Drivers Of Community Assembly Research Articles

Come to the dark side! The role of functional traits in shaping dark diversity patterns of south‐eastern European hoverflies

1. Dark diversity represents the set of species that can potentially inhabit a given area under particular ecological conditions, but are currently ‘missing’ from a site. This concept allows characterisation of the mechanisms determining why species are sometimes absent from an area that seems ecologically suitable for them.2. The aim of this study was to determine the dark diversity of hoverflies in south‐eastern Europe and to discuss the role of different functional traits that might increase the likelihood of species contributing to dark diversity. Based on expert opinion, the Syrph the Net database and known occurrences of species, the study estimated species pools, and observed and dark diversities within each of 11 defined vegetation types for 564 hoverfly species registered in south‐eastern Europe. To detect the most important functional traits contributing to species being in dark diversity across different vegetation types, a random forest algorithm and respective statistics for variable importance were used.3. The highest dark diversity was found for southwest Balkan sub‐Mediterranean mixed oak forest type, whereas the lowest was in Mediterranean mixed forest type. Three larval feeding modes (saproxylic, and phytophagous on bulbs or roots) were found to be most important for determining the probability of a species contributing to hoverfly dark diversity, based on univariate correlations and random forest analysis.4. This study shows that studying dark diversity might provide important insights into what drives community assembly in south‐eastern European hoverflies, especially its missing components, and contributes to more precise conservation prioritisation of both hoverfly species and their habitats.

Untangling the assembly of macrophyte metacommunities by means of taxonomic, functional and phylogenetic beta diversity patterns

Metacommunity ecology has broadened considerably with the recognition that measuring beta diversity beyond the purely taxonomic viewpoint may improve our understanding of the dispersal- and niche-based mechanisms across biological communities. In that perspective, we applied a novel multidimensional approach including taxonomic, functional and phylogenetic data to enhance our basic understanding of macrophyte metacommunity dynamics. For each beta diversity metric, we calculated the mean overall value and tested whether the mean value was different from that expected by chance using null models. We also employed evolutionary and spatially constrained models to first identify the degree to which the studied functional traits showed a phylogenetic signal, and then to estimate the relative importance of spatial and environmental effects on metacommunity structure. We first found that most individual ponds were inhabited by species that were merely random draws from the taxonomic and phylogenetic species pool available in the study region. Contrary to our expectations, not all measured traits were conserved along the phylogeny. We also showed that trait and phylogenetic dimensions strongly increased the amount of variation in beta diversity that can be explained by degree of environmental filtering and dispersal limitation. This suggests that accounting for functional traits and phylogeny in metacommunity ecology helps to explain idiosyncratic patterns of variation in macrophyte species distribution. Importantly, phylogenetic and functional analyses identified the influence of underlying mechanisms that would otherwise be missed in an analysis of taxonomic turnover. Together, these results let us conclude that macrophyte species have labile functional traits adapted to dispersal-based processes and some evolutionary trade-offs that drive community assembly via species sorting. Overall, our exploration of different facets of beta diversity showed how functional and phylogenetic information may be used with species-level data to test community assembly hypotheses that are more ecologically meaningful than assessments of environmental patterns based on the purely taxonomic viewpoint.

Spatial and environmental factors are minor structuring forces in a soil Collembola metacommunity in a maize agroecosystem

Understanding the processes underlying species richness across multiple sites is a major challenge in ecology. Metacommunity theory assumes that local community assemblages are largely structured by spatial and environmental factors. However, the relative importance of these factors is not clear and has varied between studies. Most studies were conducted at sampling intervals that were short (<10 m), or long (>1 km). In this study, to address a dearth of data at intermediate sampling intervals, we examined the pattern of the soil Collembola metacommunity in an agroecosystem by sampling at 40 m intervals to try to disentangle the relative influence of spatial-environmental interactions on community composition. The soil Collembola community was sampled at 121 locations arranged regularly within a 400 m × 400 m corn field, over three months (August, September, and October 2015). We used standard geospatial analysis of metacommunity structure analytical framework to identify the pattern of soil Collembola metacommunity, with three essential elements (coherence, species turnover, and boundary clumping), to provide clues to the processes driving community assembly. We used variance partitioning analysis to determine the relative contributions of spatial and environmental factors (e.g., soil pH value, soil organic matter, soil total nitrogen and soil water content). From the results of the analysis, the soil Collembola metacommunity showed a nested pattern (rather than random, checkerboards, nested subsets, evenly spaced, Clementsian and Gleasonian patterns) on all three sampling dates. Soil Collembola metacommunities have a less restricted distribution along the environmental gradient, and connectivity may be important in shaping the community composition at this intermediate sampling interval. Based on the results of the variance partitioning analysis, spatial factors only explained 7.03–14.4% of the soil Collembola community variance, while the environmental factors were not significant at this scale. Our results suggest that both spatial and environmental factors are minor drivers of soil Collembola communities at an intermediate sampling frequency, compared to other studies conducted at shorter or longer sampling intervals.

