Human land-use change is the primary force reshaping ecosystems, selectively excluding disturbance-sensitive taxa and concentrating biodiversity in human-dominated landscapes. Yet the consequences of such reconfigurations for ecosystem functioning and resilience remain uncertain. Theoretical predictions are equivocal because land-use change can both reduce functional redundancy, destabilising ecosystems, and promote disturbance-tolerant species, which may increase stability. Empirically resolving this ambiguity has proven challenging because most large-scale studies rely on static snapshots rather than time-series data, hindering our ability to directly link land-use change to alterations in functional integrity and resilience. Here, we present a continental-scale, temporally resolved analysis of how land-use intensification affects the functional integrity and stability of North American avian communities. We analysed 5,467 assemblages over 22 years, combining occupancy-modelled survey data, comprehensive morphological and dietary trait information for all species, and high-resolution annual land-cover maps of natural and human-modified habitats. We show that urbanisation—the most extreme form of land-use change—undermine community integrity and in doing so, weakens functional stability. This instability stems from erosion of functional redundancy and is amplified by increased habitat heterogeneity, despite the rise of disturbance-tolerant species. In crop-dominated landscapes, however, stability is maintained despite extreme loss of redundancy, due to the offsetting effects of habitat homogenization and gains in disturbance-tolerant species as well as direct stabilising mechanisms. Thus, land-use change can lead to communities deprived of key ecosystem functions and more exposed to future disturbances, but low redundancy alone does not necessarily imply greater vulnerability.

Abstract In the face of accelerating biodiversity loss, conservation strategies require effective tools to identify species of high conservation priority. In this context, the index of evolutionary distinctiveness (ED), which quantifies the unique contribution of individual species to the overall phylogenetic diversity of a given assemblage, has played a pivotal role. In this paper, we propose a general mathematical framework for ED based on the notion of specificity, a type of non‐probabilistic uncertainty derived from fuzzy set theory. This new perspective allows ED to be extended to other forms of distinctiveness, such as functional distinctiveness, provided that an appropriate pairwise (dis)similarity matrix between species is available. It also enables the development of new measures that capture aspects of species distinctiveness not accounted for by the ED index. Our formulation further connects species‐level distinctiveness with traditional community‐level metrics, such as alpha and beta diversity. We demonstrate how beta diversity, traditionally used to measure species turnover among sites, can be reframed as the average specificity of the sampled sites. Overall, linking ED to fuzzy specificity opens new directions for biodiversity measurement and conservation planning.

In ecology, species richness, the number of species, was a pioneer simple formula still currently most widely used as a biodiversity index. Species, functional, and phylogenetic diversity indices then emerged from the feeling that combining species richness with the distribution of species' abundances, functional and/or phylogenetic characteristics could provide indices that are more linked to ecological phenomena than species richness alone. As there are a myriad of indices developed so far, it seems impossible to explore all of them in the limited time of a research study. Selecting a single index or a limited set of indices most relevant to a given study requires methods to facilitate comparisons among indices and among their mathematical properties that reflect their different ways of summarizing biodiversity in a single numeric value. Parametric guiding indices that generalize and connect existing indices trace paths through the jungle of indices. The development of such guiding indices could thus be advantageously strengthened. As a step in this direction, I develop a parametric guiding index that generalize both well-known indices of species diversity and well-known indices of functional/phylogenetic diversity. I show under which conditions the parametric guiding index satisfies some critical mathematical properties: non-negativity; weak species monotonicity; full concentration or full similarity at minimum; evenness in species' abundance or evenness in species' effective originality at maximum; embedding of species richness and diversity. Applying the parametric guiding index on bat diversity, I show that analyzing the mathematical properties of potential biodiversity indices is critical to evaluating their relevance with regards to study objectives in ecology.

