Transcript Slajd 1

Advanced analytical approaches in
ecological data analysis
The world comes in fragments
Biogeography
Species occurrences across a
fragmented landscape
1.
2.
3.
4.
Islands
Lakes
River bed and irrigation systems
Mainlands
continental distributions
habitat islands
mountain tops and valleys
fragmented landscapes
scattered distributed host plants
5. Cities and anthropogenic habitats
6. Routes of species invasion
7. Experimental plots (natural, macro-,
meso-cosm experiments)
Galapagos Islands
The Darwin finches
The Darwin finches (Sanderson, Am. Scient. 2000)
Species
Seymour
Baltra
Isabella
Fernandina
Santiago
Rabida
Pinzon
Santa Cruz
Sante Fe
San
Cristobal
Espanola
Floreana
Genovesa
Marchena
Pinta
Darwin
Wolf
Islands
Geospiza magnirostris
0
0
1
1
1
1
1
1
1
1
0
1
1
1
1
1
1
Geospiza fortis
1
1
1
1
1
1
1
1
1
1
0
1
0
1
1
0
0
Geospiza fulignosa
1
1
1
1
1
1
1
1
1
1
1
1
0
1
1
0
0
Geospiza difficilis
0
0
1
1
1
0
0
1
0
1
0
1
1
0
1
1
1
Geospiza scandens
1
1
1
0
1
1
1
1
1
1
0
1
0
1
1
0
0
Geospiza conirostris
0
0
0
0
0
0
0
0
0
0
1
0
1
0
0
0
0
Camarhynchus psittacula
0
0
1
1
1
1
1
1
1
0
0
1
0
1
1
0
0
Camarhynchus pauper
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
Camarhynchus parvulus
0
0
1
1
1
1
1
1
1
1
0
1
0
0
1
0
0
Platyspiza crassirostris
0
0
1
1
1
1
1
1
1
1
0
1
0
1
1
0
0
Cactospiza pallida
0
0
1
1
1
0
1
1
0
1
0
0
0
0
0
0
0
Cactospiza heliobates
0
0
1
1
0
0
0
0
0
0
0
0
0
0
0
0
0
Cerrthidea olivacea
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
A presence – absence matrix reflects
the distribution of species across sites
The distribution of ground beetles across Mazuran lake islands
Species/Sites
Pterostichus nigrita (Paykull)
Platynus assimilis (Paykull)
Amara brunea (Gyllenhal)
Agonum lugens (Duftshmid)
Loricera pilicornis (Fabricius)
Pterostichus vernalis (Panzer)
Amara plebeja (Gyllenhal)
Badister unipustulatus Bonelli
Lasoitrechus discus (Fabricius)
Poecilus cupreus (Linnaeus)
Amara aulica (Panzer)
Anisodatylus binotatus (Fabricius)
Bembidion articulatum (Panzer)
Clivina collaris (Herbst)
Panagaeus cruxmajor (Linnaeus)
Poecilus versicolor (Sturm)
Pterostichus gracilis Dejean)
Stenolophus mixtus
Pseudoophonus rufipes (De Geer)
Harpalus latus (Linnaeus)
Agonum duftshmidi Shmidt
Harpalus solitaris Dejean
Colums totals
wros wron wil ter swi sos mil
0
1 1 1 0
1 1
0
0 1 0 0
1 0
1
1 0 0 1
1 0
1
1 1 1 0
0 0
0
0 1 0 0
0 1
1
1 1 1 0
1 1
0
0 0 0 1
1 0
0
0 0 0 1
1 0
0
0 0 1 0
0 1
0
0 0 0 0
1 0
0
0 0 0 0
0 0
0
0 0 0 0
0 1
0
0 0 0 0
0 1
0
0 0 0 0
0 1
0
0 0 0 0
0 0
0
0 0 0 0
0 0
0
0 0 0 0
0 0
0
0 0 1 0
0 0
0
0 1 0 0
1 1
0
0 0 0 0
1 0
0
0 1 0 0
0 0
0
0 0 0 0
0 0
3
4
7
5
3
9
lip kor hel guc
1 0 0
1
1 1 1
1
1 0 1
1
0 0 0
0
0 0 0
0
0 0 0
0
1 0 0
0
1 0 0
0
0 0 0
0
0 1 0
0
0 0 0
0
0 0 0
0
0 0 0
0
0 0 0
0
1 0 0
0
1 0 0
0
0 0 0
0
0 0 0
0
1 1 1
1
1 1 0
0
0 0 0
0
0 0 0
0
8 9
4
3
gil
1
1
0
1
1
0
1
1
0
0
0
0
0
0
0
0
1
0
1
1
0
1
ful dab 3pog 2pog 1pog Row totals
1
1
1
1
1
13
1
1
1
1
0
11
1
1
0
0
0
9
0
1
0
0
1
7
1
1
0
1
0
6
0
0
0
0
0
6
0
1
0
0
0
5
0
0
0
0
0
4
0
0
0
0
0
2
0
0
0
0
0
2
0
0
1
0
0
1
0
0
0
0
0
1
0
0
0
0
0
1
0
0
0
0
0
1
0
0
0
0
0
1
0
0
0
0
0
1
0
0
0
0
0
1
0
0
0
0
0
1
1
1
1
1
1
13
1
0
1
1
0
7
0
0
1
0
1
3
1
0
0
0
0
2
4 10 7
7
6
5
4
In presence – absence matrices
zeros denote species absence, ones denote species presences.