Trait and phylogenetic patterns reveal deterministic community assembly mechanisms on Mount St. Helens

Primary plant succession provides an excellent natural experiment to test ecological questions about community assembly following major disturbances. Temporal phylogenetic and functional trait dispersion patterns can give insight into the relative importance of stochastic and deterministic processes, as well as the potential identity of deterministic (biotic vs. abiotic) drivers (e.g. dispersal, growth, nutrient acquisition, and herbivore resistance ability). We used 28 years of plant composition data across four primary succession sites at Mount St. Helens (collected since the 1980 volcanic eruption) to examine phylogenetic dispersion and trait patterns over time. We expected to find more evidence of clustering or random phylogenetic patterns early in succession (where environmental filtering and stochasticity are thought to dominate), with a switch to overdispersion via processes such as niche differentiation later in succession. Contrary to expectations, phylogenetic relatedness and trait dispersion patterns were idiosyncratic. We found evidence of deterministic community assembly even early in succession, suggesting that both local-scale abiotic filtering and biotic interactions start playing a role shortly after the initiating disturbance. Traits were less predictive of successional patterns, with few consistent changes in trait distribution across all sites, even though the traits we examined are linked to the processes thought to be important during succession. Together, these results suggest that the drivers of community assembly during succession may be less generalizable and more complex than previously thought. We suggest that combining experiments and these analytical tools with long-term monitoring could be a useful step forward.

Seasonal strengths of the abiotic and biotic drivers of a zooplankton community

Abstract Multiple factors operate simultaneously and interact in complex ways to shape community assembly. Understanding the organisation of communities including species interactions and the importance of driving factors (food, temperature, nutrients, oxygen concentration, etc.) is a central topic in ecology. Intra‐annual variation in zooplankton and the factors that drive them are described in the Plankton Ecology Group (PEG) conceptual model. However, there has been little empirical evidence quantifying the relative contribution of abiotic and physical factors to plankton seasonality in zooplankton communities. Using a long‐term time series of zooplankton abundances and environmental conditions, we investigated which physical, chemical, and biotic factors structure zooplankton communities. We quantified their importance in seasonal changes in species composition by exploring networks of interacting species in the Římov Reservoir (Czech Republic). We investigated how these factors were associated with seasonal and intra‐annual (across all seasons) patterns of temporal variation in zooplankton. We predicted that: (1) the zooplankton community in the Římov Reservoir follows the general seasonal PEG pattern; (2) abiotic factors play an important role in the temporal distribution of zooplankton at the intra‐annual scale, but their influence on the community declines at the seasonal scale; and (3) the network of interacting species is more complex at the seasonal scale than at intra‐annual scale, so biotic drivers most strongly influence zooplankton patterns at seasonal scales. The intra‐annual pattern of zooplankton abundance was mainly determined by the physical environment. As expected, the roles of abiotic drivers of community assembly changed between seasons. There were more interactions between abiotic factors and species structuring the community at the intra‐annual scale than at the seasonal scale. Additionally, these interactions were weaker at the seasonal scale than the intra‐annual scale. The intra‐annual zooplankton community of the Římov Reservoir was the most stable, while the summer zooplankton community was the most variable. Our results provide evidence that the network of interacting zooplankton taxa is composed of positive and negative relationships, which suggests facilitative, competitive, and predator–prey interactions. Although zooplankton species interactions have an influence year‐round, the network of interacting species is more complex during the vegetative period and especially in summer, when species richness and abundance are high. Our results suggest that the zooplankton community is structured by both the biotic network at the seasonal scale and by the physical environment at the intra‐annual scale. Seasonal succession in zooplankton communities of temperate lakes is a well‐known pattern. However, the influence of interspecific interactions within seasons on this pattern has not been clearly shown until this study. Exploring the community in only one season may provide incomplete knowledge of the factors and species interactions driving the whole community.

