Distance decay 2.0 : a global synthesis of taxonomic and functional turnover in ecological communities

Aim: Understanding the variation in community composition and species abundances (i.e., β-diversity) is at the heart of community ecology. A common approach to examine β-diversity is to evaluate directional variation in community composition by measuring the decay in the similarity among pairs of communities along spatial or environmental distance. We provide the first global synthesis of taxonomic and functional distance decay along spatial and environmental distance by analysing 148 datasets comprising different types of organisms and environments. Location: Global. Time period: 1990 to present. Major taxa studied: From diatoms to mammals. Method: We measured the strength of the decay using ranked Mantel tests (Mantel r) and the rate of distance decay as the slope of an exponential fit using generalized linear models. We used null models to test whether functional similarity decays faster or slower than expected given the taxonomic decay along the spatial and environmental distance. We also unveiled the factors driving the rate of decay across the datasets, including latitude, spatial extent, realm and organismal features. Results: Taxonomic distance decay was stronger than functional distance decay along both spatial and environmental distance. Functional distance decay was random given the taxonomic distance decay. The rate of taxonomic and functional spatial distance decay was fastest in the datasets from mid-latitudes. Overall, datasets covering larger spatial extents showed a lower rate of decay along spatial distance but a higher rate of decay along environmental distance. Marine ecosystems had the slowest rate of decay along environmental distances. Main conclusions: In general, taxonomic distance decay is a useful tool for biogeographical research because it reflects dispersal-related factors in addition to species responses to climatic and environmental variables. Moreover, functional distance decay might be a cost-effective option for investigating community changes in heterogeneous environments

Distance decay 2.0 – A global synthesis of taxonomic and functional turnover in ecological communities

Trabajo elaborado por más de cincuenta autores.Aim: Understanding the variation in community composition and species abundances (i.e., β-diversity) is at the heart of community ecology. A common approach to examine β-diversity is to evaluate directional variation in community composition by measuring the decay in the similarity among pairs of communities along spatial or nvironmental distance. We provide the first global synthesis of taxonomic and functional distance decay along spatial and environmental distance by analysing 148 datasets comprising different types of organisms and environments. Location: Global.Time period: 1990 to present. Major taxa studied: From diatoms to mammals. Method: We measured the strength of the decay using ranked Mantel tests (Mantel r) and the rate of distance decay as the slope of an exponential fit using generalized linear models. We used null models to test whether functional similarity decays faster or slower than expected given the taxonomic decay along the spatial and environmental distance. We also unveiled the factors driving the rate of decay across the datasets, including latitude, spatial extent, realm and organismal features. Results: Taxonomic distance decay was stronger than functional distance decay along both spatial and environmental distance. Functional distance decay was random given the taxonomic distance decay. The rate of taxonomic and functional spatial distance decay was fastest in the datasets from mid-latitudes. Overall, datasets covering larger spatial extents showed a lower rate of decay along spatial distance but a higher rate of decay along environmental distance. Marine ecosystems had the slowest rate of decay along environmental distances. Main conclusions: In general, taxonomic distance decay is a useful tool for biogeographical research because it reflects dispersal-related factors in addition to species responses to climatic and environmental variables. Moreover, functional distance decay might be a cost-effective option for investigating community changes in heterogeneous environments

Editorial : Biodiversity in a changing world: How do species traits reflect anthropogenic changes in aquatic ecosystems?

Peer reviewe

Clumpy coexistence in phytoplankton : the role of functional similarity in community assembly

Emergent neutrality (EN) suggests that species must be sufficiently similar or sufficiently different in their niches to avoid interspecific competition. Such a scenario results in a transient pattern with clumps and gaps of species abundance along the niche axis (e.g. represented by body size). From this perspective, clumps are groups of coexisting species with negligible fitness differences and stochastic abundance fluctuations. Plankton is an excellent model system for developing and testing ecological theories, especially those related to size structure and species coexistence. We tested EN predictions using the phytoplankton community along the course of a tropical river considering 1) body size structure, 2) functional clustering of species in terms of morphology-based functional groups (MBFG) and 3) the functional similarity among species concerning their functional traits. Two main clumps in the body size axis (clump I and II) were conspicuous through time and were detected in different stretches of the river. Clump I comprised medium-sized species from the MBFGs IV, V and VI while clump II included large-bodied species from the MBFGs V and VI. Pairwise differences in species biovolume correlated with species functional similarity when the whole species pool was considered, but not among species within the same clump. Although clumps comprised multiple MBFGs, the dominant species within the clump belonged always to the same MBFG. Also, within-clump species biovolume increased with functional distinctiveness considering both seasons and stretches, except the lower course. These results suggest that species within clumps behave in a quasi-neutral state, but even minor shifts in trait composition may affect species biovolume. Our findings point that EN belongs to the plausible mechanisms explaining community assembly in river ecosystems.Peer reviewe