Absences might be caused either by real absences of species or by
incomplete detection.
98
Multivariate approaches to biodiversity
Variables
Sites
Why are species abundant or rare?
What determines community composition?
How does a community function in space and time?
Species
trait matrix
T
Species
Species
Species
Traits
Phylogenetic
distance matrix P
Environmental variable
matrix V
Sites
L
Interdependence
matrix X
Site GPS location matrix D
Sites
Species
Variables
Traits
Species abundance matrix
M
Species and
environmental data
in primary plant
succession
Measured
environmental data
WordClim, BioClim
Plant species trait data from
Bioflor and Leda
Leaf mass
[mg]
Achillea_pannonica
82.33
Agrostis_capillaris
60.97986
Agrostis_stolonifera 60.97986
Agrostis_vinealis
1.41
Ajuga_genevensis
17.99
Apera_spica-venti
60.97986
Arctium_minus_agg. 60.97986
Species
S
Achillea_pannonica
Agrostis_capillaris
Agrostis_stolonifera
Agrostis_vinealis
Ajuga_genevensis
Apera_spica_venti
Leaf size
[mm2]
567.84
1147.934
1147.934
22.75
365.5
1147.934
1147.934
S
CaCO3
Sand
pH
A1-2
Longitude 171.38
Latitude
295.09
Life
span
5
5
5
5
5
1
2
A1-2
0.27
82.54
8.16
C2-4
1.17
76.71
7.97
C2-4
205.61
275.55
C3-1
0.06
88.56
8.08
C3-1
227.46
293.74
D3-2
1.04
79.02
8.18
D3-2
239.65
271.88
D3-4
1.04
79.02
8.18
D3-4
233.65
271.88
GPS longitude and latitude data
Observed species abundances
S
Achillea_pannonica
Agrostis_capillaris
Agrostis_stolonifera
Agrostis_vinealis
Ajuga_genevensis
Apera_spica-venti
Agrosti
Agrosti Ajuga_ Apera_
Achillea_p Agrostis_c s_stolo
s_vine geneve spica_
annonica apillaris nifera_
alis
nsis venti
agg.
0.0
179.0
179.0 179.0 117.0 179.0
179.0
0.0
2.5
2.5 179.0 6.7
179.0
2.5
0.0
2.5 179.0 6.7
179.0
2.5
2.5
0.0 179.0 6.7
117.0
179.0
179.0 179.0 0.0 179.0
179.0
6.7
6.7
6.7 179.0 0.0
A1-2
0
0.1
0
0
0
0
C2-4
0
0
0
0.9
0
0
C3-1 D3-2 D3-4
0
0
0
0.15
0
0
0
0
0.3
0
0.2
0
0
0
0
0.4
0
0
Phylogenetic data
from Genbank or
own sequencing
Biogeographic matrices are static descriptions of colonization patterns.