Standardised inventories of spiders (Arachnida, Araneae) of Macaronesia I: The native forests of the Azores (Pico and Terceira islands).

BackgroundThe data presented here come from samples collected as part of two recent research projects (NETBIOME - ISLANDBIODIV and FCT - MACDIV) which aimed at understanding the drivers of community assembly in Macaronesian islands. We applied the sampling protocol COBRA (Conservation Oriented Biodiversity Rapid Assessment, Cardoso 2009) in sixteen 50 m x 50 m native forest plots in the Azorean Islands of Pico (6 plots) and Terceira (10 plots) to assess spider diversity. Through this publication, we contribute to the knowledge of the arachnofauna of the Azores and, more specifically, to that of the islands of Pico and Terceira.New informationThe collected samples yielded 8,789 specimens, of which 45% were adults (3,970) belonging to 13 families, 36 species and three morphospecies that have yet to be described. Species of the family Linyphiidae dominated the samples, with 17 species and two morphospecies that have yet to be described (48% of the taxa). Out of the identified (morpho)species, 16 were introduced, 13 Azorean endemic (three of which were undescribed) and seven native (five of them Macaronesian endemics). We report the first record of the introduced species Haplodrassus signifer and Agyneta decora in Pico Island.

A soil fungal metacommunity perspective reveals stronger and more localised interactions above the tree line of an alpine/subalpine ecotone

Dispersal affects community structure by facilitating colonisation and homogenising local communities, while species sorting along environmental gradients contributes to divergent community assembly. Fungi often have widespread distributions and are assumed to be dispersed easily across the landscape, with environmental selection being a primary driver of community assembly. To investigate the influence of spatial and environmental characteristics in shaping fungal community patterns, we characterised 143 communities of soil fungi along an altitudinal transect in Australia transitioning from subalpine to alpine vegetation (approximately 150 m difference in elevation over a distance of 1200 m). First, we inferred drivers of community assembly using canonical analyses including climate, edaphic properties, vegetation and spatial variables, all of which explained a statistically significant but very small amount of variation. We then employed an approach that defines the metacommunity with which each local community interacts via immigration and emigration and then estimates metacommunity characteristics. Using this approach, we inferred scales over which community interactions occurred along spatial, environmental and phylogenetic dimensions and the strength of community interactions based on the similarity of local communities to the metacommunity. Constructed metacommunities above the tree line consisted of local communities that were more clustered in space and more homogeneous than those at or below the tree line. Thus, mixing is likely occurring to a greater degree among fewer communities in the alpine environment. Comparisons of metacommunity estimates suggested that fungal evolutionary histories did not constrain community assembly as strongly as spatial proximity or environmental variation. This work suggests that differences exist in how fungal communities assembly along this altitudinal transect, despite site on its own explaining little compositional variation, and that the rate and the degree of species mixing among communities differs depending on the environmental context.

A functional perspective for breeding and wintering waterbird communities: temporal trends in species and trait diversity

Waterbird communities are prone to strong temporal changes both seasonally and annually, but little is known about how this affects their functional diversity and community assembly. Detecting temporal trends in taxonomic and functional diversity within (alpha diversity) and between (beta diversity) communities in breeding and wintering seasons could give insight into the ecological processes driving those trends. In this study, we investigated trends in wintering and breeding waterbirds within and between eleven wetlands in Mediterranean Spain, using a 28‐year time‐series up to 2017. We assessed the temporal trends in taxonomic and functional diversity measures, and compared observed functional diversity values with null expectations, in order to explore the mechanisms driving community assembly. We found increases over time in species richness and in the occupied functional space for both wintering and breeding communities, indicating that species with distinct functional roles were added in both seasons. However, the distribution of the abundances in the functional space was different for breeding and wintering communities. Dissimilarity of species and functional traits decreased among wetlands, suggesting that some of the same functional traits were added to the different wetlands, increasing regional homogenization through time. This is reflected in increases over time in mean body mass, diet plasticity and in the importance of fish in waterbird diets, plus declines in the dietary importance of invertebrates and in plasticity of feeding strata. Furthermore, species composition between wintering and breeding communities, but not trait composition, has become more similar through time. Our results highlight that annual changes, and especially seasonal changes, in the composition of waterbird communities have different effects on their functional diversity, and are influenced by opposing community assembly mechanisms.

