Associations among taxonomic diversity, functional diversity and evolutionary distinctiveness vary among environments

Understanding the structural concordance between taxonomic and functional diversity (FD) metrics is essential for improving the ecological interpretation of community patterns in biomonitoring programs. This study evaluated the concordance between taxonomic and FD metrics of benthic macroinvertebrates along a fluvial habitat quality gradient in the Paute River Basin, Ecuador. Macroinvertebrate communities were sampled over six years at twelve sampling points and assessed using four taxonomic metrics: Shannon diversity (H), the Margalef index (DMg), family richness (N), and the Andean Biotic Index (ABI). Functional diversity was evaluated using four metrics: weighted functional dendrogram-based diversity (wFDc), Rao's quadratic entropy (Rao), functional dispersion (FDis), and functional richness (FRic). The fluvial habitat index (FHI) was used as an environmental reference to evaluate diversity metric responses. K-means clustering was independently applied to each metric, and pairwise concordance was quantified using the Measure of Concordance (MoC) and overlap in sampling points groupings across replicates. Most metrics (except FRic and N) showed clear responsiveness to the FHI gradient, confirming their ecological relevance. Strong structural concordance was observed between H and DMg and the FD metrics Rao, FDis, and wFDc, showing that these metrics captured similar yet complementary aspects of community organization. In contrast, ABI showed marked sensitivity to the FHI gradient but low concordance with functional metrics, suggesting distinct dimensions of biological integrity not encompassed by trait-based metrics. These findings highlight the value of combining taxonomic and functional metrics to detect both broad and subtle ecological changes. Integrating metrics with differing structural properties and environmental sensitivities can enhance the robustness of freshwater biomonitoring frameworks, especially in systems undergoing ecological transition or habitat degradation.

From compositional to functional biodiversity metrics in bioassessment: A case study using stream macroinvertebrate communities

Analysis of functional diversity, based on plant traits and community structure, provides a promising approach for exploration of the adaptive strategies of plants and the relationship between plant traits and ecosystem functioning. However, it is unclear how the number of plant traits included influences functional diversity, and whether or not there are quantitatively dependent traits. This information is fundamental to the correct use of functional diversity metrics. Here, we measured 34 traits of 366 plant species in nine forests from the tropical to boreal zones in China. These traits were used to calculate seven functional diversity metrics: functional richness (functional attribute diversity (FAD), modified FAD (MFAD), convex hull hypervolume (FRic)), functional evenness (FEve), and functional divergence (functional divergence (FDiv), functional dispersion (FDis), quadratic entropy (RaoQ)). Functional richness metrics increased with an increase in trait number, whereas the relationships between the trait divergence indexes (FDiv and FDis) and trait number were inconsistent. Four of the seven functional diversity indexes (FAD, MFAD, FRic, and RaoQ) were comparable with those in previous studies, showing predictable trends with a change in trait number. We verified our hypothesis that the number of traits strongly influences functional diversity. The relationships between these predictable functional diversity metrics and the number of traits facilitated the development of a standard protocol to enhance comparability across different studies. These findings can support integration of functional diversity index data from different studies at the site to the regional scale, and they focus attention on the influence of quantitative selection of traits on functional diversity analysis.

ABSTRACTAimDespite unprecedented environmental change due to anthropogenic pressure, recent work has found increasing dissimilarity due to turnover but no overall trend in species diversity through time at the local scale. Functional diversity provides a potentially powerful alternative approach for understanding community composition by linking shifts in species identity to the characteristics that underpin ecosystem processes. Here we present the first multitaxa, multisystem analysis of functional diversity and composition through time.LocationGlobal, with a North American focus.Time Period1923–2014.Major Taxa StudiedMammals, Birds.MethodsWe paired thousands of bird and mammal assemblage time series from the BioTIME database with existing trait data representative of species' functional roles to reconstruct time series of functional diversity and composition metrics. Our dataset included 2432 time series of yearly observations from 50 studies with a maximum spatial extent of 95 km2. Using generalised linear mixed models, we estimated general and study‐level trends for those metrics.ResultsWe found no overall temporal trends in functional diversity metrics. Study characteristics such as taxa, realm, biome, or protection status did not distinguish between types of change exhibited by communities. We found evidence of a temporal increase in fish consumption across all communities but no evidence to support multiple predictions for specific traits, including decreasing body size, dietary shifts or changes in bird foraging strata.Main ConclusionsGeneral temporal trends indicate that on the aggregate, studies do not exhibit consistent changes in functional diversity across many taxa, biomes and realms. At the study level, the majority of studies showed no temporal trends in species or functional diversity, with the remainder of the studies falling into broad categories of functional diversity change independent of species richness, functional redundancy loss (species richness declines with functional richness maintained) and increasing species richness sometimes accompanied by increasing functional richness.