Downstream transport processes modulate the effects of environmental heterogeneity on riverine phytoplankton

Environmental heterogeneity (EH) in space and time promotes niche-partition, which leads to high variation in biological communities, such as in algae. In streams, EH is highly related to the intensity of the water flow and may lead to community variation mainly during the low flow conditions. Despite the wide knowledge on the responses of phytoplankton communities to EH in lentic and semi-lentic systems, studies of riverine phytoplankton community variation are still scarce. Here, we first investigated the relationship between phytoplankton community variation and EH in different courses of the river and between seasons. We expected that under low or intermediate flow conditions, there is a positive correlation between community variation and EH. Alternatively, we did not expect any relationship between EH and community variation under high flow condition because stronger downstream transport would mask environmental filtering. We sampled nine sites monthly (May 2012 to April 2013) in a tropical river of Brazilian Southeast. We calculated EH from abiotic data whereas for community variation, here community distinctiveness (CD), we used Sorensen (CDSor) and Bray-Curtis (CDBray) dissimilarities. Differences in EH, CDSor and CDBray were tested at between-season and among-course levels. We found lower distinctiveness during the dry season when EH was the highest. Contrastingly, phytoplankton CD was the highest even when EH was low during the wet season. We found that this pattern raised from the increasing in individuals dispersal during the wet season, promoting mass effects. Finally, our results thus reject the first hypothesis and show a negative relationship between EH and distinctiveness. However, results support our alternative hypothesis and show that during the wet season, distinctiveness is not driven by EH. These results provide new insights into how EH drives community variation, being useful for both basic research about riverine algal communities and biomonitoring programs using phytoplankton communities as bioindicators. (C). 2019 Elsevier B.V. All rights reserved.Peer reviewe

Calculating functional diversity metrics using neighbor-joining trees

The study of functional diversity (FD) provides ways to understand phenomena as complex as community assembly or the dynamics of biodiversity change under multiple pressures. Different frameworks are used to quantify FD, either based on dissimilarity matrices (e.g. Rao entropy, functional dendrograms) or multidimensional spaces (e.g. convex hulls, kernel-density hypervolumes), each with their own strengths and limits. Frameworks based on dissimilarity matrices either do not enable the measurement of all components of FD (i.e. richness, divergence, and regularity), or result in the distortion of the functional space. Frameworks based on multidimensional spaces do not allow for comparisons with phylogenetic diversity (PD) measures and can be sensitive to outliers.We propose the use of neighbor-joining trees (NJ) to represent and quantify FD in a way that combines the strengths of current frameworks without many of their weaknesses. Importantly, our approach is uniquely suited for studies that compare FD with PD, as both share the use of trees (NJ or others) and the same mathematical principles.We test the ability of this novel framework to represent the initial functional distances between species with minimal functional space distortion and sensitivity to outliers. The results using NJ are compared with conventional functional dendrograms, convex hulls, and kernel-density hypervolumes using both simulated and empirical datasets.Using NJ, we demonstrate that it is possible to combine much of the flexibility provided by multidimensional spaces with the simplicity of tree-based representations. Moreover, the method is directly comparable with taxonomic diversity (TD) and PD measures, and enables quantification of the richness, divergence and regularity of the functional space

Functional convergence underground? The scale‐dependency of community assembly processes in European cave spiders

Aim Quantifying the relative contribution of environmental filtering versus limiting similarity in shaping communities is challenging because these processes often act simultaneously and their effect is scale-dependent. Focusing on caves, island-like natural laboratories with limited environmental variability and species diversity, we tested: (i) the relative contribution of environmental filtering and limiting similarity in determining community assembly in caves; (ii) how the relative contribution of these driving forces changes along environmental gradients. Location Europe. Time period Present. Major taxa studied Subterranean spiders. Methods We used data on distribution and traits for European cave spiders (n = 475 communities). We estimated the trait space of each community using probabilistic hypervolumes, and obtained estimations of functional richness independent of the species richness of each community via null modelling. We model functional diversity change along environmental gradients using generalized dissimilarity modelling. Results Sixty-three percent of subterranean spider communities exhibited a prevalence of trait underdispersion. However, most communities displayed trait dispersion that did not depart significantly from random, suggesting that environmental filtering and limiting similarity were both exerting equally weak or strong, yet opposing influences. Overdispersed communities were primarily concentrated in southern latitudes, particularly in the Dinaric karst, where there is greater subterranean habitat availability. Pairwise comparisons of functional richness across caves revealed these effects to be strongly scale-dependent, largely varying across gradients of cave development, elevation, precipitation, entrance size and annual temperature range. Conversely, geographical distance weakly affected trait composition, suggesting convergence in traits among communities that are far apart. Main conclusions Even systems with stringent environmental conditions maintain the potential for trait differentiation, especially in areas of greater habitat availability. Yet, the relative influence of environmental filtering and limiting similarity change with scale, along clear environmental gradients. The interplay of these processes may explain the assembly of species-poor subterranean communities displaying high functional specialization