Host plant phylogeny and geographic distance strongly structure Betulaceae-associated ectomycorrhizal fungal communities in Chinese secondary forest ecosystems.

Environmental filtering and dispersal limitation are two of the primary drivers of community assembly in ecosystems, but their effects on ectomycorrhizal (EM) fungal communities associated with wide ranges of Betulaceae taxa at a large scale are poorly documented. In this study, we examined EM fungal communities associated with 23 species from four genera (Alnus, Betula, Carpinus and Corylus) of Betulaceae in Chinese secondary forest ecosystems, using Illumina MiSeq sequencing of the ITS2 region. Effects of host plant phylogeny, soil, climate and geographic distance on EM fungal community were explored. In total, we distinguished 1738 EM fungal operational taxonomic units (OTUs) at a 97% sequence similarity level. The EM fungal communities of Alnus had significantly lower OTU richness than those associated with the other three plant genera. The EM fungal OTU richness was significantly affected by geographic distance, host plant phylogeny, soil and climate. The EM fungal community composition was significantly influenced by host plant phylogeny (12.1% of variation explained in EM fungal community), geographic distance (7.7%), soil (4.6%) and climate (1.1%). This finding highlights that environmental filtering linked to host plant phylogeny and dispersal limitation strongly influence EM fungal communities associated with Betulaceae plants in Chinese secondary forest ecosystems.

On the relative importance of space and environment in farmland bird community assembly.

The relative contribution of ecological processes in shaping metacommunity dynamics in heavily managed landscapes is still unclear. Here we used two complementary approaches to disentangle the role of environment and spatial effect in farmland bird community assembly in an intensive agro-ecosystem. We hypothesized that the interaction between habitat patches and dispersal should play a major role in such unstable and unpredictable environments. First, we used a metacommunity patterns analysis to characterize species co-occurrences and identify the main drivers of community assembly; secondly, variation partitioning was used to disentangle environmental and geographical factors (such as dispersal limitation) on community structure and composition. We used high spatial resolution data on bird community structure and composition distributed among 260 plots in an agricultural landscape. Species were partitioned into functional classes, and point count stations were classified according to landscape characteristics before applying metacommunity and partitioning analyses within each. Overall we could explain around 20% of the variance in species composition in our system, revealing that stochasticity remains very important at this scale. However, this proportion varies depending on the scale of analysis, and reveals potentially important contributions of environmental filtering and dispersal. These conclusions are further reinforced when the analysis was deconstructed by bird functional classes or by landscape habitat classes, underlining trait-related filters, thus reinforcing the idea that wooded areas in these agroecosystems may represent important sources for a specific group of bird species. Our analysis shows that deconstructing the species assemblages into separate functional groups and types of landscapes, along with a combination of analysis strategies, can help in understanding the mechanisms driving community assembly.

Bacterial Community Assembly in a Typical Estuarine Marsh with Multiple Environmental Gradients.

Bacterial communities play essential roles in estuarine marsh ecosystems, but the interplay of ecological processes underlying their community assembly is poorly understood. Here, we studied the sediment bacterial communities along a linear gradient extending from the water-land junction toward a high marsh, using 16S rRNA gene amplicon sequencing. Bacterial community compositions differed significantly between sediment transects. Physicochemical properties, particularly sediment nutrient levels (i.e., total nitrogen [TN] and available phosphorus [AP]), as well as sediment physical structure and pH (P < 0.05), were strongly associated with the overall community variations. In addition, the topological properties of bacterial cooccurrence networks varied with distance to the water-land junction. Both node- and network-level topological features revealed that the bacterial network of sediments farthest from the junction was less intense in complexity and interactions than other sediments. Phylogenetic null modeling analysis showed a progressive transition from stochastic to deterministic community assembly for the water-land junction sites toward the emerging terrestrial system. Taken together, data from this study provide a detailed outline of the distribution pattern of the sediment bacterial community across an estuarine marsh and inform the mechanisms and processes mediating bacterial community assembly in marsh soils.IMPORTANCE Salt marshes represent highly dynamic ecosystems where the atmosphere, continents, and the ocean interact. The bacterial distribution in this ecosystem is of great ecological concern, as it provides essential functions acting on ecosystem services. However, ecological processes mediating bacterial assembly are poorly understood for salt marshes, especially the ones located in estuaries. In this study, the distribution and assembly of bacterial communities in an estuarine marsh located in south Hangzhou Bay were investigated. The results revealed an intricate interplay between stochastic and deterministic processes mediating the assembly of bacterial communities in the studied gradient system. Collectively, our findings illustrate the main drivers of community assembly, taking into consideration changes in sediment abiotic variables and potential biotic interactions. Thus, we offer new insights into estuarine bacterial communities and illustrate the interplay of ecological processes shaping the assembly of bacterial communities in estuarine marsh ecosystems.