Species/Sites
Pterostichus nigrita (Paykull)
Platynus assimilis (Paykull)
Amara brunea (Gyllenhal)
Agonum lugens (Duftshmid)
Loricera pilicornis (Fabricius)
Pterostichus vernalis (Panzer)
Amara plebeja (Gyllenhal)
Badister unipustulatus Bonelli
Lasoitrechus discus (Fabricius)
Poecilus cupreus (Linnaeus)
Amara aulica (Panzer)
Anisodatylus binotatus (Fabricius)
Bembidion articulatum (Panzer)
Clivina collaris (Herbst)
Panagaeus cruxmajor (Linnaeus)
Poecilus versicolor (Sturm)
Pterostichus gracilis Dejean)
Stenolophus mixtus
Pseudoophonus rufipes (De Geer)
Harpalus latus (Linnaeus)
Agonum duftshmidi Shmidt
Harpalus solitaris Dejean
wros wron wil ter swi sos mil
0
1 1 1 0
1 1
0
0 1 0 0
1 0
1
1 0 0 1
1 0
1
1 1 1 0
0 0
0
0 1 0 0
0 1
1
1 1 1 0
1 1
0
0 0 0 1
1 0
0
0 0 0 1
1 0
0
0 0 1 0
0 1
0
0 0 0 0
1 0
0
0 0 0 0
0 0
0
0 0 0 0
0 1
0
0 0 0 0
0 1
0
0 0 0 0
0 1
0
0 0 0 0
0 0
0
0 0 0 0
0 0
0
0 0 0 0
0 0
0
0 0 1 0
0 0
0
0 1 0 0
1 1
0
0 0 0 0
1 0
0
0 1 0 0
0 0
0
0 0 0 0
0 0
lip kor hel guc
1 0 0
1
1 1 1
1
1 0 1
1
0 0 0
0
0 0 0
0
0 0 0
0
1 0 0
0
1 0 0
0
0 0 0
0
0 1 0
0
0 0 0
0
0 0 0
0
0 0 0
0
0 0 0
0
1 0 0
0
1 0 0
0
0 0 0
0
0 0 0
0
1 1 1
1
1 1 0
0
0 0 0
0
0 0 0
0
gil
1
1
0
1
1
0
1
1
0
0
0
0
0
0
0
0
1
0
1
1
0
1
ful dab 3pog 2pog 1pog
1
1
1
1
1
1
1
1
1
0
1
1
0
0
0
0
1
0
0
1
1
1
0
1
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
1
1
1
1
1
0
1
1
0
0
0
1
0
1
1
0
0
0
0
Colonization and extinction are permanent processes.
In reality presence – absence pattern change whole the time.
It makes therefore a difference if we use temporal point data to construct our matrices or
a time series.
Time series data contain much more entries but might be ecologically unrealistic.
Species/Sites
Pterostichus nigrita (Paykull)
Platynus assimilis (Paykull)
Amara brunea (Gyllenhal)
Agonum lugens (Duftshmid)
Loricera pilicornis (Fabricius)
Pterostichus vernalis (Panzer)
Amara plebeja (Gyllenhal)
Badister unipustulatus Bonelli
Lasoitrechus discus (Fabricius)
Poecilus cupreus (Linnaeus)
Amara aulica (Panzer)
Anisodatylus binotatus (Fabricius)
Bembidion articulatum (Panzer)
Clivina collaris (Herbst)
Panagaeus cruxmajor (Linnaeus)
Poecilus versicolor (Sturm)
Pterostichus gracilis Dejean)
Stenolophus mixtus
Pseudoophonus rufipes (De Geer)
Harpalus latus (Linnaeus)
Agonum duftshmidi Shmidt
Harpalus solitaris Dejean
Colums totals
wros wron wil ter swi sos mil
0
1 1 1 0
1 1
0
0 1 0 0
1 0
1
1 0 0 1
1 0
1
1 1 1 0
0 0
0
0 1 0 0
0 1
1
1 1 1 0
1 1
0
0 0 0 1
1 0
0
0 0 0 1
1 0
0
0 0 1 0
0 1
0
0 0 0 0
1 0
0
0 0 0 0
0 0
0
0 0 0 0
0 1
0
0 0 0 0
0 1
0
0 0 0 0
0 1
0
0 0 0 0
0 0
0
0 0 0 0
0 0
0
0 0 0 0
0 0
0
0 0 1 0
0 0
0
0 1 0 0
1 1
0
0 0 0 0
1 0
0
0 1 0 0
0 0
0
0 0 0 0
0 0
3
4 7 5 3
9 8
lip kor hel guc gil
1 0 0
1 1
1 1 1
1 1
1 0 1
1 0
0 0 0
0 1
0 0 0
0 1
0 0 0
0 0
1 0 0
0 1
1 0 0
0 1
0 0 0
0 0
0 1 0
0 0
0 0 0
0 0
0 0 0
0 0
0 0 0
0 0
0 0 0
0 0
1 0 0
0 0
1 0 0
0 0
0 0 0
0 1
0 0 0
0 0
1 1 1
1 1
1 1 0
0 1
0 0 0
0 0
0 0 0
0 1
9 4 3
4 10
ful dab 3pog 2pog 1pog Row totals
1
1
1
1
1
13
1
1
1
1
0
11
1
1
0
0
0
9
0
1
0
0
1
7
1
1
0
1
0
6
0
0
0
0
0
6
0
1
0
0
0
5
0
0
0
0
0
4
0
0
0
0
0
2
0
0
0
0
0
2
0
0
1
0
0
1
0
0
0
0
0
1
0
0
0
0
0
1
0
0
0
0
0
1
0
0
0
0
0
1
0
0
0
0
0
1
0
0
0
0
0
1
0
0
0
0
0
1
1
1
1
1
1
13
1
0
1
1
0
7
0
0
1
0
1
3
1
0
0
0
0
2
7
7
6
5
4
98
Species/Sites
Pterostichus nigrita (Paykull)
Platynus assimilis (Paykull)
Amara brunea (Gyllenhal)
Agonum lugens (Duftshmid)