BackgroundStudies on the relationship between biodiversity and ecosystem productivity have suggested that species richness and functional diversity are the main drivers of ecosystem processes. Several patterns on this relationship have been found, including positive, unimodal, negative, and neutral trends, keeping the issue controversial. In this study, taxonomic diversity and functional diversity as drivers of above-ground biomass (AGB) were compared, and the mechanisms that influence biomass production were investigated by testing the complementarity and the mass-ratio hypotheses.MethodsUsing data from 414 permanent sample plots, covering 23% of temperate forest in the Sierra Madre Oriental (México), we estimated the above-gound biomass (AGB), taxonomic and functional diversity indices, as well as community weighted mean values (CWM) for three functional traits (maximum height, leaf size and wood density) for trees ≥7.5 cm DBH, in managed and unmanaged stands. To compare taxonomic diversity differences between managed and unmanaged stands we carried out a rarefaction analysis. Furthermore, we evaluated the relationship between AGB and taxonomic and functional diversity metrics, as well as CWM traits throught spatial autoregressive models.ResultsWe found a hump-shaped relationship between AGB and species richness in managed and unmanaged forests. CMW of maximum height was the most important predictor of AGB in both stands, which suggested that the mechanism underlaying the AGB-diversity relationship is the dominance of some highly productive species, supporting the mass-ratio hypothesis. Above-ground biomass was significantly correlated with three of the five functional diversity metrics, CWM maximum height and species richness. Our results show the importance of taking into account spatial autocorrelation in the construction of predictive models to avoid spurious patterns in the AGB-diversity relationship.ConclusionSpecies richness, maximum height, functional richness, functional dispersion and RaoQ indices relate with above-ground biomass production in temperate mixed-species and uneven-aged forests of northern Mexico. These forests show a hump-shaped AGB-species richness relationship. Functional diversity explains better AGB production than classical taxonomic diversity. Community weighted mean traits provide key information to explain stand biomass in these forests, where maximum tree height seems to be a more suitable trait for understanding the biomass accumulation process in these ecosystems. Although the impact of forest management on biodiversity is still debated, it has not changed the AGB-diversity relationships in the forests of the Sierra Madre Occidental, Mexico.

Biological indicators are frequently used to assess the effects of anthropogenic stressors on freshwater ecosystems. The structure of fish communities and their response to stressors have been commonly described by taxonomic richness, diversity and evenness. More recently, functional structure of communities has also been suggested to be a reliable indicator of disturbance. This article aimed at testing whether taxonomic and functional diversity metrics can provide comparable or complementary information on the response of fish communities to eutrophication and abundance of non‐native species in reservoirs. Comparison of the responses of taxonomic and functional diversities to biogeography, habitat and stressors was made in 112 French reservoirs. Widely observed effects of biogeographic and habitat variables on taxonomic and functional diversities were identified. Taxonomic and functional richness metrics notably increased with lake area and temperature respectively. Taxonomic diversity metrics did not respond to any stressor, while all functional diversity metrics were found to be impacted by non‐native species. Eutrophication was further found to decrease the impact of non‐native species on two functional diversity metrics: evenness and divergence. Our study therefore reveals that functional metrics are more sensitive than taxonomic metrics to anthropogenic stressors in the studied reservoirs. Still, the multiple linear regressions tested had overall low explanatory power. Further refinements will thus be needed to use this type of metrics in an impact assessment scheme.

