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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.

Question: Which functional diversity indices have the power to reveal changes in community assembly processes along abiotic stress gradients? Is their power affected by stochastic processes and variations in species richness along stress gradients? Methods: We used a simple community assembly model to explore the power of functional diversity indices across a wide range of ecological contexts. The model assumes that with declining stress the influence of niche complementarity on species fitness increases while that of environmental filtering decreases. We separately incorporated two trait-independent stochastic processes — mass and priority effects — in simulating species occurrences and abundances along a hypothetical stress gradient. We ran simulations where species richness was constant along the gradient, or increased, decreased or varied randomly with declining stress. We compared observed values for two indices of functional richness — total functional dendrogram length (FD) and convex hull volume (FRic) — with a matrix-swap null model (yielding indices SESFD and SESFRic) to remove any trivial effects of species richness. We also compared two indices that measure both functional richness and functional divergence — Rao quadratic entropy (Rao) and functional dispersion (FDis) — with a null model that randomizes abundances across species but within communities. This converts them to pure measures of functional divergence (SESRao and SESFDis). Results: When mass effects operated, only SESRao and SESFDis gave reasonable power, irrespective of how species richness varied along the stress gradient. FD, FRic, Rao and FDis had low power when species richness was constant, and variation in species richness greatly influenced their power. SESFRic and SESFD were unaffected by variation in species richness. When priority effects operated, FRic, SESFRic, Rao and FDis had good power and were unaffected by variation in species richness. Variation in species richness greatly affected FD and SESFD. SESRao and SESFDis had low power in the priority effects model but were unaffected by variation in species richness. Conclusions: Our results demonstrate that a reliable test for changes in assembly processes along stress gradients requires functional diversity indices measuring either functional richness or functional divergence. We recommend using SESFRic as a measure of functional richness and either SESRao or SESFDis (which are very closely related mathematically) as a measure of functional divergence. Used together, these indices of functional richness and functional divergence provide good power to test for increasing niche complementarity with declining stress across a broad range of ecological contexts.

1. Indices quantifying the functional aspect of biodiversity are essential in understanding relationships between biodiversity, ecosystem functioning and environmental constraints. Many indices of functional diversity have been published but we lack consensus about what indices quantify, how redundant they are and which ones are recommended. 2. This study aims to build a typology of functional diversity indices from artificial data sets encompassing various community structures (different assembly rules, various species richness levels) and to identify a set of independent indices able to discriminate community assembly rules. 3. Our results confirm that indices can be divided into three main categories, each of these corresponding to one aspect of functional diversity: functional richness, functional evenness and functional divergence. Most published indices are highly correlated and quantify functional richness while quadratic entropy (Q) represents a mix between functional richness and functional divergence. Conversely, two indices (FEve and FDiv respectively quantifying functional evenness and functional divergence) are rather independent to all the others. The power analysis revealed that some indices efficiently detect assembly rules while others performed poorly. 4. To accurately assess functional diversity and establish its relationships with ecosystem functioning and environmental constraints, we recommend investigating each functional component separately with the appropriate index. Guidelines are provided to help choosing appropriate indices given the issue being investigated. 5. This study demonstrates that functional diversity indices have the potential to reveal the processes that structure biological communities. Combined with complementary methods (phylogenetic and taxonomic diversity), the multifaceted framework of functional diversity will help improve our understanding of how biodiversity interacts with ecosystem processes and environmental constraints.

Understanding how ecosystem functioning is impacted by global change drivers is a central topic in ecology and conservation science. We need to assess not only how environmental change affects species richness, but also how the distribution of functional traits (i.e. functional diversity) mediate the relationship between species richness and ecosystem functioning. However, most evidence about the capacity of functional diversity to explain ecosystem functioning has been developed from studies conducted at a single spatial scale. Here, we explore theory, expectations and evidence for why and how species richness and functional diversity relationships vary with spatial scale. Despite the importance of accounting for spatial processes at multiple scales, we show that most studies of the species richness–functional diversity relationship focus on single scale analyses that ignore spatial context. Thus, we discuss the need to establish a spatially explicit, multi‐scale framework for understanding the relationship between species richness and functional diversity. As a starting point to developing such a framework, we detail some expected trajectories and mechanisms by which the diversity of species and functional traits may change across increasing spatial scales. We also explore what is known about two important gaps in the literature about this relationship: 1) the influence of spatial autocorrelation on community assembly processes and 2) the variation in the structure of species interactions across spatial extents. We present some key challenges that could be addressed by integrating approaches from community and landscape ecology. This information will help improve our understanding of the relative influence of local and large‐scale processes on community structure, while providing a foundation for improving biodiversity monitoring, policy and ecosystem function based conservation.