Loricera pilicornis (Fabricius)
Pterostichus vernalis (Panzer)
Amara plebeja (Gyllenhal)
Badister unipustulatus Bonelli
Lasoitrechus discus (Fabricius)
Poecilus cupreus (Linnaeus)
Amara aulica (Panzer)
Anisodatylus binotatus (Fabricius)
Bembidion articulatum (Panzer)
Clivina collaris (Herbst)
Panagaeus cruxmajor (Linnaeus)
Poecilus versicolor (Sturm)
Pterostichus gracilis Dejean)
Stenolophus mixtus
Pseudoophonus rufipes (De Geer)
Harpalus latus (Linnaeus)
Agonum duftshmidi Shmidt
Harpalus solitaris Dejean
Colums totals
wros wron wil ter swi sos mil
0
1 1 1 0
1 1
0
0 1 0 0
1 0
1
1 0 0 1
1 0
1
1 1 1 0
0 0
0
0 1 0 0
0 1
1
1 1 1 0
1 1
1
0 1 0 1
1 0
1
1 1 0 1
1 0
0
1 1 1 0
0 1
1
1 1 1 1
1 0
1
1 1 0 1
0 0
1
0 1 1 1
0 1
1
1 1 1 0
0 1
1
1 0 0 1
0 1
0
1 1 1 1
0 0
1
1 1 1 1
0 0
1
1 1 1 1
0 0
1
1 0 1 0
0 0
1
1 1 0 1
1 1
1
1 0 0 1
1 0
0
0 1 0 1
1 1
0
0 0 0 1
1 1
15
16 17 11 14 11 10
lip kor hel guc gil
1 0 0
1 1
1 1 1
1 1
1 0 1
1 0
0 0 0
0 1
0 1 1
1 1
0 1 1
1 0
1 1 1
1 1
1 1 1
1 1
0 1 1
1 0
0 1 1
1 0
0 1 1
1 0
0 1 1
1 0
0 1 1
1 0
0 1 1
1 0
1 0 1
1 0
1 0 1
1 0
0 0 1
1 1
0 0 1
1 0
1 1 1
1 1
1 1 0
0 1
1 1 1
1 1
1 0 1
0 1
11 14 19 19 11
ful dab 3pog 2pog 1pog Row totals
1
1
1
1
1
13
1
1
1
1
0
11
1
1
0
0
0
9
0
1
1
0
1
8
1
1
1
1
0
10
0
0
1
1
0
11
1
1
1
1
1
14
1
0
1
1
1
14
1
0
1
1
1
11
1
0
0
0
1
11
1
0
1
0
1
10
1
1
0
1
0
11
1
1
1
1
1
13
1
1
1
1
1
12
1
1
1
1
1
12
1
1
1
1
1
13
1
1
1
1
1
13
1
1
1
1
1
10
1
1
1
1
1
16
1
0
1
1
0
10
1
0
1
0
1
12
1
0
0
0
0
7
20 14
18
16
15
251
Dispersion
Extinction
Time
axis
Time series matrices
have too many entries
and do not reflect real
ecological patterns.
They do not give
information on real
species interactions
For a proper
assessment of
ecological patterns
we need point
data.
The comparison of
point and time series
matrices gives
information about
dispersion rates.
The distribution of ground beetles across Mazuran lake islands
Species/Sites
Pterostichus nigrita (Paykull)
Platynus assimilis (Paykull)
Amara brunea (Gyllenhal)
Agonum lugens (Duftshmid)
Loricera pilicornis (Fabricius)
Pterostichus vernalis (Panzer)
Amara plebeja (Gyllenhal)
Badister unipustulatus Bonelli
Lasoitrechus discus (Fabricius)
Poecilus cupreus (Linnaeus)
Amara aulica (Panzer)
Anisodatylus binotatus (Fabricius)
Bembidion articulatum (Panzer)
Clivina collaris (Herbst)
Panagaeus cruxmajor (Linnaeus)
Poecilus versicolor (Sturm)
Pterostichus gracilis Dejean)
Stenolophus mixtus
Pseudoophonus rufipes (De Geer)
Harpalus latus (Linnaeus)
Agonum duftshmidi Shmidt
Harpalus solitaris Dejean
wros wron wil ter
0
2 61 53
0
0
1 0
1
1
0 0
1
1
2 2
0
0
1 0
1
1 21 2
0
0
0 0
0
0
0 0
0
0
0 1
0
0
0 0
0
0
0 0
0
0
0 0
0
0
0 0
0
0
0 0
0
0
0 0
0
0
0 0
0
0
0 0
0
0
0 1
0
0 13 0
0
0
0 0
0
0
1 0
0
0
0 0
swi sos mil lip kor
0 18 39 2
0
0
9
0 117 76
19 40 0
1
0
0
0
0
0
0
0
0
3
0
0
0
1
7
0
0
1
2
0
4
0
4
1
0
3
0
0
0
1
0
0
0
2
0
0
1
0
0
0
0
0
0
0
2
0
0
0
0
1
0
0
0
0
2
0
0
0
0
0
1
0
0
0
0
2
0
0
0
0
0
0
0
0
0
0
0
0
5
3
2
90
0
3
0
2
1
0
0
0
0
0
0
0
0
0
0
hel guc gil
0
1 58
9
2 39
3
4
0
0
0
3
0
0
5
0
0
0
0
0
5
0
0
3
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
3
1
5
0
0 20
0
0
0
0
0
1
ful dab 3pog 2pog 1pog
1
5
2
2
30
48 4
25
7
0
10 5
0
0
0
0
2
0
0
1
5
1
0
1
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
2
1
6
3
3
0
7
11
0
0
0
2
0
1
1
0
0
0
0
Abundance matrices contain additional information. Abundance matrices might be
based on point or averaged time series data.