The Rao quadratic entropy (Q) is a fundamental measure of biodiversity, widely used in ecology, which quantifies the average dissimilarity among individuals in a community. However, Q has been sometimes criticized for not fulfilling certain properties desired in applications like conservation biology, notably: its maximum value does not necessarily correspond to maximum species richness, and its unit of measurement is not species number. For these applications, I introduce the Rich-Rao quadratic entropy (RQ), defined as the product of Q and observed species richness (S). I demonstrate that RQ satisfies key properties unsatisfied by Q, including weak species monotonicity (ensuring that the loss of any species results in a decrease in RQ). If interspecies dissimilarities are bounded between 0 and 1, RQ can be interpreted the average number of distinctive species encountered by a randomly chosen species in the community. I show that RQ also retains key statistical properties of Q, such as concavity, and can be additively partitioned into α, β, and γ components. Unlike measures of Equivalent Species Richness, RQ maintains the fundamental property that diversity is zero in the absence of inter-individual dissimilarity. Applying RQ and Q to bat and bird functional diversity across six European countries reveals that Q and RQ can provide conflicting rankings, particularly for birds, where RQ variation is strongly driven by species richness. The Q approach is best suited for mechanistic studies, while RQ provides a synthetic, readily communicable measure that balances dissimilarity and species richness, making it valuable for informing conservation priorities.

Rarefaction methods are statistical techniques used to estimate diversity across increasing number of samples, generating rarefaction curves that depict diversity as a function of sample size. These methods are widely applied in ecological research to compare taxonomic, functional, and phylogenetic diversity across samples with varying collection efforts. However, incorporating spatially explicit rarefaction methods has become essential, as accounting for spatial autocorrelation substantially influences results and alters how biodiversity hotspots or conservation priorities are identified. This paper describes Rarefy, an R package that introduces novel functions capable of handling any diversity metric, allowing users to compute the expected values of taxonomic, functional, or phylogenetic indices for reduced sample sizes under spatially constrained, distance-based sampling unit arrangements. To showcase the package's functionalities, we estimated the functional diversity of plant communities along the northern Adriatic coastline. The spatially explicit rarefaction functions consistently produced lower diversity values compared to their non-spatial counterparts, reflecting the functional redundancy typical of spatially adjacent plant communities. These differences provide a practical diagnostic signal of spatial structure in the dataset. The Rarefy package offers ecologists a robust and straightforward tool to account for spatial constraints in rarefaction analyses, yielding more ecologically meaningful diversity estimates. Future developments will further integrate null-model procedures, extending the comparison between observed and randomized community diversity patterns illustrated in this study.

Functional diversity, redundancy, rarity, and originality (or distinctiveness) are fundamental concepts in ecology and conservation biology. Despite their frequent use, the precise meaning and relationships between these measures are often unclear. This paper aims to provide a comprehensive theoretical framework to elucidate what each of these measures captures and how they interrelate. By integrating traditional community-level diversity metrics with species-level specificity measures derived from fuzzy set theory, we bridge the gap between these concepts. Our framework reveals that while all four measures address distinct aspects of community-level and species-level functional resemblance, they can all be traced back to a common conceptual and formal background. This guide is intended to help ecologists and conservationists understand the meaning of these measures and apply them more effectively in their research and conservation strategies.

Facing the myriad of indices claimed to be biodiversity indices that have been proposed by the scientific community, it becomes critical to analyze the mathematical properties that determine whether any index respond to biological necessities about biodiversity quantification. In ecology, species richness, the number of species, was a pioneer simple formula still currently most widely used as a biodiversity index. Species, functional, phylogenetic diversity indices then emerged from the feeling that combining species richness with the distribution of species’ abundances, functional and/or phylogenetic characteristics could provide indices that are more linked to ecological phenomena than species richness alone. Although there are theoretically an infinite number of potential biodiversity indices, I show here that some widely used indices of biodiversity actually take on large values in the absence of diversity. I thus claim for stricter definition of mathematical formulas that can be classified as biodiversity indices and for the use of parametric guiding indices that generalize and connect existing indices, tracing paths through the jungle of indices. As a case study I develop a parametric guiding index, and applying it on bat diversity, I show that analyzing the mathematical properties of potential biodiversity indices is critical to evaluate their relevance as regards a study objective in ecology. I come to the conclusions that to improve applications of biodiversity indices in ecology we need to: stop claiming for a single best formula; acknowledge that biodiversity indices are above all diversity indices, with the particularity that they are applied to biological data; agree on a set of minimal conditions that any biodiversity index must fulfill; integrate a large panel of diversity indices in software packages to enable ecologists to select and apply the most relevant index for their study. I propose a set of minimal conditions as a first step in this direction.

