A distance-based framework for measuring functional diversity from multiple traits
TL;DR: A highly flexible distance-based framework to measure different facets of FD in multidimensional trait space from any distance or dissimilarity measure, any number of traits, and from different trait types (i.e., quantitative, semi-quantitative, and qualitative).
Abstract: A new framework for measuring functional diversity (FD) from multiple traits has recently been proposed. This framework was mostly limited to quantitative traits without missing values and to situations in which there are more species than traits, although the authors had suggested a way to extend their framework to other trait types. The main purpose of this note is to further develop this suggestion. We describe a highly flexible distance-based framework to measure different facets of FD in multidimensional trait space from any distance or dissimilarity measure, any number of traits, and from different trait types (i.e., quantitative, semi-quantitative, and qualitative). This new approach allows for missing trait values and the weighting of individual traits. We also present a new multidimensional FD index, called functional dispersion (FDis), which is closely related to Rao's quadratic entropy. FDis is the multivariate analogue of the weighted mean absolute deviation (MAD), in which the weights are species relative abundances. For unweighted presence-absence data, FDis can be used for a formal statistical test of differences in FD. We provide the "FD" R language package to easily implement our distance-based FD framework.
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TL;DR: FD measures can explain variation in ecosystem function even when richness does not, and should be incorporated into conservation and restoration decision-making, especially for those efforts attempting to reconstruct or preserve healthy, functioning ecosystems.
Abstract: Summary 1. The goal of conservation and restoration activities is to maintain biological diversity and the ecosystem services that this diversity provides. These activities traditionally focus on the measures of species diversity that include only information on the presence and abundance of species. Yet how diversity influences ecosystem function depends on the traits and niches filled by species. 2. Biological diversity can be quantified in ways that account for functional and phenotypic differences. A number of such measures of functional diversity (FD) have been created, quantifying the distribution of traits in a community or the relative magnitude of species similarities and differences. We review FD measures and why they are intuitively useful for understanding ecological patterns and are important for management. 3. In order for FD to be meaningful and worth measuring, it must be correlated with ecosystem function, and it should provide information above and beyond what species richness or diversity can explain. We review these two propositions, examining whether the strength of the correlation between FD and species richness varies across differing environmental gradients and whether FD offers greater explanatory power of ecosystem function than species richness. 4. Previous research shows that the relationship between FD and richness is complex and context dependent. Different functional traits can show individual responses to different gradients, meaning that important changes in diversity can occur with minimal change in richness. Further, FD can explain variation in ecosystem function even when richness does not. 5. Synthesis and applications. FD measures those aspects of diversity that potentially affect community assembly and function. Given this explanatory power, FD should be incorporated into conservation and restoration decision-making, especially for those efforts attempting to reconstruct or preserve healthy, functioning ecosystems.
1,593 citations
Cites background from "A distance-based framework for meas..."
...Consensus is also lacking as to how FD should be calculated (e.g. Podani & Schmera 2006; Petchey & Gaston 2007; Villeger, Mason & Mouillot 2008; Poos, Walker & Jackson 2009; Laliberte & Legendre 2010; Mouchet et al. 2010)....
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TL;DR: Empirical evidence is synthesized and a theoretical framework, based on species positions in a functional space, as a tool to reveal the complex nature of change in disturbed ecosystems is presented.
Abstract: Understanding the processes shaping biological communities under multiple disturbances is a core challenge in ecology and conservation science. Traditionally, ecologists have explored linkages between the severity and type of disturbance and the taxonomic structure of communities. Recent advances in the application of species traits, to assess the functional structure of communities, have provided an alternative approach that responds rapidly and consistently across taxa and ecosystems to multiple disturbances. Importantly, trait-based metrics may provide advanced warning of disturbance to ecosystems because they do not need species loss to be reactive. Here, we synthesize empirical evidence and present a theoretical framework, based on species positions in a functional space, as a tool to reveal the complex nature of change in disturbed ecosystems.
1,307 citations
TL;DR: In this article, a large-scale demonstration of a strong, positive and significant effect of biodiversity on tree productivity with control for climatic and environmental conditions was presented. But the authors did not consider the effects of complementarity on ecosystem functioning.