Mutual interaction matrices
1.
2.
3.
4.
5.
6.
7.
Food web example
Parasites
Large
herbivores
Hyperparasitoids
Large
carnivores
Large
omnivores
Larger
carnivores
Parasitoids
Small
carnivores
Small
herbivores
Plant
producers
Larger
decomposer
Medium
omnivores
Bacteriophages
Bacterial
producers
Typical terrestrial food web
Smaller
decomposer
Food webs
Host – parasite networks
Plant – herbivore networks
Pollination networks
Predator – prey networks
Competition networks
Species impact networks
Translation of a food web into a matrix.
Ones denote direct links.
Prey/Predators
A
B
C
D
E
F
G
H
1
1
1
1
1
1
1
1
1
2
1
0
1
0
0
0
1
0
3
1
1
1
0
0
0
1
0
4
1
0
0
0
0
0
0
1
5
0
1
0
0
0
0
0
0
Generalist predator
Specialist predator
Predaceous birds and snakes
Parasitoid spider wasps
Songbirds
Predaceous
insects
Scorpions
Lizards
Spiders
Rodensts
Herbivorous
insects
Scavenging
insects
Detritovorous
insects
Seabird
ectoparasites
Land plands, seed detritus
Fish and bird carcasses
Seabird guano
Algal detritus
Seabirds
Marince planctonic food web
Marine macroalgae
Lower/higher level
A quantitative
food web
A
B
C
D
E
F
G
H
1
0.8
0.6
0.9
0.7
0.3
0
0.7
0.2
2
3
4
5
0.2 0.3 0.1 0.5
0.6 0.6 0 0.7
0 0.9 0
0
0
0 0.4 0
0.7 0 0.1 0
0.6 0
0
0
0
0
0
0
0
0 0.8 0
Interaction
strength is
expressed by
probabilities or by
frequencies of
interaction
Interaction matrices
Pollination networks
Plants
From Kratochwil et
al. 2009
Bees
Plant
Asclepias AsclepiasAspidonepsis
Miraglossum
Miraglossum
PachycarpusSisyranthusXysmalobium
Xysmalobium
Pollinators
cucullata
woodii diploglossa verticillare pilosum natalensistrichostomus gerrardii involucratum
Hemipepsis
0
0
0
18
9
20
2
41
1
Pompilidae sp. 2
0
0
0
0
0
0
0
1
0
Tiphia
0
1
0
0
0
0
0
0
0
Arge
0
0
0
0
0
0
1
0
0
Apis
0
0
1
0
0
0
1
3
0
Halictidae sp. 1
0
0
2
0
0
0
0
0
0
Halictidae sp. 2
1
0
0
0
0
0
0
0
0
Other wasps
0
1
1
0
0
0
0
1
3
Other bees
0
0
0
0
0
0
0
1
1
Other solitary bees
0
1
2
0
0
9
0
0
0
Atrichelaphinis
0
15
0
1
0
0
35
15
6
Cyrtothyrea
0
8
0
1
0
0
42
6
0
Lycidae sp.
0
0
0
0
0
0
0
2
0
Cantharidae sp.
0
0
0
0
0
0
0
2
0
Elateridae sp.
