Should phylogenetic and functional diversity metrics compose macroinvertebrate multimetric indices for stream biomonitoring?

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.

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.

Summary 1. Although species richness is the most common metric for biodiversity, it is important to consider that among-species differences matter for many important processes such as ecosystem functioning and assembly patterns. Thus, alternative metrics have been proposed to measure phylogenetic (PD) and functional diversity (FD). 2. Here, we analysed the correlation structure and the geographic patterns of different phylogenetic and functional diversity metrics using 1000 Carnivora (mammals) assemblages distributed world-wide. We also proposed a general approach to estimate these metrics based on phylogenetic eigenvector regressions. 3. We showed that the cumulative variance of phylogenetic eigenvectors within assemblages converges to one metric of phylogenetic clustering, the phylogenetic species variability (PSV), which was recently proposed in the literature. Phylogenetic eigenvectors have also been used to model trait variation (i.e. body mass); therefore, the same reasoning allows us to decouple trait diversity (i.e. body mass) into phylogenetic [FD(P)] and specific [FD(S)] components. The cumulative variance of these components within assemblages, for a single trait or multiple traits, offers a direct estimate of the evolutionary and ecological components of functional variation. Our results indicated that the variance of the phylogenetic component of body mass [FD(P)] estimated within assemblages was highly correlated with a common measure of functional diversity (Rao’s Q). 4. Our general approach based on phylogenetic eigenvectors provides similar results when compared to other metrics of FD and PD, but also has some important advantages. First, it allows a direct interpretation of at which hierarchical level in the phylogeny (expressed by different sets of eigenvectors) the patterns in PD and FD appear. Secondly, phylogenetic components of FD can be analysed directly because of the partition of functional diversity into FD(P) and FD(S), so it eliminates the need to generate ‘a posteriori’ phylogenetic correlations between PD and FD based on independently derived metrics, as well as of these metrics with other components of environmental variation.

Passive rewilding is increasingly seen as a promising tool to counterbalance biodiversity losses and recover native forest ecosystems. One key question, crucial to understanding assembly processes and conservation issues underlying land-use change, is the extent to which functional and phylogenetic diversity may recover in spontaneous recent woodlands. Here, we compared understorey plant communities of recent woodlands (which result from afforestation on agricultural lands during the 20th century) with those of ancient forests (uninterrupted for several centuries) in a hotspot of farmland abandonment in western Europe. We combined taxonomic, functional, and phylogenetic diversity metrics to detect potential differences in community composition, structure (richness, divergence), conservation importance (functional originality and specialization, evolutionary distinctiveness) and resilience (functional redundancy, response diversity). The recent and ancient forests harbored clearly distinct compositions, especially regarding the taxonomic and phylogenetic facets. Recent woodlands had higher taxonomic, functional and phylogenetic richness and a higher evolutionary distinctiveness, whereas functional divergence and phylogenetic divergence were higher in ancient forests. On another hand, we did not find any significant differences in functional specialization, originality, redundancy, or response diversity between recent and ancient forests. Our study constitutes one of the first empirical pieces of evidence that recent woodlands may spontaneously regain plant communities phylogenetically rich and functionally resilient, at least as much as those of ancient relict forests. As passive rewilding is the cheapest restoration method, we suggest that it should be a very useful tool to restore and conserve native forest biodiversity and functions, especially when forest areas are restricted and fragmented.

Concave trade-off curves between crop production and taxonomic, functional and phylogenetic diversity of birds

Macrophyte communities have major role in the functioning of freshwater ecosystems. However, there is gap in knowledge about how natural and anthropogenic hydro-morphological disturbances affect their functional diversity and trait structure, particularly in the temperate large rivers. In this study we investigated the effect of hydro-morphology on functional diversity and trait structure of macrophyte communities in the middle section of the Danube course. We collected macrophyte and environmental data from 947 sampling units in the main river channel and connected side waterbodies. We extracted data on 18 traits with 65 trait states and calculated seven functional diversity metrics and cumulative weighted means of trait states (CWMs). We applied redundancy analysis (RDA) to investigate the response of functional diversity metrics to the environmental variables, and Variation Partitioning to determine whether natural, or anthropogenic subset of hydro-morphological factors is more important predictor of functional diversity. To relate CWMs and environmental variables, we performed RLQ and fourth-corner analysis, followed by false discovery rate procedure. Hydro-morphological variables explained 36.7% of the variability in the functional diversity metrics. Combined effect of two subsets of environmental variables explained largest part of the variability in functional diversity metrics. Six associations between traits and environmental variables were found. We found that functional diversity metrics indicate prevailing ecological processes, from environmental to biotic filtering, along the natural—anthropogenic hydro-morphological gradient. We concluded that functional diversity metrics are potentially useful tools in the identification of the causes of ecological degradation, and could be applied in river bioassessments and management.

