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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.

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.

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.

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.

AIM: One of the main gaps in the assessment of biodiversity is the lack of a unified framework for measuring its taxonomic and functional facets and for unveiling the underlying patterns. LOCATION: Europe, 25 large river basins. METHODS: Here, we develop a decomposition of functional β‐diversity, i.e. the dissimilarity in functional composition between communities, into a functional turnover and a functional nestedness‐resultant component. RESULTS: We found that functional β‐diversity was lower than taxonomic β‐diversity. This difference was driven by a lower functional turnover compared with taxonomic turnover while the nestedness‐resultant component was similar for taxonomic and functional β‐diversity. MAIN CONCLUSIONS: Fish faunas with different species tend to share the same functional attributes. The framework presented in this paper will help to analyse biogeographical patterns as well as to measure the impact of human activities on the functional facets of biodiversity.

ContextIsland Biogeography Theory and Habitat Amount Hypothesis postulate species richness and densities to increase with connectivity and habitat amount, while niche theory highlights the importance of environmental heterogeneity for species coexistence. Additional ecological niches in heterogeneous landscapes increase species richness and functional and phylogenetic diversity, but larger, less isolated habitats are expected to enlarge species densities by mass effects without effects on functional or phylogenetic diversity.ObjectivesWe assessed the relative contribution of habitat amount, isolation and environmental heterogeneity on taxonomic, functional and phylogenetic diversity of the particular canga vegetation, i.e., rupestrian savannas associated to banded ironstone outcrops from the Carajás Massif, Eastern Amazon.MethodsWe sampled vegetation at 48 sampling points comprising different physiognomies from 5 canga patches. Diversity measures were modelled as response variables in linear mixed models, using non-collinear predictors of habitat amount, isolation and environmental heterogeneity.ResultsDiversity and species composition differed among canga physiognomies, indicating that environmental filters segregate canga plant metacommunity in physiognomy-specific species pools. Landscape roughness, a proxy for heterogeneity on the landscape level, increases species densities and functional richness. Additionally, habitat amount was positively associated with the degree of phylogenetic relatedness and functional diversity in communities.ConclusionsOur results suggest that configurational landscape heterogeneity increases the number of available ecological niches, while larger habitat amounts select for functionally and phylogenetically convergent species. These different underlying mechanisms need to be considered for management plans and reserve design for canga ecosystems, so that functional canga portions can be protected.

Aim: Niche theory proposes that increases in species richness along an environmental gradient are associated with a packing of species inside the niche space or an expansion of the niche space. We test whether and under what conditions an increase in bird species richness along a gradient of resource availability is associated with an expansion or packing of the niche as measured based on traits related to resource use. Location: Global. Time period: Current. Major taxa studied: Birds. Methods: We measured birds’ realized niche space as the standardized departure between observed total trait range and its null expectation (functional richness: SES.FRic) in 12,188 cells worldwide. We first correlated both species richness and this measurement along the global net primary productivity (NPP) gradient using linear regressions. Second, we investigated the nonstationarity of the species richness–NPP relationship with Lee’s bivariate correlation, a measure of the spatial association of two variables. We then assessed the number of cells exhibiting a significant positive species richness–NPP association and a significant negative or positive SES.FRic. Third, we assessed whether species of species-rich assemblages occur within or outside the niche space of species-poor assemblages. Results: At a global scale, we found that species richness and SES.FRic increased with NPP. We also showed that cells with a significant positive association between species richness and NPP exhibited niche packing (1,699 assemblages out of 12,188) more than niche expansion (five assemblages). Niche packing was associated with complex biomes such as tropical rain forests. Finally, by showing that species in species-rich assemblages predominantly occur within the niche space of species-poor assemblages, we showed that the increase in SES.FRic with NPP contributed little to the increase in species richness. Main conclusion: Although niche volume increases with species richness along an NPP gradient, we confirmed that niche packing is the pattern most associated with the species richness–NPP relationship at a global scale.

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.

Characterizing the spatial structure of taxonomic and functional diversity (FD) of marine organisms across regional and latitudinal scales is essential for improving our understanding of the processes driving species richness and those that may constrain or enhance the set of species traits that define the functional structure of communities. Here, we present the functional diversity of coastal invertebrate macrofaunal species along the south‐eastern Pacific from 7°N to 56°S, describe spatial variation of species traits, and examine the relationship with environmental variables. For that, we defined the functional traits and distribution ranges of 2350 marine macroinvertebrates calculated eight metrics of FD. Random forest regression was applied to identify significant relationships between FD and six environmental variables. Finally, functional β‐turnover was estimated to detect alongshore shifts in functional structure and their coincidence with biogeographical domains. Our results show, in contrast with taxonomic richness that measures of trait differences, functional space and functional specialisation increase with latitude, while functional evenness exhibits a non‐linear shape, peaking at mid latitudes. Functional redundancy decreased significantly poleward, while indicators of vulnerability increase. In contrast to taxonomic richness, FD was tightly connected to variables indicative of stress and productivity, such as dissolved oxygen and nutrients. Sea surface temperature and coastal area best explained the increased FD redundancy and richness towards the tropics. The high spatial correlation between taxonomic and functional turnover suggests environmental filters play an important role in the functional structure of the seascape. Our findings suggest that processes favouring taxonomic richness are latitudinally divergent from those favouring functional diversity. Correlations with environmental variables suggest that increased sea surface temperature and measures of stability increase redundancy, while variations in dissolved oxygen and nutrients positively affect functional diversification. Moreover, the functional diversity patterns suggest low resilience of high latitude coastal ecosystems, which are heavily exploited and threatened by climate change, hence highlighting the urgent need for effective conservation policies.