0
0
0
0
0
0
0
0
4
Chrysomelidae sp. 1
0
0
0
0
0
1
0
0
1
Chrysomelidae sp. 2
0
0
0
0
0
0
1
1
1
Scarabaeinae sp. 1
0
0
0
0
0
0
0
3
0
Scarabaeinae sp. 2
0
0
0
0
0
0
0
3
1
Scarabaeinae sp. 3
0
0
0
0
0
0
0
1
0
Curculionidae sp. 1
0
0
0
0
0
0
10
4
1
Curculionidae sp. 2
0
2
0
0
0
0
0
0
0
Coleoptera sp. 3
0
0
0
0
0
0
0
2
0
Coleoptera sp. 8
0
0
0
0
0
0
1
0
0
Other Coleoptera
0
0
0
0
0
0
0
4
4
Aspilocoryphus
1
0
0
1
0
4
1
139
1
Lygaeidae sp. 2
0
0
0
1
0
1
0
8
2
Coreidae sp.
0
0
0
0
0
0
0
1
0
Spilostethus
0
0
0
0
0
1
0
0
0
Homoecerus
0
0
0
0
0
1
0
0
0
Pentatomoidea sp.
0
0
0
0
0
0
0
1
0
Other Heteroptera
0
0
0
0
0
0
0
1
0
Calliphoridae genus 1
0
0
0
0
0
0
0
1
0
Calliphoridae genus 2
0
0
0
0
0
0
2
6
0
Calliphoridae genus 3
0
0
0
0
0
0
0
1
0
Sarcophaga sp.
0
1
0
6
0
11
0
53
1
Musca
0
0
2
0
0
0
0
3
0
Muscidae genus 2
0
0
1
0
0
0
0
0
0
Empididae sp. 1
2
0
0
0
0
1
0
0
0
Empididae sp. 2
0
0
0
0
0
0
0
1
0
Chloropidae
0
0
1
0
0
0
0
1
0
Microphthalma
0
0
0
0
0
1
0
0
0
Microphthalma
0
0
0
0
0
0
0
1
0
Tachinidae subfamily Goniinae
0
0
0
0
0
0
0
1
0
Tachinidae genus 2
0
0
0
0
0
0
0
1
0
Actea
0
0
0
0
0
0
0
1
0
Sepsidae sp. 1
0
0
0
0
0
0
0
3
1
Sepsidae sp. 2
0
0
0
0
0
0
0
0
1
Sepsidae sp. 3
0
0
0
1
0
0
0
0
0
Dacus
0
0
0
0
0
1
0
0
0
Bibionidae
0
0
0
0
0
0
0
1
0
Diptera sp. 3
0
0
0
0
0
0
1
0
0
Diptera sp. 22
0
0
0
0
0
1
0
0
0
Other Diptera
0
1
0
1
0
1
0
15
0
Unidentified butterfly
0
0
0
0
0
0
1
0
0
Unidentified micromoth
2
0
0
0
0
0
0
0
0
From Ollerton et
al. 2003
How to present a presence – absence matrix?
Unsorted raw data
S
1
2
3
4
5
6
7
8
9
10
1
1
1
0
0
0
0
0
0
0
1
2
0
0
1
1
0
0
0
1
1
0
3
0
0
1
1
0
1
0
0
0
0
4
1
0
1
0
1
0
0
1
1
0
5
0
0
0
0
0
1
0
1
1
0
6
0
1
1
0
0
0
0
1
0
0
7
0
1
0
0
0
1
0
0
1
1
8
1
0
0
0
0
0
1
1
0
0
S
3
4
3
5
3
3
4
3
Sorted according to marginal totals
S
3
3
4
2
1
3
1
5
4
2
S
8
3
9
1
2
6
4
10
5
7
4
1
1
1
1
0
0
0
0
1
0
2
1
1
1
0
0
0
1
0
0
0
7
0
0
1
0
1
1
0
1
0
0
1
0
0
0
1
1
0
0
1
0
0
3
0
1
0
0
0
1
1
0
0
0
5
1
0
1
0
0
1
0
0
0
0
6
1
1
0
0
1
0
0
0
0
0
8
1
0
0
1
0
0
0
0
0
1
S
5
4
4
3
3
3
3
3
S
5
4
4
3
3
3
2
2
1
1
Sorted to maximize species turnover
S
7
1
10
2
5
8
9
3
6
4
8
1
1
0
0
0
1
0
0
0
0
1
0
1
1
1
0
0
0
0
0
0
7
0
0
1
1
0
0
1
0
1
0
4
0
1
0
0
1
1
1
1
0
0
6
0
0
0
1
0
1
0
1
0
0
5
0
0
0
0
0
1
1
0
1
0
2
0
0
0
0
0
1
1
1
0
1
3
0
0
0
0
0
0
0
1
1
1
S
3
3
4
5
3
3
4
3
S
1
3
2
3
1
5
4
4
3
2
Correspondence
analysis
Reciprocal averaging
(seriation)
Ecological gradients
Species
ful
guc 3pog sos 2pog
dabwros gil ter 1pogwil mil swi kor hel lip
wron Sum
Pterostichus nigrita (Paykull)
1
1
2 18 2 5
0 58 53 30 61 39 0 0 0
2
2
Platynus assimilis (Paykull)
48
2
25
9 7 4
0 39 0
0 1
0 0 76 9 117
0
Amara brunea (Gyllenhal)
10
4
0 40 0 5
1 0 0
0 0
0 19 0 3
1
1
Agonum lugens (Duftshmid)
0
0
0
0 0 2
1 3 2
1 2
0 0 0 0
0
1
Loricera pilicornis (Fabricius)
5
0
0
0 1 1
0 5 0
0 1
3 0 0 0
0
0
Pterostichus vernalis (Panzer)
0
0
0
1 0 0
1 0 2
0 21