Biodiversity has been linked to reduced disease transmission through the dilution effect process. Traditional ecological measures of biological diversity, such as species richness, are most commonly used to test for the dilution effect. However, such metrics of species diversity do not consider the evolutionary relationship between species, which has important implications for host immune processes and disease transmission. Phylogenetic diversity incorporates the evolutionary relationships of a wildlife community. Host reservoir competency is partly determined by their capacity to mount effective immune responses, which may be phylogenetically determined. As a result, phylogenetic diversity may be a better metric to evaluate the relationship between host diversity and disease transmission, given that closely related species may have more similar pathogen competencies than distantly related ones. Few studies have examined the relationship between phylogenetic diversity and disease transmission, particularly in vector‐borne transmission systems. This study seeks to quantify phylogenetic diversity in the western United States Lyme disease system, where the causal agent Borrelia burgdorferi is vectored by the western black‐legged tick, Ixodes pacificus. We empirically measured mammalian diversity and tick data over seven years. We collected data on ticks, host community, and infection prevalence with Borrelia burgdorferi and constructed generalized linear mixed‐effect models to evaluate the utility of phylogenetic diversity in predicting the prevalence of a tick‐borne pathogen. We found that phylogenetic diversity metrics improved our disease prediction models. Predictions of the overall density and infection prevalence of ticks were improved by the addition of phylogenetic metrics, whereas the density of infected nymphs was solely predicted by a phylogenetic metric over traditional species diversity or richness. Our study found that phylogenetic diversity improves statistical predictions of the Lyme disease pathogen and entomological risk in the western United States and may be informative in other contexts and systems as well.

Understanding the mechanisms that influence the assembly of natural communities has become a central issue in ecological studies, especially because of the influence of diversity on ecosystem functioning. These mechanisms may be related to niche and neutral processes. Niche-related processes include selection imposed by the abiotic environment and biotic interactions, whereas neutral effects are related to chance or historical events. Mountain ecosystems are among the most suitable models for unraveling the interactions between the facets of biodiversity. The overall aim of this project was to understand the assembly processes of alpine and forest plant communities through phylogenetic and functional diversity across altitudinal gradients in tropical mountains. To respond to this approach, we selected areas from several tropical mountains worldwide. We used lists with altitude records from three tropical montane mountains of tropical ecosystems: Mount Puracé, Colombia; Mount Kilimanjaro, Tanzania; and Mount Haleakalā, Hawaii, USA (CAP. 1). In addition, six sampling sites were established along an elevation gradient of (3200-4100 m). At each station, 10 plots measuring 2.5 m x 4 m were established (CAP. 2 and 3). In addition, 28 isolated individuals of Espeletia lopezii (Asteraceae) were selected; a 70 cm diameter metal ring was centered on each caulescent rosette. In addition, 28 rings were established in the open areas (control) (CAP. 4). The alpha taxonomic diversity was estimated using Hill's numbers (q=0, q=1, q=2) (CAP. 2 and 4). For phylogenetic diversity, six phylogenetic metrics were calculated: lineage diversity as the total length of the phylogenetic branch (PD), mean pairwise phylogenetic distance (MPD), mean nearest taxon phylogenetic distance (MNTD), and standardized effect size of these metrics (CAP. 1, 2 and 4). To determine the functional responses that drive the assembly of communities along the elevation gradient, five functional traits were measured: leaf area, leaf length, leaf thickness, leaf dry matter content, and maximum plant height. The weighted community mean (CWM) of the traits and functional diversity (FD) were estimated (CAP. 3). Different statistical models were used to test the main effects of altitude and soil depth on taxonomic, phylogenetic, and functional metrics. In the three tropical mountains, an environmental filtering effect was observed with increasing altitude, causing phylogenetic clustering, decreasing phylogenetic diversity, and decreasing species richness. The decreasing phylogenetic distances between close relatives are congruent with neo-endemism, suggesting recent diversification of plants at high altitudes in tropical mountains, possibly driven by geographical isolation and environmental heterogeneity (CAP. 1). In Chapter 2, the results showed that as soil depth decreased and altitude increased, páramo plant communities showed a general pattern of decreasing phylogenetic diversity. These results are consistent with the general expectation that community assemblage attributes become more closely related as stressful environmental conditions increase along a gradient. In Chapter 3, the results showed that several functional traits (CWM) and several indices of functional diversity varied significantly along the altitude and soil gradient in the area. Three of the five functional traits showed the potential to describe how the functional composition of páramo communities responded to increasing environmental severity along these environmental gradients. The two functional diversity indices, FDis and FRic, significantly decreased with increasing elevation and decreasing soil depth. In Chapter 4, the vegetation under the canopy of the facilitator plants (E. lopezii) was found to have a positive impact on taxonomic diversity, compared to the control areas. Regarding phylogenetic diversity, the dominant pattern observed was mainly random. These results suggest that, at these altitudes, the metacommunity is strongly filtered by climatic and edaphic factors, and despite the benefits of the facilitation exerted by stem rosettes, it is difficult to detect a pattern of phylogenetic overdispersion. In Chapter 5, as a general trend, a greater number of species were found in locations at higher altitudes, decreasing in locations at lower altitudes, and where climatic seasonality is more marked and filters out species from lineages that are less tolerant to stressful environments. Nitrogen-fixing Fabaceae species were prominent among the important species, especially at low altitudes and more stressful sites. Keywords: Tropical mountains, altitudinal gradient, phylogenetic diversity, functional diversity, plant-plant interaction, community assembly.

