Advanced analytical approaches in ecological data analysis The world comes in fragments 1

Species occurrences across a fragmented landscape Biogeography Species occurrences across a fragmented landscape Islands Lakes River bed and irrigation systems Mainlands continental distributions habitat islands mountain tops and valleys fragmented landscapes scattered distributed host plants Cities and anthropogenic habitats Routes of species invasion Experimental plots (natural, macro-, meso-cosm experiments)

Galapagos Islands The Darwin finches

The Darwin finches (Sanderson, Am. Scient. 2000) Sanderson JG (2000) Testing ecological patterns. American Scientist 88:332-339 A presence – absence matrix reflects the distribution of species across sites

The distribution of ground beetles across Mazuran lake islands 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.

Multivariate approaches to biodiversity Traits Sites Interdepen-dence matrix X Environmental variable matrix V Variables Variables Why are species abundant or rare? What determines community composition? How does a community function in space and time? Sites Site GPS location matrix D L Traits Species Sites Species trait matrix T Phylogenetic distance matrix P Species abundance matrix M Species Species Species

Species and environmental data in primary plant succession Measured environmental data WordClim, BioClim S A1-2 C2-4 C3-1 D3-2 D3-4 CaCO3 0.27 1.17 0.06 1.04 Sand 82.54 76.71 88.56 79.02 pH 8.16 7.97 8.08 8.18 Plant species trait data from Bioflor and Leda A1-2 C2-4 C3-1 D3-2 D3-4 Longitude 171.38 205.61 227.46 239.65 233.65 Latitude 295.09 275.55 293.74 271.88 GPS longitude and latitude data Species Leaf mass [mg] Leaf size [mm2] Life span Achillea_pannonica 82.33 567.84 5 Agrostis_capillaris 60.97986 1147.934 Agrostis_stolonifera Agrostis_vinealis 1.41 22.75 Ajuga_genevensis 17.99 365.5 Apera_spica-venti 1 Arctium_minus_agg. 2 Observed species abundances S A1-2 C2-4 C3-1 D3-2 D3-4 Achillea_pannonica Agrostis_capillaris 0.1 0.15 Agrostis_stolonifera 0.3 Agrostis_vinealis 0.9 0.2 Ajuga_genevensis Apera_spica-venti 0.4 S Achillea_pannonica Agrostis_capillaris Agrostis_stolonifera_agg. Agrostis_vinealis Ajuga_genevensis Apera_spica_venti 0.0 179.0 117.0 2.5 6.7 Agrostis_stolonifera Phylogenetic data from Genbank or own sequencing

Biogeographic matrices are static descriptions of colonization patterns. 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.

They do not give information on real species interactions Dispersion 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 Dispersion Extinction 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 Abundance matrices contain additional information. Abundance matrices might be based on point or averaged time series data.

Mutual interaction matrices Food webs Host – parasite networks Plant – herbivore networks Pollination networks Predator – prey networks Competition networks Species impact networks Food web example Translation of a food web into a matrix. Ones denote direct links. Typical terrestrial food web Generalist predator Specialist predator

A quantitative food web Interaction strength is expressed by probabilities or by frequencies of interaction A quantitative food web

Interaction matrices Pollination networks Plants Bees Kratochwil A., Beil M., Schwabe A. 2009. Complex structure of pollinator-plant interaction –webs: random, nested, with gradients or modules. Apodologie 40: 634-650. Ollerton, J., S. D. Johnson, L. Cranmer, and S. Kellie. 2003. The pollination ecology of an assemblage of grassland asclepiads in South Africa. Annals of Botany 92: 807-834. Plants From Ollerton et al. 2003 From Kratochwil et al. 2009 Bees

How to present a presence – absence matrix? Unsorted raw data Sorted according to marginal totals Sorted to maximize species turnover Correspondence analysis Reciprocal averaging (seriation)

Spatial or ecological distance Ecological gradients Spatial or ecological distance Sorting of matrix columns according to ecological gradients allows for an assessment of the importance of environmental variables.

Ordinated presence – absence matrix 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 Ordinated presence – absence matrix Spatial distance between species Unexpected occurrences Ecological distance between sites

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. 0.0 179.0 117.0 44.0 122.0 2.5 6.7 Artemisia_campestris_agg. 32.7 Artemisia_vulgaris_agg. Berteroa_incana 127.0 Betula_pendula

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 Leaf mass [mg] Leaf size [mm2] Life span Min releasing height [m] Max releasing height [m] Stem erect % Stem ascending to prostrate % Emergents attached to substrate Terminal velocity m/s Achillea_pannonica 82.33 567.84 5 0.2 0.8 100 1.934717 Agrostis_capillaris 60.97986 1147.934 0.83 50 0.98 Agrostis_stolonifera_agg. 0.1 0.7 25 1.11 Agrostis_vinealis 1.41 22.75 0.4 1.59 Ajuga_genevensis 17.99 365.5 0.07 0.3 75 Apera_spica-venti 1 1.31

Literature Zaplata M. K., Winter S., Fischer A., Kollmann J., Ulrich W. 2013. Species-driven phases and increasing structure in early-successional 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 meta-community analysis. Turnover – A Fortran program for the analysis of species associations. NODF – a Fortran program for nestedness analysis. Past Matrix Excel add in