0 2 0 12 0 0 14 0 12Patrobus atrorufus (Stroem) 348 11 37 35 11 9 22 0 81 2 0 0 6 0 7 2 0 12Carabus nemoralis Muller 8 14 5 12 10 6 1 16 5 2 0 0 0 0 6 0 0 11Pterostichus antracinus 21 0 2 0 2 1 0 11 0 0 274 46 1 1 0 0 11 10Pterostichus minor (Gyllenhal) 48 0 0 21 0 7 1 0 0 2 5 28 0 2 1 0 5 10Notiophilus palustris (Duftshmid) 1 2 7 1 4 0 2 2 0 1 0 0 0 0 0 0 0 8Stomis pumicatus (Panzer) 1 1 2 50 14 0 1 2 5 0 0 0 0 0 0 0 0 8Clivina fossor (Linnaeus) 2 0 0 0 0 0 3 0 2 1 1 1 1 0 0 0 0 7Epaphius secalis (Paykull) 15 127 8 8 0 4 0 0 3 0 0 0 0 4 0 0 0 7Leistus rufomarginatus (Duftshmid) 77 10 3 4 0 0 2 3 0 0 0 0 0 0 0 0 0 6

Notiophilus biguttatus (Fabricius) 1 2 2 0 0 1 0 1 0 0 0 0 0 0 0 0 0 5Calathus melanocephalus (Linnaeus) 0 1 0 0 1 0 0 0 0 0 2 1 0 0 0 0 0 4

Carabus hortensis Linnaeus 52 75 0 0 0 109 0 0 0 0 0 0 0 0 0 0 0 3Calathus mollis (Marsham) 0 9 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 2Calathus micropterus (Duftschmid) 0 20 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2

Dischirius globosus (Herbst) 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 1Leistus ferrugineus (Linnaeus) 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1Calathus fuscipes (Goeze) 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 1Carabus cancelatus Illiger 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1Occurrences 18 17 16 13 13 13 12 11 11 10 10 9 8 7 6 6 3 24

Ground beetles species with limited dispersal ability on Mazuran lake island

Core and satellite species

Species gil ful lip sos kor guc 3pog hel dab wron mil wil 2pog ter wros swi 1pog Occurren-ces

Carabus granulatus 110 12 113 59 154 25 52 11 11 18 0 77 11 11 19 1 0 15Pterostichus melanarius 345 187 704 428 1199 60 13 169 17 26 394 29 36 4 0 13 0 15Pterostichus strennus (Panzer) 30 13 24 14 28 5 3 6 47 3 22 7 5 0 5 4 0 15Oxypselaphus obscurus (Herbst) 166 27 7 278 96 80 27 0 96 85 48 25 0 13 37 0 1 14Pterostichus diligens (Sturm) 18 1 1 5 4 11 0 1 12 5 0 4 1 1 0 3 0 13Synuchus vivalis (Illiger) 24 19 5 1 4 1 2 10 51 0 2 0 12 0 0 14 0 12Patrobus atrorufus (Stroem) 348 11 37 35 11 9 22 0 81 2 0 0 6 0 7 2 0 12Carabus nemoralis Muller 8 14 5 12 10 6 1 16 5 2 0 0 0 0 6 0 0 11Pterostichus antracinus 21 0 2 0 2 1 0 11 0 0 274 46 1 1 0 0 11 10Pterostichus minor (Gyllenhal) 48 0 0 21 0 7 1 0 0 2 5 28 0 2 1 0 5 10Notiophilus palustris (Duftshmid) 1 2 7 1 4 0 2 2 0 1 0 0 0 0 0 0 0 8Stomis pumicatus (Panzer) 1 1 2 50 14 0 1 2 5 0 0 0 0 0 0 0 0 8Clivina fossor (Linnaeus) 2 0 0 0 0 0 3 0 2 1 1 1 1 0 0 0 0 7Epaphius secalis (Paykull) 15 127 8 8 0 4 0 0 3 0 0 0 0 4 0 0 0 7Leistus rufomarginatus (Duftshmid) 77 10 3 4 0 0 2 3 0 0 0 0 0 0 0 0 0 6Notiophilus biguttatus (Fabricius) 1 2 2 0 0 1 0 1 0 0 0 0 0 0 0 0 0 5Calathus melanocephalus (Linnaeus) 0 1 0 0 1 0 0 0 0 0 2 1 0 0 0 0 0 4Carabus hortensis Linnaeus 52 75 0 0 0 109 0 0 0 0 0 0 0 0 0 0 0 3Calathus mollis (Marsham) 0 9 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 2Calathus micropterus (Duftschmid) 0 20 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2Dischirius globosus (Herbst) 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 1Leistus ferrugineus (Linnaeus) 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1Calathus fuscipes (Goeze) 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 1Carabus cancelatus Illiger 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1Occurrences 18 17 16 13 13 13 12 11 11 10 10 9 8 7 6 6 3 24