7 0 0 0
0
1
Amara plebeja (Gyllenhal)
0
0
0
2 0 1
0 5 0
0 0
0 1 0 0
4
0
Badister unipustulatus Bonelli
0
0
0
1 0 0
0 3 0
0 0
0 4 0 0
3
0
Lasoitrechus discus (Fabricius)
0
0
0
0 0 0
0 0 1
0 0
1 0 0 0
0
0
Poecilus cupreus (Linnaeus)
0
0
0
2 0 0
0 0 0
0 0
0 0 1 0
0
0
Sum
4
3
2
7 3 6
3 6 4
2 5
4 3 2 2
5
4
Area
Isolation
Habitat heterogeneity
10
10 2.1 20 1 7 0.2 10 0
0 1 0.2 2.1 2 1 4.19 0.15
0.01 0.01 0.1 0.1 0 0 0.1 0 0 0.1 0 0.1 0.1 0 0 0.09 0.09
10
10 8.4 8 7 7 6.8 6 4 4.3 4 3.1 3.1 3 1 1.23 0.91
Spatial or ecological distance
Sorting of matrix columns according to ecological gradients allows for an
assessment of the importance of environmental variables.
13
11
9
7
6
6
5
4
2
2
Basic patterns
Species turnover
Species turnover or beta diversity is a special case of species segregation
where there is an ordering change in species composition across the sites.
Raw matrix
Species
ful
guc 3pog sos 2pog
dabwros gil ter 1pogwil mil swi kor hel lip
wron
Pterostichus nigrita (Paykull)
1
1
2 18 2 5
0 58 53 30 61 39 0 0 0
2
2
Platynus assimilis (Paykull)
48
2
25
9 7 4
0 39 0
0 1
0 0 76 9 117
0
Amara brunea (Gyllenhal)
10
4
0 40 0 5
1 0 0
0 0
0 19 0 3
1
1
Agonum lugens (Duftshmid)
0
0
0
0 0 2
1 3 2
1 2
0 0 0 0
0
1
Loricera pilicornis (Fabricius)
5
0
0
0 1 1
0 5 0
0 1
3 0 0 0
0
0
Pterostichus vernalis (Panzer)
0
0
0
1 0 0
1 0 2
0 21
7 0 0 0
0
1
Amara plebeja (Gyllenhal)
0
0
0
2 0 1
0 5 0
0 0
0 1 0 0
4
0
Badister unipustulatus Bonelli
0
0
0
1 0 0
0 3 0
0 0
0 4 0 0
3
0
Lasoitrechus discus (Fabricius)
0
0
0
0 0 0
0 0 1
0 0
1 0 0 0
0
0
Poecilus cupreus (Linnaeus)
0
0
0
2 0 0
0 0 0
0 0
0 0 1 0
0
0
Ordinated presence – absence matrix
.
kor swi lip
sos hel guc3poggil ful dab 2pogwil wronwros1pogmil
Poecilus_cupreus_(Linnaeus)
1
0
0
1 0 0
0 0 0
0 0
0 0 0 0
Badister_unipustulatus_Bonelli
0
1
1
1 0 0
0 1 0
0 0
0 0 0 0
Amara_plebeja_(Gyllenhal)
0
1
1
1 0 0
0 1 0
1 0
0 0 0 0
Platynus_assimilis_(Paykull)
1
0
1
1 1 1
1 1 1
1 1
1 0 0 0
Amara_brunea_(Gyllenhal)
0
1
1
1 1 1
0 0 1
1 0
0 1 1 0
Pterostichus_nigrita_(Paykull)
0
0
1
1 0 1
1 1 1
1 1
1 1 0 1
Loricera_pilicornis__(Fabricius)
0
0
0
0 0 0
0 1 1
1 1
1 0 0 0
Pterostichus_vernalis_(Panzer)
0
0
0
1 0 0
0 0 0
0 0
1 1 1 0
Agonum_lugens_(Duftshmid)
0
0
0
0 0 0
0 1 0
1 0
1 1 1 1
Lasoitrechus_discus_(Fabricius)
0
0
0
0 0 0
0 0 0
0 0
0 0 0 0
Unexpected occurrences
ter
0
0
0
0
0
1
1
1
0
1
Ecological distance
between sites
0
0
0
0
0
1
0
1
1
1
Spatial
distance
between
species
The data of our lecture
Small scale spatial variability in phylogenetic signals during early plant succession
depends on soil properties
Werner Ulrich, Marcin Piwczyński, Markus Klemens Zaplata, Susanne Winter, Wolfgang
Schaaf, Anton Fischer
Phylogenetic distance matrix according to the classification contained in APG III (Angiosperm Phylogeny
Group 2009)
S
Achillea_pannonica
Agrostis_capillaris
Agrostis_stolonifera_agg.