Abstract: Aim An important issue regarding biodiversity concerns its influence on ecosystem functioning.Experimental work has led to the proposal of mechanisms such as niche complementarity.However,few attempts have been made to confirm these in natural systems, especially in forests. Furthermore, one of the most interesting unresolved questions is whether the effects of complementarity on ecosystem functioning (EF) decrease in favour of competitive exclusions over an increasing productivity gradient. Using records from permanent forest plots, we asked the following questions.(1) Is tree productivity positively related to diversity? (2) Does the effect of diversity increase in less productive forests? (3) What metric of diversity (e.g. functional or phylogenetic diversity) better relates to tree productivity? Location Temperate, mixed and boreal forests of eastern Canada. Methods Over 12,000 permanent forest plots, from temperate to boreal forests, were used to test our hypotheses in two steps.(1) Stepwise regressions were used to identify the best explanatory variables for tree productivity. (2) The selected climatic and environmental variables,as well as density and biodiversity indices,were included in a structural equation model where links (paths) between covarying variables are made explicit, making structural equation modelling the best tool to explore such complicated causal networks. Results This is the first large-scale demonstration of a strong, positive and significant effect of biodiversity on tree productivity with control for climatic and environmental conditions. Important differences were noted between the two forest biomes investigated. Main conclusions We show for the first time that complementarity may be less important in temperate forests growing in a more stable and productive environment where competitive exclusion is the most probable outcome of species interactions, whereas in the more stressful environment of boreal forests, beneficial interactions between species may be more important. The present work is also a framework for the analysis of large datasets in biodiversity‐ecosystem functioning (B-EF) research.
722 citations
Cites background or methods from "A distance-based framework for meas..."
...Functional diversity (FD) indices were then computed using an index called functional dispersion (FDis) (Laliberté & Legendre, 2010)....
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...There is a strong and lasting debate over what element of biodiversity matters to ecosystem functioning (Diaz et al., 2007; Mokany et al., 2008) and how it should be quantified (Poos et al., 2009; Laliberté & Legendre, 2010)....
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TL;DR: This work uses BioGeoBEARS on a large sample of island and non-island clades to show that founder-event speciation is a crucial process in almost every clade, and that most published datasets reject the non-J models currently in widespread use.
Abstract: Historical biogeography has been characterized by a large diversity of methods and unresolved debates about which processes, such as dispersal or vicariance, are most important for explaining distributions. A new R package, BioGeoBEARS, implements many models in a common likelihood framework, so that standard statistical model selection procedures can be applied to let the data choose the best model. Available models include a likelihood version of DIVA (“DIVALIKE”), LAGRANGE’s DEC model, and BAYAREA, as well as “+J” versions of these models which include founder-event speciation, an important process left out of most inference methods. I use BioGeoBEARS on a large sample of island and non-island clades (including two fossil clades) to show that founder-event speciation is a crucial process in almost every clade, and that most published datasets reject the non-J models currently in widespread use. BioGeoBEARS is open-source and freely available for installation at the Comprehensive R Archive Network at http://CRAN.R-project.org/package=BioGeoBEARS. A step-by-step tutorial is available at http://phylo.wikidot.com/biogeobears.
676 citations
Additional excerpts
... The maxent function of the package FD (Laliberté & Legendre 2010; Laliberté & Shipley 2011) was used in the above-‐described calculation of descendant daughter range size weights....
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TL;DR: The progression of food-web ecology and the challenges in using the food- web approach are summarized and five areas of research are identified where advances can continue, and be applied to global challenges.
Abstract: The global biodiversity crisis concerns not only unprecedented loss of species within communities, but also related consequences for ecosystem function. Community ecology focuses on patterns of species richness and community composition, whereas ecosystem ecology focuses on fluxes of energy and materials. Food webs provide a quantitative framework to combine these approaches and unify the study of biodiversity and ecosystem function. We summarise the progression of food-web ecology and the challenges in using the food-web approach. We identify five areas of research where these advances can continue, and be applied to global challenges. Finally, we describe what data are needed in the next generation of food-web studies to reconcile the structure and function of biodiversity.
530 citations
References
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Western Washington University1, University of Alaska Fairbanks2, United States Forest Service3, University of Zurich4, Centre national de la recherche scientifique5, Natural Environment Research Council6, University of Notre Dame7, École Normale Supérieure8, Columbia University9, University of Helsinki10, United States Geological Survey11, University of Michigan12, Swedish University of Agricultural Sciences13, Landcare Research14
TL;DR: Understanding this complexity, while taking strong steps to minimize current losses of species, is necessary for responsible management of Earth's ecosystems and the diverse biota they contain.