The matrix sorted according to row and column totals (numbers of occurrences) containes two triangles. One contain species and site with very high matrix fill (numbers

of occurrences, the second contains species and site with very low matrix fill.

We call such a matrix nested.

A SitesSpecies A C F D G E B H Sum

1 1 1 1 1 1 1 1 1 8

2 1 1 1 1 1 1 1 0 7

3 1 1 1 1 1 1 0 0 6

4 1 1 1 1 0 0 0 0 4

5 1 1 1 0 0 0 0 0 3

6 1 1 1 0 0 0 0 0 3

7 1 1 1 0 0 0 0 0 3

8 1 1 0 0 0 0 0 0 2

9 1 1 0 0 0 0 0 0 2

10 1 1 0 0 0 0 0 0 2

11 1 0 0 0 0 0 0 0 1

12 1 0 0 0 0 0 0 0 1Sum 12 10 7 4 3 3 2 1 42

A perfectly nested matrix

A perfectly nested (ordered) matrix can be divided into a completely filled

and an empty part.

A SitesSpecies A C F D G E B H Sum

1 1 1 1 0 1 1 1 1 7

2 1 1 1 1 1 1 1 0 7

3 0 1 1 1 1 1 0 0 5

4 1 1 1 1 0 0 0 0 4

5 1 1 1 0 0 0 0 0 3

6 1 1 1 0 0 1 0 0 4

7 1 1 1 0 0 0 0 0 3

8 1 1 0 0 0 0 0 0 2

9 1 1 0 0 0 0 0 0 2

10 1 1 0 0 0 0 0 0 2

11 1 0 0 0 0 1 0 0 2

12 1 0 0 0 0 0 0 0 1Sum 11 10 7 3 3 5 2 1 42

Imperfectly nested matrices have holes (unexpected absences) and outliers (unexpected occurrences).

The number of holes and outlier with respect to the perfectly ordered state is a measure of the degree of nestedness.

The discrepancy metric counts the number of holes that have to be filled by outliers of the same row or column to form a perfectly nested matrix.

Species gil ful lip sos kor guc 3pog hel dab wron mil wil 2pog ter wros swi 1pog Occurren-ces