Functional distinctiveness is a key concept in ecology, reflecting the extent to which a species exhibits unique functional traits relative to other species in the assemblage. While functionally distinct species often contribute disproportionately to ecosystem processes, their role in shaping community functioning remains underexplored. In this study, we propose an integrated framework that links functional distinctiveness to rarity functions, a fundamental component of diversity measures, thereby generalizing distinctiveness metrics beyond the simple calculation of mean trait distance. The main advantage of the proposed framework lies in its ability to adjust the sensitivity of distinctiveness to changes in the abundance of rare or common species, thus providing a more accurate representation of community structure. We apply this approach to an Alpine plant succession, examining changes in functional distinctiveness across six successional stages. Our results reveal a gradual decline in functional diversity along the succession, driven by a progressive reduction in the functional distinctiveness of the most abundant species within plots. Additionally, we demonstrate that measures of functional distinctiveness that are more sensitive to rare species provide a more refined understanding of changes in the functional structure of communities during succession. This study highlights the importance of integrating distinctiveness and rarity functions to better capture the ecological roles of functionally distinct species and inform biodiversity conservation strategies.

This article is a discussion on Shinto Eguchi's article published in Sankhya A (Eguchi 2025).

Several studies have revealed species that constitute conservation paradoxes because they are invasive in some areas and threatened in others. However, those studies only considered ecological impacts of invasions and species' threat category as a criterion that makes them conservation priorities. Here, our aim was to highlight further species that cause economic costs because of their invasiveness in some areas while being in need of priority protection in their native ranges. We used the InvaCost database to calculate an economic cost for each invasive alien species (IAS) in this database and explored the threat category, as well as the phylogenetic and functional distinctiveness of these IAS. We also focused on the costliest IAS to reveal their threat category and distinctiveness. Among the 355 species of mammals, birds, and plants constituting IAS with sufficient data on economic costs, we found that 10 species are also conservation priorities because they are threatened in their native range, therefore constituting conservation paradoxes. We further found that 27 IAS with economic costs are also conservation priorities because they are among the most phylogenetically or functionally distinctive, thus constituting conservation challenges. One IAS with economic costs is a conservation priority both because it is threatened in its native range and phylogenetically distinctive: the koala. Finally, we found three conservation paradoxes or challenges among the costliest IAS. Our work stresses to an unprecedented level that some species simultaneously need to be controlled in their invasive range and protected in their native range.

It is crucial to document biodiversity data and to take actions to halt the ongoing massive loss of biodiversity. Yet, these data are poorly defined. We propose a definition of biodiversity data and discuss its implications for data management, enabling enhanced data mobilization for integrated research and efficient conservation strategies.

Abstract In recent decades, research on biodiversity in community ecology has been marked by the consideration of species' evolutionary histories and functional traits. Among the different spatial levels at which functional or phylogenetic (hereafter FP) diversity can be quantified, the definition of the general concept of between‐community (β) diversity has been given less attention than that of local, within‐community (α) and regional, merged‐community (γ) diversities. Here, we develop a new method for partitioning FP β diversity into elementary components to determine how and why FP β diversity differs from species β diversity, with the latter reflecting only differences in species' abundances between communities. As a reference example, we consider two distinct measures of FP β diversity: Rao's dissimilarity coefficient (Qβ), which expresses the average FP dissimilarity between communities, and its transformation (Eβ), which expresses the effective number of distinct communities. Through analytical partitioning and simulations, we show that Qβ and Eβ are connected differently to typical patterns of community structure. The search for the ecological and evolutionary processes that drive community assembly and the assessment of community resilience and stability have indeed revealed typical community structures: the local clustering of species with similar traits or shared evolutionary histories and the local (α) or regional (γ) presence of functionally or phylogenetically redundant versus unique species. We show that while Qβ and Eβ are both increasing functions of species β diversity and FP γ uniqueness, Qβ increases with FP clustering, while Eβ increases with FP α redundancy. We also show that the component of FP clustering included in Qβ partitioning formula allows the detection of an overall trend of overdispersion or clustering in a dataset without the need to use null models. To facilitate and secure the selection of an index of β diversity for a given study, we call, through our study, for the development of formal and precise definitions for FP β diversity in light of the concepts of clustering versus overdispersion and redundancy versus uniqueness. In particular, we call for further research on when and why FP β diversity should increase with FP clustering.