Abstract: Humans are altering the composition of biological communities through a variety of activities that increase rates of species invasions and species extinctions, at all scales, from local to global. These changes in components of the Earth's biodiversity cause concern for ethical and aesthetic reasons, but they also have a strong potential to alter ecosystem properties and the goods and services they provide to humanity. Ecological experiments, observations, and theoretical developments show that ecosystem properties depend greatly on biodiversity in terms of the functional characteristics of organisms present in the ecosystem and the distribution and abundance of those organisms over space and time. Species effects act in concert with the effects of climate, resource availability, and disturbance regimes in influencing ecosystem properties. Human activities can modify all of the above factors; here we focus on modification of these biotic controls. The scientific community has come to a broad consensus on many aspects of the re- lationship between biodiversity and ecosystem functioning, including many points relevant to management of ecosystems. Further progress will require integration of knowledge about biotic and abiotic controls on ecosystem properties, how ecological communities are struc- tured, and the forces driving species extinctions and invasions. To strengthen links to policy and management, we also need to integrate our ecological knowledge with understanding of the social and economic constraints of potential management practices. Understanding this complexity, while taking strong steps to minimize current losses of species, is necessary for responsible management of Earth's ecosystems and the diverse biota they contain.
6,891 citations
TL;DR: A general coefficient measuring the similarity between two sampling units is defined and the matrix of similarities between all pairs of sample units is shown to be positive semidefinite.
Abstract: A general coefficient measuring the similarity between two sampling units is defined. The matrix of similarities between all pairs of sample units is shown to be positive semidefinite (except possibly when there are missing values). This is important for the multidimensional Euclidean representation of the sample and also establishes some inequalities amongst the similarities relating three individuals. The definition is extended to cope with a hierarchy of characters.
4,204 citations
"A distance-based framework for meas..." refers background or methods in this paper
...In particular, they proposed to use the principal coordinate analysis (PCoA) axes from a Gower dissimilarity matrix (Gower 1971) among the species as the new traits to compute their FD indices when there are qualitative traits in the original (species 3 trait) matrix....
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...We add that it is also useful when some traits are semi-quantitative, when missing trait values are present, and when individual traits need to be weighted differently, because the Gower dissimilarity index can handle all of these situations (Gower 1971, Legendre and Legendre 1998, Podani 1999)....
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TL;DR: Active adaptive management and governance of resilience will be required to sustain desired ecosystem states and transform degraded ecosystems.
Abstract: ▪ Abstract We review the evidence of regime shifts in terrestrial and aquatic environments in relation to resilience of complex adaptive ecosystems and the functional roles of biological diversity in this context. The evidence reveals that the likelihood of regime shifts may increase when humans reduce resilience by such actions as removing response diversity, removing whole functional groups of species, or removing whole trophic levels; impacting on ecosystems via emissions of waste and pollutants and climate change; and altering the magnitude, frequency, and duration of disturbance regimes. The combined and often synergistic effects of those pressures can make ecosystems more vulnerable to changes that previously could be absorbed. As a consequence, ecosystems may suddenly shift from desired to less desired states in their capacity to generate ecosystem services. Active adaptive management and governance of resilience will be required to sustain desired ecosystem states and transform degraded ecosystems...
3,297 citations
"A distance-based framework for meas..." refers background in this paper
...Functional diversity (FD) is a key driver of ecosystem processes (Hooper et al. 2005), ecosystem resilience to environmental change (Folke et al. 2004), and ecosystem services (Dı́az et al. 2007)....
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TL;DR: This paper provides an international methodological protocol aimed at standardising this research effort, based on consensus among a broad group of scientists in this field, and features a practical handbook with step-by-step recipes, for 28 functional traits recognised as critical for tackling large-scale ecological questions.
Abstract: There is growing recognition that classifying terrestrial plant species on the basis of their function (into 'functional types') rather than their higher taxonomic identity, is a promising way forward for tackling important ecological questions at the scale of ecosystems, landscapes or biomes. These questions include those on vegetation responses to and vegetation effects on, environmental changes (e.g. changes in climate, atmospheric chemistry, land use or other disturbances). There is also growing consensus about a shortlist of plant traits that should underlie such functional plant classifications, because they have strong predictive power of important ecosystem responses to environmental change and/or they themselves have strong impacts on ecosystem processes. The most favoured traits are those that are also relatively easy and inexpensive to measure for large numbers of plant species. Large international research efforts, promoted by the IGBP–GCTE Programme, are underway to screen predominant plant species in various ecosystems and biomes worldwide for such traits. This paper provides an international methodological protocol aimed at standardising this research effort, based on consensus among a broad group of scientists in this field. It features a practical handbook with step-by-step recipes, with relatively brief information about the ecological context, for 28 functional traits recognised as critical for tackling large-scale ecological questions.
3,288 citations