Carabus granulatus 110 12 113 59 154 25 52 11 11 18 0 77 11 11 19 1 0 15Pterostichus melanarius 345 187 704 428 1199 60 13 169 17 26 394 29 36 4 0 13 0 15Pterostichus strennus (Panzer) 30 13 24 14 28 5 3 6 47 3 22 7 5 0 5 4 0 15Oxypselaphus obscurus (Herbst) 166 27 7 278 96 80 27 0 96 85 48 25 0 13 37 0 1 14Pterostichus diligens (Sturm) 18 1 1 5 4 11 0 1 12 5 0 4 1 1 0 3 0 13Synuchus vivalis (Illiger) 24 19 5 1 4 1 2 10 51 0 2 0 12 0 0 14 0 12Patrobus atrorufus (Stroem) 348 11 37 35 11 9 22 0 81 2 0 0 6 0 7 2 0 12Carabus nemoralis Muller 8 14 5 12 10 6 1 16 5 2 0 0 0 0 6 0 0 11Pterostichus antracinus 21 0 2 0 2 1 0 11 0 0 274 46 1 1 0 0 11 10Pterostichus minor (Gyllenhal) 48 0 0 21 0 7 1 0 0 2 5 28 0 2 1 0 5 10Notiophilus palustris (Duftshmid) 1 2 7 1 4 0 2 2 0 1 0 0 0 0 0 0 0 8Stomis pumicatus (Panzer) 1 1 2 50 14 0 1 2 5 0 0 0 0 0 0 0 0 8Clivina fossor (Linnaeus) 2 0 0 0 0 0 3 0 2 1 1 1 1 0 0 0 0 7Epaphius secalis (Paykull) 15 127 8 8 0 4 0 0 3 0 0 0 0 4 0 0 0 7Leistus rufomarginatus (Duftshmid) 77 10 3 4 0 0 2 3 0 0 0 0 0 0 0 0 0 6Notiophilus biguttatus (Fabricius) 1 2 2 0 0 1 0 1 0 0 0 0 0 0 0 0 0 5Calathus melanocephalus (Linnaeus) 0 1 0 0 1 0 0 0 0 0 2 1 0 0 0 0 0 4Carabus hortensis Linnaeus 52 75 0 0 0 109 0 0 0 0 0 0 0 0 0 0 0 3Calathus mollis (Marsham) 0 9 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 2Calathus micropterus (Duftschmid) 0 20 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2Dischirius globosus (Herbst) 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 1Leistus ferrugineus (Linnaeus) 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1Calathus fuscipes (Goeze) 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 1Carabus cancelatus Illiger 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1Occurrences 18 17 16 13 13 13 12 11 11 10 10 9 8 7 6 6 3 24

Nestedness analysis surves to find idiosyncratic species that means species that deviate from the general trend of community organization.

.Often these species do not belong to the guild of species under study while having different habitat requirements.

Variable 3pog sos 2pog dab wros gil ter 1pog wil mil swi kor hel lip wronOrganic matter content 8.40 7.98 7.48 7.27 6.79 6.17 4.28 4.26 4.03 3.15 3.13 2.73 1.29 1.23 0.91Temperature 0.82 3.75 1.20 2.14 1.92 2.19 1.23 0.33 1.66 0.89 2.60 2.24 3.50 2.06 1.43

Species 3pog sos 2pog dab wros gil ter 1pog wil mil swi kor hel lip wron Occurrences

Carabus granulatus 52 59 11 11 19 110 11 0 77 0 1 154 11 113 18 13Pterostichus melanarius 13 428 36 17 0 345 4 0 29 394 13 1199 169 704 26 13Pterostichus strennus (Panzer) 3 14 5 47 5 30 0 0 7 22 4 28 6 24 3 13Oxypselaphus obscurus (Herbst) 27 278 0 96 37 166 13 1 25 48 0 96 0 7 85 12Pterostichus diligens (Sturm) 0 5 1 12 0 18 1 0 4 0 3 4 1 1 5 11Synuchus vivalis (Illiger) 2 1 12 51 0 24 0 0 0 2 14 4 10 5 0 10Patrobus atrorufus (Stroem) 22 35 6 81 7 348 0 0 0 0 2 11 0 37 2 10Pterostichus antracinus 0 0 1 0 0 21 1 11 46 274 0 2 11 2 0 9Pterostichus minor (Gyllenhal) 1 21 0 0 1 48 2 5 28 5 0 0 0 0 2 9Carabus nemoralis Muller 1 12 0 5 6 8 0 0 0 0 0 10 16 5 2 9Notiophilus palustris (Duftshmid) 2 1 0 0 0 1 0 0 0 0 0 4 2 7 1 7Clivina fossor (Linnaeus) 3 0 1 2 0 2 0 0 1 1 0 0 0 0 1 7Stomis pumicatus (Panzer) 1 50 0 5 0 1 0 0 0 0 0 14 2 2 0 7Leistus rufomarginatus (Duftshmid) 2 4 0 0 0 77 0 0 0 0 0 0 3 3 0 5Epaphius secalis (Paykull) 0 8 0 3 0 15 4 0 0 0 0 0 0 8 0 5Notiophilus biguttatus (Fabricius) 0 0 0 0 0 1 0 0 0 0 0 0 1 2 0 3