Tropical species richness is threatened by habitat degradation associated with land-use conversion, yet the consequences for functional diversity remain little understood. Progress has been hindered by difficulties in obtaining comprehensive species-level trait information to characterize entire assemblages and insufficient appreciation that increasing land-cover heterogeneity potentially compensates for species loss. We examined the impacts of tropical deforestation associated with land-use heterogeneity on bird species richness, functional redundancy, functional diversity, and associated components (i.e., alpha diversity, species dissimilarity, and interaction strength of the relationship between abundance and functional dissimilarity). We analyzed over 200 georeferenced bird assemblages in the Atlantic Forest of Brazil. We characterized the functional role of the species of each assemblage and modeled biodiversity metrics as a function of forest cover and land-cover heterogeneity. Replacement of native Atlantic Forest with a mosaic of land uses (e.g., agriculture, pastures, and urbanization) reduced bird species richness in a nonrandom way. Core forest species, or species considered sensitive to edges, tended to be absent in communities in heterogenous environments. Overall, functional diversity and functional redundancy of bird species were not affected by forest loss. However, birds in highly heterogenous habitats were functionally distinct from birds in forest, suggesting a shift in community composition toward mosaic-exclusive species led by land-cover heterogeneity. Threatened species of the Atlantic Forest did not seem to tolerate degraded and heterogeneous environments; they remained primarily in areas with large forest tracts. Our results shed light on the complex effects of native forest transformation to mosaics of anthropogenic landscapes and emphasize the importance of considering the effects of deforestation and land-use heterogeneity when assessing deforestation effects on Neotropical biodiversity.

Given the current accelerating extinction rates, an increasing number of species-based conservation strategies have emerged because of the public interest in helping save particular species by funding rescue actions. Although public interest has focused mainly on well-studied, charismatic species, conservation scientists have developed tools to help prioritize species conservation from a more objective perspective, preserving ecosystem functioning and human well-being for future generations. For that purpose, species-centered biodiversity indicators that account not only for the extinction risk of a species but also for its evolutionary and/or functional distinctiveness have been developed. A species is considered irreplaceable and distinctive if it is isolated on the phylogenetic tree and/or if it has distinct traits, especially functional traits that determine the species' effects on ecosystems. The quantitative values representing extinction risk and distinctiveness of species have often been multiplied to define a quantitative conservation priority score. However, there is a plethora of ways to combine several conservation criteria into a single quantitative priority score, and the product of this multiplication is one such possibility. Each possible way of combining extinction risk and distinctiveness provides a different point of view on which of these should prevail to set conservation priorities. We set up an axiomatic framework on how a species' distinctiveness could be combined with its extinction risk via a tool used to define conservation priorities. By doing so, we show that further work is still needed to better communicate biodiversity indicators to the public and ensure an informed choice of indicators.

Snake response to habitat changes is frequently investigated at the species level, but it is still poorly known how snakes respond to habitat changes at the community level and at which spatial scale. Here, we used a multi-model inference approach to evaluate the effects of local and landscape composition (percentage of forest cover and silviculture) and habitat fragmentation (number of forest patches and total edge) on species, functional, and phylogenetic diversity of snake communities in tropical fragmented landscapes. Additionally, we tested whether silviculture acted as an environmental filter for snakes. Species and functional diversity responded primarily to landscape elements: species richness, abundance, and functional diversity decreased with deforestation. In addition, species richness and abundance increased with the proportion of forest and the number of patches in the landscape. In contrast, phylogenetic diversity was driven by the local habitat composition. Although habitat types did not filter entire clades and functional groups, each species tended to have a co-occurring species with similar traits (at landscape level) and a close relative (at both levels) in impacted habitats. In contrast, the co-occurrence of close relatives and functionally similar species was avoided in the native forest. Our findings indicate that snake responses to habitat changes occur on multiple scales and highlight the importance of conserving native forests to maintain multiple components of biodiversity. Strategies for conserving snake diversity in tropical fragmented landscapes should therefore consider management practices at both the local and landscape scales.