Disentangling the processes driving tree community assembly in a tropical biodiversity hotspot (New Caledonia)

AbstractAimUnderstanding the drivers of community diversity and composition is a major question in ecology, which is of particular significance for the conservation of narrowly distributed taxa facing habitat alteration. In this study, we examined three ecological processes (environmental and biotic filtering, and dispersal limitation) hypothesized to drive community assembly in the island biodiversity hotspot of New Caledonia, and whether the relative importance of these processes changes along environmental gradients.MethodsFirst, we assessed environmental filtering by stacking binary presence/absence species distribution models generated for 678 tree species from c. 40,000 occurrences. Second, we acknowledged the influence of dispersal limitation by applying a buffer around each occurrence. Third, we modelled a local hierarchy of performances by ranking species in decreasing order of their predicted habitat suitability, up to the predicted local species richness. Predictions of stacked species distribution models (S‐SDMs) accounting for different combinations of the filtering processes were compared with the composition of 12 forest plots.ResultsThe three filters appear to be important driving forces. Accounting for environmental filtering provided fairly accurate assemblage predictions but species richness was overestimated. Considering dispersal limitation increased assemblage specificity (the proportion of correctly predicted absences) while considering differences in local performances increased assemblage sensitivity (the proportion of correctly predicted presences). The predictive ability of all S‐SDMs decreased with elevation, which suggests that unpredictable stochastic processes influenced biodiversity dynamics in more productive mountain habitats.Main conclusionsNew Caledonian tree communities appear to be similar to those of other tropical regions in their structuring processes (important role of dispersal and biotic filtering, increasing role of neutral processes with productivity). Our findings stress the potential of using S‐SDMs to understand and predict current and future biodiversity patterns.

Adjacency and Area Explain Species Bioregional Shifts in Neotropical Palms.

Environmental and geographical variables are known drivers of community assembly, however their influence on phylogenetic structure and phylogenetic beta diversity of lineages within different bioregions is not well-understood. Using Neotropical palms as a model, we investigate how environmental and geographical variables affect the assembly of lineages into bioregions across an evolutionary time scale. We also determine lineage shifts between tropical (TRF) and non-tropical (non-TRF) forests. Our results identify that distance and area explain phylogenetic dissimilarity among bioregions. Lineages in smaller bioregions are a subset of larger bioregions and contribute significantly to the nestedness component of phylogenetic dissimilarity, here interpreted as evidence for a bioregional shift. We found a significant tendency of habitat shifts occurring preferentially between TRF and non-TRF bioregions (31 shifts) than from non-TRF to TRF (24) or from TRF to TRF (11) and non-TRF to non-TRF (9). Our results also present cases where low dissimilarity is found between TRF and non-TRF bioregions. Most bioregions showed phylogenetic clustering and larger bioregions tended to be more clustered than smaller ones, with a higher species turnover component of phylogenetic dissimilarity. However, phylogenetic structure did not differ between TRF and non-TRF bioregions and diversification rates were higher in only two lineages, Attaleinae and Bactridinae, which are widespread and overabundant in both TRF and non-TRF bioregions. Area and distance significantly affected Neotropical palm community assembly and contributed more than environmental variables. Despite palms being emblematic humid forest elements, we found multiple shifts from humid to dry bioregions, showing that palms are also important components of these environments.

Fire? They don't give a dung! The resilience of dung beetles to fire in a tropical savanna

1. Disturbance is a strong driver of community assembly and fire has long been recognised as one of the main disturbances of terrestrial ecosystems. This study tested the resilience of dung beetles to fire events in campos rupestres, which is a tropical savanna ecosystem that evolved under a frequent fire regime, by assessing the resistance and recovery of their communities.2. Dung beetles were sampled before and after a fire event and the effect of fire on dung beetle richness, abundance, mean community biomass and composition was tested. The effects of time since last fire and fire frequency on the community were also tested.3. No effect of fire occurrence, time since last fire and fire frequency on any community variable was found.4. Some non‐mutually exclusive mechanisms promoting the resistance and recovery of dung beetles in campos rupestres could be acting in synergy. One potential mechanism is the mismatched seasonality between fire events and dung beetle occurrence, as fires occur during the dry season and dung beetles are present above ground during the rainy season. Furthermore, dung beetles are insects that remain buried during most of their lifetime, which could protect individuals from being burned. Another potential mechanism is the replacement of species in burned areas by the movement of individuals from unburned areas, attracted by resources and/or by metacommunity dynamics.5. It is concluded that in this ‘fire‐dependent’ ecosystem, dung beetle communities are resilient to fire and seem not to be structured by this disturbance.