Alaskan Arctic shelf communities are currently experiencing dramatic changes that will likely affect ecosystem functioning of Arctic marine benthic communities. Here, functional diversity based on biological traits was used to assess differences and similarities in ecosystem functioning between 2 shelf systems that are geographically close but vary in many environmental influences: the Arctic Beaufort and Chukchi Sea epibenthic communities. We hypothesized that (1) patterns of functional composition and diversity metrics reflect patterns in taxonomic composition and diversity metrics in these 2 shelf communities; and (2) patterns in functional diversity metrics are distinct between the 2 shelves. We evaluated 9 biological traits (body form, body size, feeding habit, fragility, larval development, living habit, movement, reproductive strategy, sociability) for 327 taxa in 2014 and 2015. For each trait, multiple modalities (specific expressions within a trait) were considered. Patterns in functional diversity metrics on both shelves reflected those in taxonomic diversity metrics. However, shelf communities were more similar in functional- than in taxonomic composition. Beaufort Sea communities had higher functional dissimilarity and functional evenness driven by differences in the modalities within body form, body size, larval development, and reproductive strategy. These traits primarily affect nutrient cycling, energy turnover, and recovery from disturbances, suggesting a stronger potential for future maintenance of ecosystem function, and indicating a more even use of resources in the Beaufort Sea. The combination of functional and taxonomic diversity metrics enabled a comprehensive understanding of how ecological niche space is used and how epibenthic communities function in Alaskan Arctic shelf systems.

While taxonomic metrics are common indicators for assessing impact of acid mine drainage (AMD) on macroinvertebrates, functional diversity metrics are scarcely used. We tested the hypothesis that functional diversity metrics could be used as indicators for assessing impact of AMD on macroinvertebrates. Differences in both taxonomic metrics and functional diversity metrics were examined among sites with varying levels of AMD impact. AMD led to loss of sensitive functional groups and resulted in low functional diversity in the impacted sites. Functional richness, functional Shannon's index and functional Brillouin's index were significantly correlated with all key AMD parameters. Compared to taxonomic metrics, functional diversity metrics had higher correlations with most key AMD parameters. Functional diversity metrics were more informative than taxonomic metrics for assessing impact of AMD on macroinvertebrates since they were more effective at indicating mild or moderate AMD pollution. Functional Shannon's index and functional Brillouin's index were the most precise metrics.

Forest biodiversity world‐wide is affected by climate change, habitat loss and fragmentation, and today 20% of the forest area is located within 100 m of a forest edge. Still, forest edges harbour a substantial amount of terrestrial biodiversity, especially in the understorey. The functional and phylogenetic diversity of forest edges have never been studied simultaneously at a continental scale, in spite of their importance for the forests' functioning and for communities' resilience to future change. We assessed nine metrics of taxonomic, phylogenetic and functional diversity of understorey plant communities in 225 plots spread along edge‐to‐interior gradients in deciduous forests across Europe. We then derived the relative effects and importance of edaphic, stand and landscape conditions on the diversity metrics. Here, we show that taxonomic, phylogenetic and functional diversity metrics respond differently to environmental conditions. We report an increase in functional diversity in plots with stronger microclimatic buffering, in spite of their lower taxonomic species richness. Additionally, we found increased taxonomic species richness at the forest edge, but in forests with intermediate and high openness, these communities had decreased phylogenetic diversity. Functional and phylogenetic diversity revealed complementary and important insights in community assembly mechanisms. Several environmental filters were identified as potential drivers of the patterns, such as a colder macroclimate and less buffered microclimate for functional diversity. For phylogenetic diversity, edaphic conditions were more important. Interestingly, plots with lower soil pH had decreased taxonomic species richness, but led to increased phylogenetic diversity, challenging the phylogenetic niche conservatism concept. Synthesis . Taxonomic, phylogenetic and functional diversity of understorey communities in forest edges respond differently to environmental conditions, providing insight into different community assembly mechanisms and their interactions. Therefore, it is important to look beyond species richness with phylogenetic and functional diversity approaches when focusing on forest understorey biodiversity.