Calathus melanocephalus (Linnaeus) 0 0 0 0 0 0 0 0 1 2 0 1 0 0 0 3Calathus mollis (Marsham) 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1Dischirius globosus (Herbst) 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 1Leistus ferrugineus (Linnaeus) 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1Carabus hortensis Linnaeus 0 0 0 0 0 52 0 0 0 0 0 0 0 0 0 1Calathus micropterus (Duftschmid) 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1Calathus fuscipes (Goeze) 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 1Carabus cancelatus Illiger 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1

Analysis of ecological gradients

Nestedness analysis helps to identify species that run counter to

ecological gradients

Nestedness analysis is particulalry an analysis of ecological gradients

A SitesSpecies A C F D G E B H Sum1 1 1 1 1 1 1 1 1 82 1 1 0 1 1 1 0 0 53 1 0 1 0 1 0 1 1 54 1 0 1 1 1 1 0 0 55 1 1 1 0 0 0 1 0 46 1 1 1 0 0 1 0 0 47 0 1 0 1 0 0 0 0 28 0 1 1 0 0 0 0 0 29 1 1 0 0 0 0 0 0 210 1 0 0 0 1 0 0 0 211 0 0 0 1 0 0 0 1 212 1 0 0 0 0 0 0 0 1Sum 9 7 6 5 5 4 3 3 42

Statistical inference using null models

Species A C F D G E B H Sum1 1 1 1 1 1 1 1 1 82 1 1 0 1 1 1 0 0 53 1 0 1 0 1 0 1 1 54 1 0 1 1 1 1 0 0 55 1 1 1 0 0 0 1 0 46 1 1 1 0 0 1 0 0 47 0 1 0 1 0 0 0 0 28 0 1 1 0 0 0 0 0 29 1 1 0 0 0 0 0 0 210 1 0 0 0 1 0 0 0 211 0 0 0 1 0 0 0 1 212 1 0 0 0 0 0 0 0 1Sum 9 7 6 5 5 4 3 3 43

We have to infer how many discrepancies are expected just by chance.

0 1 1 01 0 0 1

Checkerboards

We randomize the matrix switching

checkerboards. This retains row and column

totals and therefore basic matrix properties.

0

0.05

0.1

0.15

0.2

0.25

1 3 5 7 9 11 13 15 17 19 21

Freq

uency

Discrepancy

Observed discrepancy D = 11

Nested Antinested

Lower 5% CL

Upper 5% CL

Observed

1. Use 10*sites*species checkerboard swaps per matrix to randomize.2. Calculate discrepancy.3. Repeat steps 1 and 2 1000 times to get the null distribtuion.4. Compare the observed discepancy with the expected one.

Both matrices are not significantly nested.There are not more idiosyncratic sites and

species than expected just by chance.

Low dispersal Carabidae do not colonize lake island according to

organic matter content (soil fertility).Our first eysight impression was wrong.

Always ask whether an observed pattern or process might exist just by chance.

Today’s reading

Local and regional species richness: http://www.springerlink.com/content/ugm5380764049730/

Nestedness and null models: www.uvm.edu/~ngotelli/manuscriptpdfs/UlrichConsumersGuide.pdf

Community assembly: www.msstate.edu/courses/etl5/Community%20Assembly1.ppt