Do all roads lead to Rome? Exploring community trajectories in response to anthropogenic salinization and dilution of rivers.

Abiotic stress shapes how communities assemble and support ecological functions. However, it remains unclear whether artificially increasing or decreasing stress levels would lead to communities assembling predictably along a single axis of variation or along multiple context-dependent trajectories of change. In response to stress intensity alterations, we hypothesize that a single trajectory of change occurs when trait-based assembly prevails, while multiple trajectories of change arise when dispersal-related processes modify colonization and trait-filtering dynamics. Here, we tested these hypotheses using aquatic macroinvertebrates from rivers exposed to gradients of natural salinity and artificially diluted or salinized ion contents. Our results showed that trait-filtering was important in driving community assembly in natural and diluted rivers, while dispersal-related processes seemed to play a relevant role in response to salinization. Salinized rivers showed novel communities with different trait composition, while natural and diluted communities exhibited similar taxonomic and trait compositional patterns along the conductivity gradient. Our findings suggest that the artificial modification of chemical stressors can result in different biological communities, depending on the direction of the change (salinization or dilution), with trait-filtering, and organism dispersal and colonization dynamics having differential roles in community assembly. The approach presented here provides both empirical and conceptual insights that can help in anticipating the ecological effects of global change, especially for those stressors with both natural and anthropogenic origins.This article is part of the theme issue 'Salt in freshwaters: causes, ecological consequences and future prospects'.

Non-random processes determine the colonization of groundwater sediments by microbial communities in a pristine porous aquifer.

Sediments accommodate the dominating share of groundwater microbiomes, however the processes that govern the assembly and succession of sediment-attached microbial communities in groundwater aquifers are not well understood. To elucidate these processes, we followed the microbial colonization of sterile sediments in in situ microcosms that were exposed to groundwater for almost 1 year at two distant but hydrologically connected sites of a pristine, shallow, porous aquifer. Our results revealed intriguing similarities between the community succession on the newly-colonized sediments and succession patterns previously observed for biofilms in other more dynamic aquatic environments, indicating that the assembly of microbial communities on surfaces may be governed by similar underlying mechanisms across a wide range of different habitats. Null model simulations on spatiotemporally resolved 16S rRNA amplicon sequencing data further indicated selection of specific OTUs rather than random colonization as the main driver of community assembly. A small fraction of persistent OTUs that had established on the sediments during the first 115 days dominated the final communities (68%-85%), suggesting a key role of these early-colonizing organisms, in particular specific genera within the Comamonadaceae and Oxalobacteraceae, for community assembly and succession during the colonization of the sediments. Overall, our study suggests that differences between planktonic and sediment-attached communities often reported for groundwater environments are not the result of purely stochastic events, but that sediment surfaces select for specific groups of microorganisms that assemble over time in a reproducible, non-random way.

Small-scale Variation of Testate Amoeba Assemblages: the Effect of Site Heterogeneity and Empty Shell Inclusion

Studies on testate amoeba species distribution at small scales (i.e., single peatland sites) are rare and mostly focus on bogs or mineral-poor Sphagnum fens, leaving spatial patterns within mineral-rich fens completely unexplored. In this study, two mineral-rich fen sites of contrasting groundwater chemistry and moss layer composition were selected for the analysis of testate amoeba compositional variance within a single site. At each study site, samples from 20 randomly chosen moss-dominated plots were collected with several environmental variables being measured at each sampling spot. We also distinguished between empty shells and living individuals to evaluate the effect of empty shell inclusion on recorded species distribution. At the heterogeneous-rich Sphagnum-fen, a clear composition turnover in testate amoebae between Sphagnum-dominated and brown moss-dominated samples was closely related to water pH, temperature and redox potential. We also found notable species composition variance within the homogeneous calcareous fen, yet it was not as high as for the former site and the likely drivers of community assembly remained unidentified. The exclusion of empty shells provided more accurate data on species distribution as well as their relationship with some environmental variables, particularly moisture. Small-scale variability in species composition of communities seems to be a worthwhile aspect in testate amoeba research and should be considered in future sampling strategies along with a possible empty shell bias for more precise understanding of testate amoeba ecology and paleoecology.