South America has undergone complex environmental and geological events that ultimately made it the most climatically and biodiverse continent on the planet, including anuran amphibians. Though biogeographical studies with anurans in South America have been continuously performed during the last decades, most of them focus on specific clades and/or regions. Moreover, no systematic compilation has been performed since the first synthesis of patterns of amphibian distribution, conducted by William E. Duellman by the end of the twentieth century. Here, we perform a systematic species survey of anurans in South America that allow us to revisit previously documented biogeographic patterns of species distribution (e.g., geographical patterns of species richness, species range size) and uncover novel biogeographic patterns, such as mapping anuran phylogenetic and functional diversity metrics across the continent. In summary, this book is made up of seven chapters spanning a wide range of topics that integrate herpetology, biogeography, ecology, and conservation biology. This chapter provides an overview of South American anurans and details the methodology used to generate the species list used in all subsequent chapters, as well as how different environmental variables were gathered and processed to be assessed as potential predictors of the biodiversity metrics explored through this book.

Climate change and anthropogenic alteration of landscapes negatively impact the abundance and species diversity of plant and animal communities worldwide. Much less is known about the effects on phylogenetic diversity and community functioning. Here we use long‐term butterfly data (1980–2022) from the Austrian Alps along an elevation gradient. We assessed how communities adjust structures and functionality to increasing temperatures, and how these changes are linked to trait expression and community functioning. Species diversity decreased at low and intermediate altitudes, and increased at high ones. Functional diversity was lower than expected by a random model at intermediate and high altitudes and increased with time at high, but not at intermediate and low altitudes. Phylogenetic diversity did not show significant temporal trends at low altitude, but increased with time at intermediate and high altitudes. Multifunctionality significantly decreased at intermediate and high altitudes and was not significantly correlated with functional diversity, but was negatively correlated with phylogenetic diversity. We argue that the ongoing homogenisation of Alpine butterfly communities strongly affects species, functional and phylogenetic diversity. The assessment of species richness and diversity alone, as provided by common species surveys, might give a false impression about the state and functional diversity of Alpine insect communities in the course of climate change. The directions of faunal changes heavily depend on altitude and therefore on specific climatic conditions. Higher altitudes face decreasing butterfly multifunctionality despite of increasing species richness due to climate induced altitudinal up‐hill shifts of many species. We conclude that studies on community time series should include phylogenetic and functional diversity besides of being focused on richness and endangerment. Red lists might be extended by categories on functional importance and phylogenetic distinctness.

How much matching there is in functional, phylogenetic and taxonomic optima of epiphytic macrolichen communities along a European climatic gradient?

Biocrusts are major contributors to dryland diversity, functioning, and services. However, little is known about how habitat degradation will impact multiple facets of biocrust diversity and measurable functional traits. We evaluated changes in taxonomic, functional, and phylogenetic diversity of biocrust-forming lichens along a habitat degradation gradient related to the presence of linear infrastructure (i.e., a road) and a profound agricultural driven transformation. To do so, we selected 50 remnants of a Mediterranean shrubland. We considered several surrogates of habitat quality and causal disturbance on the various diversity facets of biocrusts by using structural equation modeling, hypothesizing that habitat degradation primarily affects functional diversity, which in turn regulates changes in taxonomic and phylogenetic diversities, and also that taxonomic and phylogenetic diversities are coupled. Fragment connectivity, distance to linear infrastructure (i.e., a road) and, particularly, soil fertility (i.e., soil P concentration), had mostly negative effects on biocrust functional diversity, which in turn affected both taxonomic and phylogenetic diversities. However, we found no direct effects of habitat degradation variables on the taxonomic and phylogenetic diversities. We also found that increases in phylogenetic diversity had a positive effect on taxonomic diversity along the habitat degradation gradient. Our results indicate that functional diversity of biocrusts is strongly affected by habitat degradation, which may profoundly alter their contribution to ecosystem functioning and services. Furthermore, functional diversity regulates the response of biocrust taxonomic and phylogenetic diversity to habitat degradation. These findings indicate that habitat degradation alters and simplifies the diversity of functional traits of biocrust-forming lichens, leading to biodiversity loss, with important consequences for the conservation of global drylands biodiversity.

