Linking patterns in phylogeny, traits, abiotic variables and space: a novel approach to linking environmental filtering and plant community assembly

Abstract

Summary 1.We introduce a novel method that analyses environmental filtering of plant species in a geographic and phylogenetic context. By connecting species traits with phylogeny, traits with environment, and environment with geography, this comprehensive approach partitions the ecological and evolutionary processes that influence community assembly. 2. Our analysis extends RLQ ordination, which connects site attributes in matrix R (here environmental variables and spatial positions) with species attributes in matrix Q (here biological traits and phylogenetic positions), through the composition of sites in terms of species presences or abundances (matrix L). This methodology, which explores and identifies environmental filters that organize communities, was developed to answer four questions: which combinations of trait states are filtered by the environment, which lineages are affected by these filters, which environmental variables contribute to the assemblage of local communities and where do these filters act? 3. At La Mafragh in north-eastern Algeria, our approach shows that plant species traits were distributed according to environmental filters associated with a salinity gradient. Traits associated with the salinity gradient were convergent among Juncaceae, Cyperaceae and Amaranthaceae. The observed phylogenetic and trait patterns were related to how species survived the xeric season. Juncaceae and Cyperaceae, being perennials and anemogamous, tolerate the xeric hot season by restricting their range to the humid centre of the study area (where conditions are close to a subtropical climate). Several Amaranthaceae species co-occur with the Juncaceae and Cyperaceae in two areas with the highest salinity. Most dicots were observed at higher elevations (up to 7 m a.s.l.), had hairy structures that can retain water and reflect solar radiation and were mostly annual or biennial, completing their life cycle before the onset of the xeric season. 4. Synthesis. Our methodology describes environmental filters in terms of identified combinations of traits and environmental factors. It allows spatial and phylogenetic signals to be determined by identifying convergent and conserved patterns in the evolution of traits and spatial scales that structured the environment. Our statistical framework is generic and can be readily extended to a wide range of exciting issues, such as host-parasite, plant-pollinator and predatorprey interactions.

CSR analysis of plant functional types in highly diverse tropical grasslands of harsh environments

“…To conduct the RLQ analysis, a correspondence analysis was used for the floristic matrix, while a principal component analysis (PCA) was used for the functional and environmental matrices. In the functional PCA, the species were weighted by their overall relative abundance over both habitats, while in the environmental PCA, the areas were weighted by the relative number of plants observed (Dolédec et al 1996;Dray and Dufour 2007;Pavoine et al 2011). Both analyses were carried out in the R (R Development Core Team 2012) software with the "ade4" package (Chessel et al 2004;Dray and Dufour 2007) and some functions provided by Pavoine et al (2011).…”

Assessing the effects of spatial contingency and environmental filtering on metacommunity phylogenetics

“…While our approach certainly has some analytical and/or heuristical commonalities with previous ones (Ackerly and Cornwell 2007, Leibold et al 2010, Ives and Helmus 2011, Pavoine et al 2011; see Discussion for further details), we present some interesting novel features including the coupling of evolutionary stochastic simulations within a modeling framework, how to consider spatial variation in the analysis of phylogenetic/trait associations and the decomposition of phylogenetic/trait means and variances.…”

“…There are several statistics that have been suggested to measure the degree of phylogenetic structure based on patterns of phylogenetic clustering and eveness (see Kembel 2009 and references therein) and different ways of representing phylogenetic composition (Pillar and Duarte 2010, Pavoine et al 2011, Ricotta and Moretti 2011. However, none of these methods allows decomposing the total variation in metacommunity phylogenetic (and trait for that matter) structure (P L ) using a single unified approach that includes the two separate components of interest (i.e.,X P and s P ).…”

Biodiversity in a Rapidly Changing World: How to Manage and Use Information?

“…New approaches are necessary to analyze the importance of these complex features. Recently, Pavoine et al (2011) suggested a framework based on a mathematical method of ordination to analyze phylogeny, traits, abiotic variables and space in a plant community. Another example can be found in Diniz Filho et al (2009) proposing an integrated framework to study spatial patterns in genetic diversity within local populations, coupling genetic data, SDM and landscape genetics.…”