Temporal taxonomic shifts have been documented in bird communities within protected areas. However, the potential impact of these changes on functional diversity and phylogenetic diversity remains poorly understood. In this study, we monitored bird communities in Qiyunshan National Nature Reserve in southern China for nine years (2014-2022). We examined temporal trends in taxonomic, functional and phylogenetic diversity metrics and compared observed phylogenetic diversity values with expected values to determine the mechanisms driving community assembly. Additionally, we evaluated the temporal trend of beta diversity. A total of 118 bird species were recorded, with the dominant species including Chestnut Bulbul (Hemixoscastanonotus), Grey-cheeked Fulvetta (Alcippemorrisonia) and Great Tit (Parusmajor). We found that species turnover was the principal driver of temporal variations in species composition. However, species richness, functional diversity and phylogenetic diversity fluctuated throughout the study period, showing no clear trend of increase or decrease. Our findings indicate that the composition of bird communities is shaped by environmental filtering and neutral processes. The changes in taxonomics may be due to changes in the availability of resources and random substitution arising from the dispersion process. Protected areas have the potential to attract new bird species with similar functional and genetic relationships to those already present. This leads to minimal changes to overall functional and phylogenetic diversity, suggesting a degree of functional redundancy amongst species that are replaced or added. Notably, we observed a persistent increase in species loss over time, raising concerns about the potential impact on the future functional stability of the system. We highlight that the asynchronous patterns of taxonomic, functional and phylogenetic diversity in birds emphasise the importance of multidimensional diversity metrics. Consequently, we suggest that functional and phylogenetic diversity should be regarded as essential indicators alongside species richness when evaluating conservation outcomes in nature reserves. This approach provides a more comprehensive understanding of the complexity of ecological communities and provides information for more effective conservation strategies.

Background and aims - Recent methodological and theoretical advances in community ecology have allowed more robust exploration of complementary facets of biodiversity in plant communities. Focusing on semi-natural permanent grasslands of the French Jura Mountains, we assessed how taxonomic, phylogenetic and functional diversity metrics vary among three phytosociological vegetation units. Methods - We selected a sample of 135 relevés out of a phytosociological database, depicting three phytosociological orders (Brometalia erecti, Arrhenatheretalia elatioris and Trifolio repentis-Phleetalia pratensis) and including 381 vascular plant species. We built a phylogenetic tree based on sequences of two genes encoding chloroplast proteins, from which we computed phylogenetic diversity metrics that we compared to various taxonomic, single-trait and multi-trait functional metrics, including communityweighted means of functional traits (CWMs). Key results - Most diversity metrics and CWMs significantly differed among vegetation units. Within each facet of biodiversity, the different metrics showed complementary results. Moreover, even when considering diversity metrics comparable in mathematical terms, i.e. based on Rao quadratic entropy, the results were largely non-redundant among the facets of biodiversity. Phylogenetic diversity and multi-trait functional diversity show opposite responses to vegetation units, as well as a low phylogenetic signal. These two results suggest that phylogenetic diversity cannot be used as a simple proxy for functional diversity. Conclusion - This study highlights the importance of taking into consideration different facets for a better understanding of biodiversity. In particular, phylogenetic and functional facets appear highly informative, and could thus be used in addition to taxonomic diversity metrics as indicators of conservation value. © 2014 Botanic Garden Meise and Royal Botanical Society of Belgium.