Context The spectral variation hypothesis (SVH) suggests that remotely sensed spectral variation correlates with biodiversity. However, conflicting evidence has been presented regarding the SVH, it has not been widely tested in high-latitude landscapes, and its assessments mainly employ species richness, omitting other aspects of biodiversity. Objectives We examine plant diversity, spectral variation and the SVH across a northern boreal landscape utilizing high-spatial-resolution satellite imagery. We incorporate taxonomic, phylogenetic, functional, and indicator-based plant diversity metrics and visualize spatial differences between proposed plant diversity proxies. Methods We surveyed plant community composition in peatlands, forests, and tundra in northwest Finland and calculated 14 diversity metrics for 355 sites. We compared observed diversity with (1) spatial, (2) temporal, (3) multivariate spatiotemporal spectral variation, and (4) multivariate machine learning. We used statistical relationships and machine learning models to create continuous maps of plant diversity. Results While forests were generally more biodiverse than peatlands or tundra, each of these ecosystems obtained the highest values in some metrics. Spectral variation had positive correlations (0.14–0.72) across most dimensions of plant diversity, but relationships varied between ecosystems and were sometimes insignificant or negative. For example, plant diversity in forests was largely uncorrelated with spatial spectral variation. Temporal spectral variation was more strongly correlated with plant diversity than spatial spectral variation in a majority (41 of 56) of cases. Conclusions While spectral variation was usually correlated with plant diversity, correlations varied among peatlands, forests, and tundra. Thus, methods for estimating plant diversity should be tailored to different biodiversity metrics and ecosystem types.

AimTo explore the impact of island area and isolation on multiple dimensions of ant biodiversity (taxonomic, phylogenetic and functional diversity) and the underlying processes of community assembly on islands.LocationThousand Island Lake, Zhejiang, China, created by dam construction in 1959.TaxonAnts.MethodsWe sampled ants on 33 islands, built a species‐level phylogenetic tree and measured five morphological traits of all species collected to estimate taxonomic, phylogenetic and functional diversity. We used multiple linear regression models and null models to examine the relationships between diversity metrics and island variables (area and isolation).ResultsWe recorded 97 ant species on the study islands. We verified positive diversity–area relationships for species richness, phylogenetic diversity and functional diversity. However, although functional and phylogenetic community structure were indistinguishable from random communities, phylogenetic structure tended to be clustered, whereas functional structure tended to be overdispersed. Additionally, we found the structure of ant communities shifted from phylogenetic and functional clustering on smaller islands to phylogenetic and functional overdispersion on larger islands.Main conclusionsOur results support the hypothesis that environmental filtering is the dominant process structuring ant communities on smaller islands, and that competitive exclusion becomes more important on larger islands. Thus, island area acts as an important filter even though ant community structure on the study islands was indistinguishable from random communities. Moreover, our results show that environmental filtering influences phylogenetic community structure of ants, whereas competitive exclusion influences functional community structure of ants. These findings highlight the need to examine both phylogenetic and functional diversity in order to understand the mechanisms that govern the assembly of natural communities on islands.

1. Despite the fact that insects are suffering a global decline, little is known about the extent to which species loss affects functional diversity. Thus, to understand the relationship between taxonomic and functional diversity metrics, we focused on saproxylic beetles, which perform vital functions in forest ecosystems.2. Beetles were collected monthly for a year using flight interception traps placed in three protected areas of mature evergreen MediterraneanQuercusforests. Five morphological traits, one phenological trait, and one physiological surrogate trait were measured, and trophic guild identities were determined. Two taxonomic and six functional metrics were assessed to determine their relationships.3. Taxonomic and functional diversity patterns, as well as trait patterns, differed depending on the protected areas, as they were influenced by habitat and microhabitat characteristics. Generally, a high number of species tended to support high values of functional richness, but did not ensure high values of functional redundancy, thus affecting the resilience of communities.4. A 5% of species loss strongly affected the functional redundancy of communities, making them more vulnerable. Functional richness, however, was not affected, since it was associated with a high number of redundant species. Thus, the way species loss affected communities is highly dependent on the presence of rare or redundant species.5. Taxonomic and functional diversity metrics should be used as complementary tools for conservation purposes. In this way, the comparative analysis of taxonomic and functional patterns may help to predict the vulnerability of saproxylic assemblages to changes or disturbances.