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... Just as different measures of functional diversity capture different aspects of trait variation in communities (Petchey et al. 2009), researchers must consider how the details of a phylogenetic diversity calculation, including the variation in rates of character divergence, impact the answer to the research question. Previous studies have evaluated the performance of different diversity metrics in predicting biodiversity– ecosystem-function relationships, notably Petchey et al. (2004), who demonstrated that FD was a stronger predictor of aboveground biomass production than S or FGR. Notably, Cadotte et al. (2009) assessed PD, several versions of FD, and other diversity metrics as predictors of the biodiversity effect in one of the studies included in this meta-analysis. They found that FD and PD were weakly correlated, but that PD and combinations of PD and other metrics were always superior predictors of ecosystem functioning. This contrasts with our results, but their study differed from the current study because they used a different set of traits, fewer species, and focused on a single biodiversity experiment. These contrasting results highlight the need for a mechanistic understanding of which tr...

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...d the study context. Here we propose a guideline, following our results, concerning two issues: the influence of biodiversity on ecosystem functioning which is mainly investigated with controlled communities in experiments and the elucidation of processes governing biodiversity patterns at local, regional and continental scales. For the former issue, the crucial question is no longer whether species richness influences ecosystem processes such as productivity or resilience but which facet of biodiversity has the strongest influence on ecosystem processes and in which environmental conditions (Cadotte et al. 2009). For instance, Villeger et al. (2010) demonstrated how habitat degradation differentially impacts each of the three components of functional diversity 2010 The Authors. Journal compilation 2010 British Ecological Society, Functional Ecology, 24, 867–876 874 M. A. Mouchet et al. with a loss of functional divergence while species richness increases. To test the effect of a set of biodiversity facets on ecosystem functioning ecologists usually rely on regression methods (e.g. Cadotte et al. 2009). However multicollinearity among explanatory variables is known to generate spurious results wi...

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...variate trait di!erences within a community, generically referred to as ‘functional diversity’. Functional diversity (FD) is measured in a multitude of ways (see Appendix S1 Supporting Information). Technically, it represents the diversity of traits but is taken to represent the diversity of species’ niches or functions (Petchey, Hector & Gaston 2004; McGill et al. 2006; Petchey &Gaston 2006; Villeger, Mason & Mouillot 2008). As a representation of niches or functions, FD has been used to understand how species richness or diversity relates to ecosystem function (Petchey, Hector &Gaston 2004; Cadotte et al. 2009; Flynn et al. 2011) and how diversity responds to environmental stress or disturbance (Norberg et al. 2001; Suding et al. 2008). The power of FD is that unlike traditional measures of species richness or diversity, it presupposes a mechanistic link between diversity and the ecological phenomena in question. This intuitive link is attractive, and FD is appearing in the literature with increasing frequency (Fig. 1). To advocate for the use of FD measures assumes mechanistic links with niche and functional aspects of species diversity. Here, we review the literature to determine how FD di!ers fr...

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... called ‘Ecophylogenetics’ (Cadotte, 2009). Appealing as this new research program might be, it suffers from its ever-increasing richness while each ecological sub-discipline integrates the phylogenetic information from very different perspectives (Webb et al., 2002; Chave, Chust Fig. 1. Results of a search in the ISI Web of Science using the key words ‘Phylogenetics OR phylogeny’ AND ‘community ecology’. The black column indicates the year of publication of the influential paper by Webb et al. (2002) on phylogenetic community ecology. & Thebaud, 2007; Emerson & Gillespie, 2008; Avise, 2009; Cadotte et al., 2009; Cavender-Bares et al., 2009; Leibold, Economo & Peres-Neto, 2010; Matthews et al., 2011). There are also still a number of critical assumptions that have been only partly discussed in the recent literature (Cavender-Bares et al., 2009; Mayfield & Levine, 2010; Pavoine & Bonsall, 2011). It is now important to assess how the use of phylogenetic information can help ecology to be a more integrative science. Herein we provide a critical evaluation of the various ways that phylogeny has been used to gain insight in community and ecosystems ecology. We focus on community assembly rules, the struct...