Agrostis_vinealis
Ajuga_genevensis
Apera_spica_venti
Arctium_minus_agg.
Arenaria_serpyllifolia_agg.
Artemisia_campestris_agg.
Artemisia_vulgaris_agg.
Berteroa_incana
Betula_pendula
Arenaria
Achillea Agrostis Agrostis
Ajuga_g Apera_s Arctium_ _serpyllif
_pannon _capillari _stolonif Agrostis enevensi pica_ven minus_a olia_agg
ica
s
era_agg. _vinealis s
ti
gg.
.
0.0
179.0
179.0
179.0
117.0
179.0
44.0
122.0
179.0
0.0
2.5
2.5
179.0
6.7
179.0
179.0
179.0
2.5
0.0
2.5
179.0
6.7
179.0
179.0
179.0
2.5
2.5
0.0
179.0
6.7
179.0
179.0
117.0
179.0
179.0
179.0
0.0
179.0
117.0
122.0
179.0
6.7
6.7
6.7
179.0
0.0
179.0
179.0
44.0
179.0
179.0
179.0
117.0
179.0
0.0
122.0
122.0
179.0
179.0
179.0
122.0
179.0
122.0
0.0
32.7
179.0
179.0
179.0
117.0
179.0
44.0
122.0
32.7
179.0
179.0
179.0
117.0
179.0
44.0
122.0
127.0
179.0
179.0
179.0
127.0
179.0
127.0
127.0
127.0
179.0
179.0
179.0
127.0
179.0
127.0
127.0
Small scale spatial variability in phylogenetic signals during early plant
succession depends on soil properties
Werner Ulrich, Marcin Piwczyński, Markus Klemens Zaplata, Susanne
Winter, Wolfgang Schaaf, Anton Fischer
Database containing a total of 33 plant functional, genetic and morphological
traits complied from the Leda (Kleyer et al. 2008) and BioFlor (Klotz et al.
2002) trait bases.
Species
Achillea_pannonica
Agrostis_capillaris
Agrostis_stolonifera_agg.
Agrostis_vinealis
Ajuga_genevensis
Apera_spica-venti
Leaf
mass
[mg]
Leaf
size
[mm2]
82.33 567.84
60.9798 1147.93
6
4
60.9798 1147.93
6
4
1.41 22.75
17.99 365.5
60.9798 1147.93
6
4
Life
span
Emerge
Stem
nts
Min
Max
ascendi attache Termina
releasin releasin
ng to
d to
l
g height g height Stem
prostrat substrat velocity
[m]
[m]
erect % e %
e
m/s
1.93471
5
0.2
0.8
100
0
0
7
5
0.2
0.83
50
50
0
5
5
0.1
0.2
0.7
0.4
50
50
25
50
25
0
5
0.07
0.3
75
25
1
0.3
1
100
0
0.98
1.11
1.59
1.93471
0
7
0
1.31
Literature
• Zaplata M. K., Winter S., Fischer A.,
Kollmann J., Ulrich W. 2013. Species-driven
phases and increasing structure in earlysuccessional plant communities. Am. Nat.
181: E17-E27.
• Ulrich W., Gotelli N. J. 2013. Pattern
Detection in Null Model Analysis. Oikos 122:
2-18.
• Gotelli N. J., Ulrich W. 2012. Statistical
challenges in null model analysis. Oikos 121:
171-180.
• Ulrich W., Gotelli N. J. 2012. A null model
algorithm for presence – absence matrices
based on proportional resampling. Ecol.
Modell. 244: 20-27.
• Ulrich W., Piwczyński, M., Maestre F. T.,
Gotelli N. J. 2012. Null model tests for niche
conservatism, phylogenetic assortment and
habitat filtering. Meth. Ecol. Evol. 3: 930-939.
• Ulrich W., Almeida-Neto M., Gotelli N. G.
2009. A consumer’s guide to nestedness
analysis. Oikos 118: 3-17.
Software
• Niche – A Fortran program for metacommunity analysis.
• Turnover – A Fortran program for the
analysis of species associations.
• NODF – a Fortran program for
nestedness analysis.
• Past
• Matrix Excel add in