Functional diversity is the diversity of species traits in ecosystems. This concept is increasingly used in ecological research, yet its formal definition and measurements are currently under discussion. As the overall behavior and consistency of functional diversity indices have not been described so far, the novice user risks choosing an inaccurate index or a set of redundant indices to represent functional diversity. In our study we closely examine functional diversity indices to clarify their accuracy, consistency, and independence. Following current theory, we categorize them into functional richness, evenness, or divergence indices. We considered existing indices as well as new indices developed in this study. The new indices aimed at remedying the weaknesses of currently used indices (e.g., by taking into account intraspecific variability). Using virtual data sets, we test (1) whether indices respond to community changes as expected from their category and (2) whether the indices within each category are consistent and independent of indices from other categories. We also test the accuracy of methods proposed for the use of categorical traits. Most classical functional richness indices either failed to describe functional richness or were correlated with functional divergence indices. We therefore recommend using the new functional richness indices that consider intraspecific variability and thus empty space in the functional niche space. In contrast, most functional evenness and divergence indices performed well with respect to all proposed tests. For categorical variables, we do not recommend blending discrete and real-valued traits (except for indices based on distance measures) since functional evenness and divergence have no transposable meaning for discrete traits. Nonetheless, species diversity indices can be applied to categorical traits (using trait levels instead of species) in order to describe functional richness and equitability.

Functional diversity is an important aspect of biodiversity, but its relationship to species diversity in time and space is poorly understood. Here we compare spatial patterns of functional and taxonomic diversity across marine and terrestrial systems to identify commonalities in their respective ecological and evolutionary drivers. We placed species-level ecological traits into comparable multi-dimensional frameworks for two model systems, marine bivalves and terrestrial birds, and used global species-occurrence data to examine the distribution of functional diversity with latitude and longitude. In both systems, tropical faunas show high total functional richness (FR) but low functional evenness (FE) (i.e. the tropics contain a highly skewed distribution of species among functional groups). Functional groups that persist toward the poles become more uniform in species richness, such that FR declines and FE rises with latitude in both systems. Temperate assemblages are more functionally even than tropical assemblages subsampled to temperate levels of species richness, suggesting that high species richness in the tropics reflects a high degree of ecological specialization within a few functional groups and/or factors that favour high recent speciation or reduced extinction rates in those groups.

Human activities have strong impacts on ecosystem functioning through their effect on abiotic factors and on biodiversity. There is also growing evidence that species functional traits link changes in species composition and shifts in ecosystem processes. Hence, it appears to be of utmost importance to quantify modifications in the functional structure of species communities after human disturbance in addition to changes in taxonomic structure. Despite this fact, there is still little consensus on the actual impacts of human-mediated habitat alteration on the components of biodiversity, which include species functional traits. Therefore, we studied changes in taxonomic diversity (richness and evenness), in functional diversity, and in functional specialization of estuarine fish communities facing drastic environmental and habitat alterations. The Terminos Lagoon (Gulf of Mexico) is a tropical estuary of primary concern for its biodiversity, its habitats, and its resource supply, which have been severely impacted by human activities. Fish communities were sampled in four zones of the Terminos Lagoon 18 years apart (1980 and 1998). Two functions performed by fish (food acquisition and locomotion) were studied through the measurement of 16 functional traits. Functional diversity of fish communities was quantified using three independent components: richness, evenness, and divergence. Additionally, we measured the degree of functional specialization in fish communities. We used a null model to compare the functional and the taxonomic structure of fish communities between 1980 and 1998. Among the four largest zones studied, three did not show strong functional changes. In the northern part of the lagoon, we found an increase in fish richness but a significant decrease of functional divergence and functional specialization. We explain this result by a decline of specialized species (i.e., those with particular combinations of traits), while newly occurring species are redundant with those already present. The species that decreased in abundance have functional traits linked to seagrass habitats that regressed consecutively to increasing eutrophication. The paradox found in our study highlights the need for a multifaceted approach in the assessment of biodiversity changes in communities under pressure.