The variability in species composition among a set of sampling sites, or beta diversity, is considered a key signature of the ecological processes that shape the spatial structure of species assemblages. In this paper, we propose to decompose this variability into three additive components: i) the standard similarity in the (relative) abundances of species among sites, ii) the degree of functional dissimilarity between individuals of distinct species among sites, and iii) the degree of functional similarity between individuals of distinct species among sites, or beta redundancy. These three components can be used to portray the functional resemblance among sites on a ternary diagram. With the resulting ternary diagram of ‘functional resemblance’ we can relate various aspects of taxonomic and functional variability among sites to community assembly processes more completely than just looking at individual components. The potential of this method is shown with real data on the functional turnover of Alpine species along a primary succession on glacial deposits in northern Italy.

Among the many diversity indices in the ecologist toolbox, measures that can be partitioned into additive terms are particularly useful as the different components can be related to different ecological processes shaping community structure. In this paper, an additive diversity decomposition is proposed to partition the diversity structure of a given community into three complementary fractions: functional diversity, functional redundancy and species dominance. These three components sum up to one. Therefore, they can be used to portray the community structure in a ternary diagram. Since the identification of community‐level patterns is an essential step to investigate the main drivers of species coexistence, the ternary diagram of functional diversity can be used to relate different facets of diversity to community assembly processes more exhaustively than looking only at one index at a time. The value of the proposed diversity decomposition is demonstrated by the analysis of actual abundance data on plant assemblages sampled in grazed and ungrazed grasslands in Tuscany (Central Italy).

Specialization refers to a species adaptation to a restricted range of environmental conditions. While generalist species are able to exploit a wide variety of resources in a broad range of habitats, specialist species tend to have narrower niche breadths. From an evolutionary perspective, specialization is the result of a functional syndrome in which a suite of traits covary to allow the effective exploitation of specific resources. Accordingly, the measurement of specialization should be based on a multi-trait approach. In plant ecology, a well-known classification of the adaptive strategies of plants is Grime's competitor, stress tolerator, ruderal (CSR) theory in which the three principal strategies represent relatively easily measurable trait combinations from the global spectrum of plant form and function arising under conditions of competition, abiotic restriction to growth or periodic disturbance, respectively. In this paper, we thus introduce a method to summarize the functional specialization of plant species and communities by applying inequality measures to Grime's CSR strategies. The general idea is that a plant species that can be exclusively assigned to one CSR strategy can be considered a specialist (as it adopts only one adaptive strategy to access resources), while species that share functional characteristics of multiple CSR strategies can be considered more generalist. The behavior of the proposed measures is shown with one case study on the functional changes of six Alpine vegetation types ordered along a gradient, from pioneer to more stable communities.

Functional traits determine species' responses to environmental change and/or determine species' effects on ecosystem functions. When species with distinctive functional traits are threatened, there is a risk that ecosystem properties are also threatened. This is because functionally distinctive species may be those that have irreplaceable roles in an ecosystem and/or those that would be able to survive unusual environmental disturbances. To include functional distinctiveness as a criterion in conservation strategies, we need formal quantification of species' degree of distinctiveness while incorporating extinction risk. Based on previously developed quantitative methods, we develop a framework that links different metrics of functional distinctiveness and accounts for all species' extinction probabilities. Our framework is particularly relevant at the local scale, where species extinctions impact ecosystem functioning and where conservation policies are developed. As a case study, we thus applied our framework to the mammals of Indian dry forests known to be threatened with a drastic decrease in functional diversity and identified top-priority species as the threatened, most functionally distinctive species. We notably highlight that although some of the top-priority species we identified are charismatic and targeted by conservation actions, others are not. On the basis of this case study, we note that less charismatic, less known species that may be key for ecosystems could be revealed by applying our framework to a range of ecosystems and taxa.