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Species assemblages often have a non-random nested organization, which in vertebrate scavenger (carrion-consuming) assemblages is thought to be driven by facilitation in competitive environments. However, not all scavenger species play the same role in maintaining assemblage structure, as some species are obligate scavengers (i.e., vultures) and others are facultative, scavenging opportunistically. We used a database with 177 vertebrate scavenger species from 53 assemblages in 22 countries across five continents to identify which functional traits of scavenger species are key to maintaining the scavenging network structure. We used network analyses to relate ten traits hypothesized to affect assemblage structure with the “role” of each species in the scavenging assemblage in which it appeared. We characterized the role of a species in terms of both the proportion of monitored carcasses on which that species scavenged, or scavenging breadth (i.e., the species “normalized degree”), and the role of that species in the nested structure of the assemblage (i.e., the species “paired nested degree”), therefore identifying possible facilitative interactions among species. We found that species with high olfactory acuity, social foragers, and obligate scavengers had the widest scavenging breadth. We also found that social foragers had a large paired nested degree in scavenger assemblages, probably because their presence is easier to detect by other species to signal carcass occurrence. Our study highlights differences in the functional roles of scavenger species and can be used to identify key species for targeted conservation to maintain the ecological function of scavenger assemblages.

The present study aimed to evaluate the variation in the composition and diversity of the fish assemblages (beta diversity) along the east-west axis of the Paranaguá Estuarine Complex and the Adjacent Continental Shelf. To this end, seasonal collections were carried out between 2014 and 2016 at 12 sampling sites, totaling 144 collections. These sites were distributed in 4 sectors (External, Lower, Middle, and Upper) on an axis from the continental shelf to the interior of the estuary. Beta diversity (βSOR), calculated by the Sørensen index, was divided into the components turnover (βSIM) and nestedness (βSNE) and evaluated the contributions of each to the total heterogeneity. βratio, the ratio of βSNE to βSOR, was estimated to identify the components with the greatest contribution to the total beta diversity. To corroborate the results, nestedness estimates were made using the NODF (Nestedness metric based on Overlap and Decreasing Filling), compared to the null model. For the Upper, Lower, and External sectors, βratio values were lower than 0.5, indicating that the turnover was predominant for variations in total beta diversity, as expected for these environments. Unlike the other sectors, in the Middle sector, βratio values were greater than 0.5, indicating that nestedness was predominant for variations in total beta diversity, which may reflect possible natural or human stressors since innumerable disturbances have already been detected in this environment.

1. In 2003, 24 presence–absence β-diversity metrics were reviewed and a number of trade-offs and redundancies identified. We present a parallel investigation into the performance of abundance-based metrics of β-diversity. 2. β-diversity is a multi-faceted concept, central to spatial ecology. There are multiple metrics available to quantify it: the choice of metric is an important decision. 3. We test 16 conceptual properties and two sampling properties of a β-diversity metric: metrics should be 1) independent of α-diversity and 2) cumulative along a gradient of species turnover. Similarity should be 3) probabilistic when assemblages are independently and identically distributed. Metrics should have 4) a minimum of zero and increase monotonically with the degree of 5) species turnover, 6) decoupling of species ranks and 7) evenness differences. However, complete species turnover should always generate greater values of β than extreme 8) rank shifts or 9) evenness differences. Metrics should 10) have a fixed upper limit, 11) symmetry (βA,B = βB,A), 12) double-zero asymmetry for double absences and double presences and 13) not decrease in a series of nested assemblages. Additionally, metrics should be independent of 14) species replication 15) the units of abundance and 16) differences in total abundance between sampling units. When samples are used to infer β-diversity, metrics should be 1) independent of sample sizes and 2) independent of unequal sample sizes. We test 29 metrics for these properties and five 'personality' properties. 4. Thirteen metrics were outperformed or equalled across all conceptual and sampling properties. Differences in sensitivity to species' abundance lead to a performance trade-off between sample size bias and the ability to detect turnover among rare species. In general, abundance-based metrics are substantially less biased in the face of undersampling, although the presence–absence metric, βsim, performed well overall. Only βBaselga R turn, βBaselga B-C turn and βsim measured purely species turnover and were independent of nestedness. Among the other metrics, sensitivity to nestedness varied >4-fold. 5. Our results indicate large amounts of redundancy among existing β-diversity metrics, whilst the estimation of unseen shared and unshared species is lacking and should be addressed in the design of new abundance-based metrics.