1. Functional diversity (FD) metrics are widely used to assess invasion ecosystem impacts, but we have limited theory to predict how FD should respond to invasion. A key challenge to effectively using FD metrics is the complexity of conceptualizing alterations to multidimensional trait space, making it difficult to select a priori the most appropriate metric for specific ecological questions. 2. Here, we provide expectations on how invasion should change four commonly used FD metrics—functional richness (FRic), evenness (FEve), divergence (FDiv) and dispersion (FDis)—and then test these expectations in a laboratory decomposition experiment. We simulate invasion of a forest by understorey plants by adding leaf litter from 18 natives and non-natives to a representative canopy tree litter mixture to test changes in FD and decomposition. 3. All four metrics changed predictably with invasion. Species that were more functionally unique or when added at greater proportions had larger impacts on FD. Overall, FRic, FEve and FDiv were poor choices for understanding impacts of non-native species. FDis was the only metric that both changed predictably with addition of understorey litter and correlated intuitively with changes in carbon mineralization. Furthermore, ranking species based upon how much they changed FDis of the litter mixture provided a fair assessment of which species had the largest impact on decomposition. As such, functional dispersion may be a key tool for predicting a priori which non-natives will have the greatest impact on ecosystem processes. 4. Synthesis. We highlight the need to assess the suitability of each functional diversity metric for the specific ecological question at hand. Our work reveals the pitfalls of considering multiple metrics or randomly choosing a single metric without suitability assessments. At the same time, it suggests a framework for metric assessment that should help lead to selection of a metric or metrics that provide robust a priori insights into how invasion by non-native species can impact ecosystem processes.

Functional traits are characteristics of an organism that represents how it interacts with its environment and can influence the structure and function of ecosystems. Ecological stoichiometry provides a framework to understand ecosystem structure and function by modeling the coupled flow of elements (e.g. carbon [C], nitrogen [N], phosphorus [P]) between consumers and their environment. Animals tend to be homeostatic in their nutrient requirements and preferentially sequester the element in shortest supply relative to demand, and release relatively more of the element in excess. Tissue stoichiometry is an important functional trait that allows for predictions among the elemental composition of animals, their diet, and their waste products, with important effects on the cycling and availability of nutrients in ecosystems. Here, we examined the tissue stoichiometric niches (C:N:P) and nutrient recycling stoichiometries (N:P) of several filter-feeding freshwater mussels in the subfamily Ambleminae. Despite occupying the same functional-feeding group and being restricted to a single subfamily-level radiation, we found that species occupied distinct stoichiometric niches and that these niches varied, in part, as a function of their evolutionary history. The relationship between phylogenetic divergence and functional divergence suggests that evolutionary processes may be shaping niche complementarity and resource partitioning. Tissue and excretion stoichiometry were negatively correlated as predicted by stoichiometric theory. When scaled to the community, higher species richness and phylogenetic diversity resulted in greater functional evenness and reduced functional dispersion. Filter-feeding bivalves are an ecologically important guild in freshwater ecosystems globally, and our study provides a more nuanced view of the stoichiometric niches and ecological functions performed by this phylogenetically and ecologically diverse assemblage.

AimSpecies shift their ranges as a consequence of climate change, hence modifying the structure of local assemblages. This may have important consequences for ecosystem functioning in the case of ecosystem engineers such as earthworms, especially when community restructuring leads to an alteration of their functional diversity. Here, we aimed to model the potential modification of the functional diversity of French earthworm assemblages in a context of climate change.LocationMetropolitan France.MethodsWe fitted boosted regression trees to earthworm data collected using a standardized protocol across France in the 1960s. We used model projections constrained by a macroecological model of species richness to predict the composition of earthworm assemblages in the present and in two scenarios of climate change and two future time periods. We coupled these results with a large set of species traits to calculate predicted changes in functional diversity, which we summarized by ecoregion.ResultsModels predicted a clear decline in functional richness between the period of sampling and nowadays which are expected to continue in the future, with substantial differences depending on ecoregions and on whether species will be able to disperse or not. However, predicted changes in functional evenness and divergence are much weaker, suggesting that climate change will not affect all facets of functional diversity in the same way.Main ConclusionsOur results mostly pointed to a potential reduction of the functional richness of earthworm communities in the future, but this predicted loss of diversity could be weaker if species are able to colonize new suitable sites or to persist in microclimate refugia. There are concerns, though, that these changes lead to an alteration of soil processes and of the ecosystem services they provide.