Understanding how habitat structures species assemblages in a community is one of the main goals of community ecology. To relate community patterns to particular factors defining habitat conditions, ecologists often use canonical ordinations such as canonical redundancy analysis (RDA). It is a common practice to use dissimilarity coefficients to perform canonical ordinations through distance-based RDA (db-RDA) or transformation-based RDA (tb-RDA). Dissimilarity coefficients are measures of resemblance where the information about species communities is condensed into a symmetric square matrix of dissimilarities among sites. In this paper we compared 16 of the most commonly used dissimilarity coefficients to evaluate if the species abundance distribution (SAD) of a community can be used to select an appropriate coefficient. Of these, 11 are designed to be used primarily with abundance data although they can also be used with presence-absence data, whereas five can only be applied to presence-absence data. Using simulations, we compared the explained variance of RDAs differing only by their coefficients to evaluate how the abundance patterns of communities influence coefficient choice. We found that coefficients are largely equivalent, independently of the community SAD. In light of these findings, we propose the consensus RDA method, a new canonical ordination procedure that performs a consensus of RDAs across several coefficients. This new method focuses on the common relations found by independent RDAs differing only by their dissimilarity coefficients; this ensures the absence of a coefficient-related bias when interpreting the canonical ordination result. Also, because in our simulations the presence-absence data were directly derived from the abundance data, we were able to evaluate if the information in presence-absence data was equivalent to that in abundance data. We found that although some information was lost by converting abundance data into presence-absence, both data formats may be complementary. When applying consensus RDA to abundance and presence-absence data independently, a more complete understanding and interpretation of the ecological patterns is obtained. An ecological example illustrating consensus RDA and the conclusions of our simulations is presented, using Carabidae data collected at the Ecosystem Management Emulating Natural Disturbances (EMEND) project in northwestern Alberta, Canada.
Standardized abundances of carabid species caught in every sites
This table contains the standardized abundances of each carabid species captured in each of the 192 sites. Carabids were collected using three pitfall traps in each site and beetle abundances were divided by the number of days each trap was active to remove the effect of trap disturbance. The code for each species is available in table E1 of the associated publication (Blanchet et al. Consensus RDA across dissimilarity coefficients for canonical ordination of community composition data, Ecological Monographs) as well as the detailed description of sampling protocol. More details about sampling and analysis of this data may be found in: Blanchet FG, JAC Bergeron, JR Spence, F He, 2013. Landscape effects of disturbance, habitat heterogeneity and spatial autocorrelation for a ground beetle (Carabidae) assemblage in mature boreal forest. Ecography, 36(5): 636-647; Bergeron JAC, GF Blanchet, JR Spence, WJA Volney, 2012. Ecosystem classification and inventory maps as surrogates for ground-beetle assemblages in boreal forest, Journal of Plant Ecology, 5(1): 97-108; and Bergeron JAC, JR Spence, WJA Volney, 2011. Landscape patterns of species-level association between ground-beetles (Coleoptera: Carabidae) and overstory trees in boreal forests of western Canada, Zookeys, 147: 577-600. This data and the analysis procedures associated with this paper are also available in the R package ordiconsensus (https://r-forge.r-project.org/R/?group_id=68).
beetles.txt
Relative basal area for each tree species recorded in every sites
This table contains the relative basal area for each tree species sampled at each site. In each of the 192 sites, the diameter at breast height (dbh) and species of the 25 trees closest to the centre of the plot and over 5 cm bdh were recorded. Total basal area was calculated for each species in each site and divided by the total basal area of all species in each site to produce the relative basal area. Refer to the associated publication (Blanchet et al. Consensus RDA across dissimilarity coefficients for canonical ordination of community composition data, Ecological Monograph) for more details on sampling protocol and table E2 of this same publication for the abbreviation of the tree species. More details about sampling and analysis of this data may be found in: Blanchet FG, JAC Bergeron, JR Spence, F He, 2013. Landscape effects of disturbance, habitat heterogeneity and spatial autocorrelation for a ground beetle (Carabidae) assemblage in mature boreal forest. Ecography, 36(5): 636-647; Bergeron JAC, GF Blanchet, JR Spence, WJA Volney, 2012. Ecosystem classification and inventory maps as surrogates for ground-beetle assemblages in boreal forest, Journal of Plant Ecology, 5(1): 97-108; and Bergeron JAC, JR Spence, WJA Volney, 2011. Landscape patterns of species-level association between ground-beetles (Coleoptera: Carabidae) and overstory trees in boreal forests of western Canada, Zookeys, 147: 577-600. This data and the analysis procedures associated with this paper are also available in the R package ordiconsensus (https://r-forge.r-project.org/R/?group_id=68).
beetle_expl.txt