Aim: To develop a new probabilistic model that can be used to test for statistically significant pair-wise patterns of species co-occurrence. The model gives the probability that two species would co-occur at a frequency less than (or greater than) the observed frequency if the two species were distributed independently of one another among a set of sites. The model can be used to classify species associations as negative, positive or random. Innovation: Historically, the analysis of species co-occurrence has involved the use of data randomization. An observed species presence-absence matrix is compared with randomized matrices to determine if the observed matrix has structure, either an excess or deficit of species positively or negatively associated with each other. The computer algorithms used to randomize matrices can sometimes produce Type I and Type II errors (when the randomization algorithm produces a biased set of all possible matrices) due to the randomization process itself. The probabilistic model does not rely on any data randomization, hence it has a very low Type I error rate and is powerful having a low Type II error rate. Main conclusions: When applied to 10 different data sets the probabilistic model revealed significant positive and negative species associations in most of the data sets. Compared with previous analyses the model tended to find fewer significant associations; this may indicate a generally low rate of Type I error in the model. The model is easy to implement and requires no special software. The model could potentially transform the way that ecologists test for species co-occurrence in a wide range of ecological studies.

AimTwo frameworks (BASVIL and PODCAR), based on two different functional representations (ordination and dendrogram), have been proposed for partitioning overall functional beta diversity into two analogous components: turnover and nestedness‐resultant dissimilarity, or replacement and difference of functional richness, respectively. We compared the two frameworks by testing the influence of functional representations and partitioning methods on the measurement of overall functional beta diversity and its components.InnovationWe computed beta‐diversity indices from the two frameworks on a set of communities simulated according to five scenarios of assembly: random, richness gradient, pure nestedness, pure turnover and mixed turnover/loss scenarios. To disentangle the effects of the partitioning approach and those of the functional representation on measurement of functional beta diversity, we also computed PODCAR indices in multidimensional space.Main conclusionsBASVIL and PODCAR frameworks led to different results for overall functional beta diversity and their analogous partitioning components. Most of the difference between the two frameworks was due to the functional representation used. The goodness‐of‐fit measure (mean squared deviation, mSD) to assess the quality of functional spaces showed that the one computed on the basis of the dendrogram used in PODCAR remained lower than that of the functional ordination considered in BASVIL. In addition, only functional turnover derived from the BASVIL framework is independent of difference in functional richness. Finally, BASVIL measured functional variations derived from nested phenomena while PODCAR did not allow separation of this variation derived from richness difference. However, the sensitivity of BASVIL to functionally extreme species may make it difficult to know whether variations of the nestedness‐resultant dissimilarity components are due to a turnover with few extreme species or a loss in functional richness. Particular attention with regard to the properties of the two frameworks is required before drawing conclusions regarding processes that structure communities.

Aim Mountain systems offer excellent opportunities to understand β‐diversity patterns and the processes driving them. However, β‐diversity patterns and the underlying mechanisms that lead to dissimilarity in mountain amphibian communities across elevational gradients remain elusive. We aimed to evaluate how amphibian communities respond to environmental gradients with elevation and to explore how different ecological mechanisms drive elevational β‐diversity. Location A 2600‐m elevational gradient along Mount Emei in southwestern China. Methods We investigated elevational patterns and assembly processes of pairwise β‐diversity across three dimensions (taxonomic, phylogenetic, and functional) in turnover (i.e., species replacement) and nestedness‐resultant (i.e., species lose/gain) for amphibians. We compared multifaceted β‐diversity components and assessed the extent to which β‐diversity responded to environmental and elevational distances. We also quantified the standardized effect size of β‐diversity and its components using null models to examine the dynamics of niche‐based and neutral processes. Results The turnover component dominated taxonomic β‐diversity, whereas nestedness was relatively more important for phylogenetic and functional dissimilarity. Moreover, taxonomic total dissimilarity and turnover were higher than their phylogenetic and functional analogues. Our results indicated a significant distance‐decay effect for multifaceted β‐diversity of amphibians on Mount Emei and found that effects and directions of predictors on multifaceted β‐diversity were different, with temperature seasonality, annual precipitation, and elevational distance acting as the most important factors. Comparing observed patterns with null‐model expectations, environmental filtering, and competitive exclusion may jointly drive elevational patterns of β‐diversity. Main conclusions Our study emphasizes the importance of partitioning taxonomic, phylogenetic, and functional components of β‐diversity and community assembly when determining β‐diversity drivers. Although it is difficult to distinguish random communities from outcomes of niche‐based processes, this work highlights the potential roles of environmental filtering and competitive exclusion in controlling elevational communities and provides insights into amphibian community assembly in a biodiversity hotspot.

Environmental filtering is a major mechanism structuring ecological communities. However, it is still not clear how different abiotic drivers composing the environmental filter interact with each other to determine local species assemblage and create spatial patterns in species distribution. Here, we evaluated the effects of two strong and uncorrelated environmental variables (salinity and sediment properties) on the β-diversity of an estuarine macrobenthic community while accounting for spatial effects. Our results show that the benthic community composition has a strong spatial structure along the estuary, which can be greatly explained by salinity and sediment variation. Salinity is most associated with species replacement (turnover), whereas sediment is more important for species loss (nestedness). However, the effects of sediment variation on nestedness are mainly detected at a smaller spatial scale (estuarine sectors), whereas the effects of salinity on species turnover are stronger as spatial scale increases (entire estuary). Our findings suggest that environmental filters can drive both turnover and nestedness components of β-diversity, but that their relative importance depends on the spatial scale of investigation. Although abiotic drivers associated with detrimental effects (sediment) usually result in nestedness, larger spatial scales encompass abiotic drivers associated with different suitable conditions (salinity), increasing the relative importance of the replacement component of species β-diversity.