Ciliate Communities Respond via Their Traits to a Wastewater Treatment Plant With a Combined UASB-Activated Sludge System

Assessing functional diversity of communities is an efficient method to link community composition to ecosystem quality. Still, studies using functional traits of microeukaryote ciliate communities in biological wastewater treatment plants are lacking. The present work explores the functional diversity of the ciliate protist community in a wastewater treatment plant (WWTP) operating with a combined UASB-activated sludge system, and specifically to: 1) investigate the taxonomic and functional composition of the ciliate communities over time; 2) compare taxonomic and functional diversity indices with regard to its applicability in WWPS; 3) assess the relationship between the ciliate community's functional composition and the WWTPs temporal conditions; and 4) investigate the potential use of functional diversity as an indicator of WWTP efficiency. Totally, we recorded 21 ciliate species throughout 37 samplings. The number of species was low compared to other plants. Bacterivorous and flake-forming species were the main functional strategies found in the samples. The correlation between taxonomic and functional richness was significant, indicating a functionally redundant community. There was a correlation between the Simpson and Rao's quadratic entropy indexes suggesting that loss of taxonomic diversity leads to a loss of functional diversity. The homogeneity of the measured physical and chemical data led to functional homogenization and redundancy (homogenous CWM) of the ciliate community. The functional diversity is positively correlated with parameters of removal efficiency, indicating a promising application in WWTPs. Future studies will broaden knowledge on functional diversity in biological wastewater treatment systems, this being a first step with the unprecedented application of this methodology in artificial ecosystems.Peer reviewe

A trait database and updated checklist for European subterranean spiders

Species traits are an essential currency in ecology, evolution, biogeography, and conservation biology. However, trait databases are unavailable for most organisms, especially those living in difficult-to-access habitats such as caves and other subterranean ecosystems. We compiled an expert-curated trait database for subterranean spiders in Europe using both literature data (including grey literature published in many different languages) and direct morphological measurements whenever specimens were available to us. We started by updating the checklist of European subterranean spiders, now including 512 species across 20 families, of which at least 192 have been found uniquely in subterranean habitats. For each of these species, we compiled 64 traits. The trait database encompasses morphological measures, including several traits related to subterranean adaptation, and ecological traits referring to habitat preference, dispersal, and feeding strategies. By making these data freely available, we open up opportunities for exploring different research questions, from the quantification of functional dimensions of subterranean adaptation to the study of spatial patterns in functional diversity across European caves.Peer reviewe

A protocol for reproducible functional diversity analyses

The widespread use of species traits in basic and applied ecology, conservation and biogeography has led to an exponential increase in functional diversity analyses, with > 10 000 papers published in 2010-2020, and > 1800 papers only in 2021. This interest is reflected in the development of a multitude of theoretical and methodological frameworks for calculating functional diversity, making it challenging to navigate the myriads of options and to report detailed accounts of trait-based analyses. Therefore, the discipline of trait-based ecology would benefit from the existence of a general guideline for standard reporting and good practices for analyses. We devise an eight-step protocol to guide researchers in conducting and reporting functional diversity analyses, with the overarching goal of increasing reproducibility, transparency and comparability across studies. The protocol is based on: 1) identification of a research question; 2) a sampling scheme and a study design; 3-4) assemblage of data matrices; 5) data exploration and preprocessing; 6) functional diversity computation; 7) model fitting, evaluation and interpretation; and 8) data, metadata and code provision. Throughout the protocol, we provide information on how to best select research questions, study designs, trait data, compute functional diversity, interpret results and discuss ways to ensure reproducibility in reporting results. To facilitate the implementation of this template, we further develop an interactive web-based application (stepFD) in the form of a checklist workflow, detailing all the steps of the protocol and allowing the user to produce a final 'reproducibility report' to upload alongside the published paper. A thorough and transparent reporting of functional diversity analyses ensures that ecologists can incorporate others' findings into meta-analyses, the shared data can be integrated into larger databases for consensus analyses, and available code can be reused by other researchers. All these elements are key to pushing forward this vibrant and fast-growing field of research.Peer reviewe