The transformation of natural habitats for farming is a major driver of tropical biodiversity loss. To mitigate impacts, two alternatives are promoted: intensifying agriculture to offset protected areas (land sparing) or integrating wildlife‐friendly habitats within farmland (land sharing). In the montane and dry tropics, phylogenetic and functional diversity, which underpin evolutionary values and the provision of ecosystem functioning and services, are best protected by land sparing. A key question is how these components of biodiversity are best conserved in the more stable environments of lowland moist tropical forests. Focusing on cattle farming within the Colombian Amazon, we investigated how the occupancy of 280 bird species varies between forest and pasture spanning gradients of wildlife‐friendly features. We then simulated scenarios of land‐sparing and land‐sharing farming to predict impacts on phylogenetic and functional diversity metrics. Predicted metrics differed marginally between forest and pasture. However, community assembly varied significantly. Wildlife‐friendly pastures were inadequate for most forest‐dependent species, while phylogenetic and functional diversity indices showed minimal variation across gradients of wildlife‐friendly features. Land sparing consistently retained higher levels of Faith's phylogenetic diversity (~30%), functional richness (~20%) and evolutionarily distinct lineages (~40%) than land sharing, and did so across a range of landscape sizes. Securing forest protection through land‐sparing practices remains superior for conserving overall community phylogenetic and functional diversity than land sharing. Synthesis and applications: To minimise the loss of avian phylogenetic diversity and functional traits from farming in the Amazon, it is imperative to protect large blocks of undisturbed and regenerating forests. The intensification required within existing farmlands to make space for spared lands while meeting agricultural demand needs to be sustainable, avoiding long‐term negative impacts on soil quality and other ecosystem services. Policies need to secure the delivery of both actions simultaneously.

The idea behind multimetric indices is to integrate information from several metrics to provide a general classification of water bodies without losing the particularities of each individual metric. Historically, multimetric indices use information on richness, taxon sensitivity, and taxonomic diversity. Recently, functional and phylogenetic diversity proved to capture different dimensions of biodiversity. Here we asked if these new metrics provide complementary information to classical metrics and should be included in multimetric indices. We used an index construction protocol based on statistical filters to test candidate metrics for range, sensitivity, and redundancy. We used macroinvertebrate data from streams located in a Savanna region of Brazil, encompassing a gradient of impact, to test our ideas. Of 41 candidate metrics, functional dispersion of functional diversity, mean nearest neighbor distance of phylogenetic diversity, and four classical metrics passed the filter selection composing the final multimetric index. Our results indicated that functional and phylogenetic diversity metrics indeed responded to environmental impact and complemented the information provided by classical metrics. We suggest that future indices should consider including new metrics of functional and phylogenetic diversity to properly monitor multiple dimensions of biodiversity.

Mammal functional diversity and habitat heterogeneity: Implications for hominin habitat reconstruction

Characterising changes in functional diversity at large spatial scales provides insight into the impact of human activity on ecosystem structure and function. However, the approach is often based on trait data sets that are incomplete and unrepresentative, with uncertain impacts on functional diversity estimates. To address this knowledge gap, we simulated random and biased removal of data from three empirical trait data sets: an avian data set (9579 species), a plant data set (2185 species) and a crocodilian data set (25 species). For these data sets, we assessed whether functional diversity metrics were robust to data incompleteness with and without using imputation to fill data gaps. We compared two metrics each calculated with two methods: functional richness (calculated with convex hulls and trait probabilities densities) and functional divergence (calculated with distance‐based Rao and trait probability densities). Without imputation, estimates of functional diversity (richness and divergence) for birds and plants were robust when 20%–70% of species had missing data for four out of 11 and two out of six continuous traits, respectively, depending on the severity of bias and method used. However, when missing traits were imputed, functional diversity metrics consistently remained representative of the true value when 70% of bird species were missing data for four out of 11 traits and when 50% of plant species were missing data for two out of six traits. Trait probability densities and distance‐based Rao were particularly robust to missingness and bias when combined with imputation. Convex hull‐based estimations of functional richness were less reliable. When applied to a smaller data set (crocodilians, 25 species), all functional diversity metrics were much more sensitive to missing data. Expanding global morphometric data sets to represent more taxa and traits, and to quantify intraspecific variation, remains a priority. In the meantime, our results show that widely used methods can successfully quantify large‐scale functional diversity even when data are missing for half of species, provided that missing traits are estimated using imputation. We recommend the use of trait probability densities or distance‐based Rao when working with large incomplete data sets and filling data gaps with imputation.