Nestedness and modularity have been recurrently observed in species interaction networks. Some studies argue that those topologies result from selection against unstable networks, and others propose that they likely emerge from processes driving the interactions between pairs of species. Here we present a model that simulates the evolution of consumer species using resource species following simple rules derived from the integrative hypothesis of specialization (IHS). Without any selection on stability, our model reproduced all commonly observed network topologies. Our simulations demonstrate that resource heterogeneity drives network topology. On the one hand, systems containing only homogeneous resources form generalized nested networks, in which generalist consumers have higher performance on each resource than specialists. On the other hand, heterogeneous systems tend to have a compound topology: modular with internally nested modules, in which generalists that divide their interactions between modules have low performance. Our results demonstrate that all real-world topologies likely emerge through processes driving interactions between pairs of species. Additionally, our simulations suggest that networks containing similar species differ from heterogeneous networks and that modules may not present the topology of entire networks.

Aims: Patterns of spatial community dissimilarity have inspired a large body of theory in ecology and biogeography. Yet key gaps remain in our understanding of the local-scale ecological processes underlying species replacement and species nestedness, the two fundamental components of spatial community dissimilarity. Here, we examined the relative influence of dispersal limitation, habitat filtering and interspecific species interactions on local-scale patterns of the replacement and nestedness components in eight stem-mapped temperate forest mega-plots at different ontogenetic stages (large versus small trees). Location: Eight large (20–35 ha), fully mapped temperate forest plots in northern China and northern U.S.A. Time period: 2004–2016. Major taxa studied: Woody plants. Methods: We combined decomposition of community dissimilarity (based on the Ružička index) and spatial point-pattern analysis to compare the spatial (i.e., distance-dependent) replacement and nestedness components of each plot with that expected under five spatially explicit null models representing different hypotheses on community-assembly mechanisms. Results: Our analyses revealed complex results. In all eight forests, spatial community dissimilarity was best explained by species replacement among local tree assemblages and by a null model based on dispersal limitation. In contrast, spatial nestedness for large and small trees was best explained by random placement and habitat filtering, respectively, in addition to dispersal limitation. However, interspecific interactions did not contribute to local replacement and nestedness. Main conclusions: Species replacement is the predominant process accounting for spatial community dissimilarity in these temperate forests and caused largely by local-scale species clustering associated with dispersal limitation. Nestedness, in contrast, is less prevalent and primarily associated with larger variation in local species richness as caused by spatial richness gradients or 'hotspots' of local species richness. The novel use of replacement and nestedness measures in point pattern analysis is a promising approach to assess local-scale biodiversity patterns and to explore their causes.

Aim Understanding how biotic communities are spatially distributed is essential for biodiversity conservation in human‐modified landscapes. The large‐scale subsidence wetlands generated by underground coal mining in China have been increasingly used by large numbers of waterbirds, which remain understudied. We aimed to explore the role of non‐random assembly in shaping the regional waterbird diversity in non‐breeding seasons, providing insights for the conservation. Location The North China Plain. Methods Taxonomic β‐diversity and functional β‐diversity (both multiple‐site and pairwise) of the waterbird communities were quantified and decomposed into turnover (i.e. species replacement) and nestedness components (i.e. the poorer sites being subsets of the richer sites). Observed functional α‐diversity and pairwise β‐diversity, as well as the two components, were compared with simulated means under random assembly processes in null models, which maintained the species richness, pairwise taxonomic dissimilarity, and its turnover and nestedness components as the observed. Results The communities exhibited similar multiple‐site taxonomic and functional β‐diversity, which were primarily contributed by taxonomic and functional turnover, respectively. The pairwise functional β‐diversity, as well as its turnover and nestedness components, was positively correlated with their taxonomic counterparts. The pairwise functional β‐diversity was higher than the taxonomic β‐diversity, with the former mainly reflecting nestedness of functional strategies and the latter reflecting species replacement. The observed functional α‐diversities in most communities were lower, and most of the observed pairwise functional β‐diversities were higher than the simulated means in null models. Main conclusions The above patterns suggest the existence of non‐random assembly of the waterbird communities across the subsidence wetlands. To protect waterbirds in the subsidence wetlands, we suggest that most wetlands should be protected via increasing habitat diversity. Furthermore, considering the changing environmental conditions, changes in the multiple biodiversity metrics should be monitored to inform the ongoing management plans.