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...ations. In 2001–2008 and in 2010, for each plot, biomass from one strip was sorted by individual species and weighed. Data from this experiment (e120) are available through the Cedar Creek Long Term Ecological Research (LTER) website.6 Monthly snowfall, precipitation, and maximum and minimum temperature for the duration of the experiment were obtained from Minnesota Climatology Working Group of the State Climatology Office for the Cedar weather station (latitude, 45.31288; longitude, 93.28832; available online).7 Phylogeny construction We used the phylogeny produced in a previous publication (Cadotte et al. 2009). Briefly, GenBank (Benson et al. 2005) was queried for four gene sequences (matK, rbcl, ITS1, and 5.8s) for 31 species used in two experiments at Cedar Creek, and two representatives of early-diverging angiosperm lineages as outgroup species, Amborella trichopoda and Magnolia grandiflora. Fourteen species were represented by at least one gene in GenBank. For the remaining species, we used gene sequences from a congeneric relative not included in these experiments. All sequences were aligned using MUSCLE (Edgar 2004). A maximum-likelihood phylogeny was estimated using the PHYML algorithm with ...

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...e topology [56]. However, we observed that areas with a high proportion of species experiencing global declines correspond to areas of unique evolutionary history, suggesting that whilst extinction risk might not demonstrate strong phylogenetic structure, the loss of currently threatened species might still have a disproportionate impact on mangrove phylogenetic diversity regionally. The loss of phylogenetic diversity may be of concern because it captures the functional and ecological diversity represented along the branches of the tree-of-life, and has been linked to ecosystem function (e.g. [57,58]) and stability [57]. As the tree-of-life is pruned through extinctions we would then lose Figure 2. Geographical distribution of phylogenetic diversity within mangrove ecosystem for (A) mean terminal branch lengths, and (B) mean evolutionary distinctiveness across the same six biogeographical regions depicted in Figure 1. doi:10.1371/journal.pone.0066686.g002 Loss of Evolutionarily Unique Mangrove Species PLOS ONE |www.plosone.org 4 June 2013 |Volume 8 |Issue 6 |e66686 these services associated with the functional and ecological diversity represented along its branches. We evaluated various p...

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...008; Isbell, Polley & Wilsey 2009; Wittebolle et al. 2009); species’ and functional group interactions (Kirwan et al. 2007, 2009) and phylogenetic and functional trait diversity (Petchey et al. 2004; =-=Cadotte et al. 2009-=-; Connolly et al. 2011; Flynn et al. 2011). In addition to describing BEF relationships in detail, linking coefficients of BEF models to underlying mechanisms and process should be one of the aims of ...

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...ime or whether specific clades are dominant at a particular point in succession, an important factor in restoration efforts. Recently, phylogenetic approaches have been used to interpret the forces structuring communities following disturbance (CavenderBares et al. 2004; Letcher 2010; Verdu, Gomez-Aparicio & Valiente-Banuet 2012; Whitfeld et al. 2012; Mo et al. 2013; Purschke et al. 2013). Phylogenetics can provide information on species ecological similarity and function in the environment (Faith 1992), therefore having potential to aid restoration and habitat management (Webb et al. 2002; Cadotte et al. 2009; Cavender-Bares et al. 2009). Metrics of phylogenetic diversity (PD) were first developed to capture underlying diversity in phenotypic features (Faith 1992) and later to describe evolutionary relationships among species in a community (Webb et al. 2002). Phylogenetic community structure is typically quantified with respect to either clustering (community members are more closely related than expected by chance) or overdispersion (community members are more evenly distributed throughout the phylogeny than expected by chance). Assuming that traits are evolutionarily conserved and that phylogen...