Drivers of species turnover vary with species commonness for native and alien plants with different residence times.

Communities comprising alien species with different residence times are natural experiments allowing the assessment of drivers of community assembly over time. Stochastic processes (such as dispersal and fluctuating environments) should be the dominant factors structuring communities of exotic species with short residence times. In contrast, communities should become more similar, or systematically diverge, if they contain exotics with increasing resident times, due to the increasing importance of deterministic processes (such as environmental filtering). We use zeta diversity (the number of species shared by multiple assemblages) to explore the relationship between the turnover of native species and two categories of alien species with different residence times (archaeophytes [introduced between 4000 BC and 1500 AD] and neophytes [introduced after 1500 AD]) in a network of nature reserves in central Europe. By considering multiple assemblages simultaneously, zeta diversity allows us to determine the contribution of rare and widespread species to turnover. Specifically, we explore the relative effects of assembly processes representing isolation by distance, environmental filtering, and environmental stochasticity (fluctuating environments) on zeta diversity using Multi-Site Generalized Dissimilarity Modelling (MS-GDM). Four clusters of results emerged. First, stochastic processes for structuring plant assemblages decreased in importance with increasing residence time. Environmental stochasticity only affected species composition for neophytes, offering possibilities to predict the spread debt of recent invasions. Second, native species turnover was well explained by environmental filtering and isolation by distance, although these factors did not explain the turnover of archaeophytes and neophytes. Third, native and alien species compositions were only correlated for rare species, whereas turnover in widespread alien species was surprisingly unrelated to the composition of widespread native species. Site-specific approaches would therefore be more appropriate for the monitoring and management of rare alien species, whereas species-specific approaches would suit widespread species. Finally, the size difference of nature reserves influences not only native species richness, but also their richness-independent turnover. A network of reserves must therefore be designed and managed using a variety of approaches to enhance native diversity, while controlling alien species with different residence times and degrees of commonness.

Testing and interpreting the shared space‐environment fraction in variation partitioning analyses of ecological data

Variation partitioning analyses combined with spatial predictors (Moran's eigenvector maps, MEM) are commonly used in ecology to test the fractions of species abundance variation purely explained by environment and space. However, while these pure fractions can be tested using a classical residuals permutation procedure, no specific method has been developed to test the shared space‐environment fraction (SSEF). Yet, the SSEF is expected to encompass a major driver of community assembly, that is, an induced spatial dependence effect (ISD; i.e. the reflection of a spatially structured habitat filter on a species distribution). A reliable test of this fraction is therefore crucial to properly test the presence of an ISD on ecological data. To bridge the gap, we propose to test the SSEF through spatially‐constrained null models: torus‐translations, and Moran spectral randomisations. We investigated the type I error rate and statistical power of our method based on two real environmental datasets and simulations of tree distributions. Ten types of tree distribution displaying contrasted aggregation properties were simulated, and their abundances were sampled in 153 regularly‐distributed 20 × 20 m quadrats. The SSEF was tested for 1000 simulated tree distributions either unrelated to the environment, or filtered by environmental variables displaying contrasting spatial structures. The method proposed provided a correct type I error rate (&lt; 0.05). The statistical power was high (&gt; 0.9) when abundances were filtered by an environmental variable structured at broad scale. However, the spatial resolution allowed by the sampling design limited the power of the method when using a fine‐scale filtering variable. This highlighted that an ISD can be properly detected providing that the spatial pattern of the filtering process is correctly captured by the sampling design of the study. An R function to apply the SSEF testing method is provided and detailed in a tutorial.

Disentangling the influence of aridity and salinity on community functional and phylogenetic diversity in local dryland vegetation

One of the key hypothesized drivers of community assembly and dynamics is environmental filtering, where environmental stress limits species migration and survival as a result of functional trait convergence. Whereas most such studies focus on large-scale variation in functional traits along a single-factor environmental gradient, the mutual effects of small-scale multiple environmental filtering remain unclear. Furthermore, it has rarely been tested whether the combined effect of aridity and salinity on local dryland vegetation constrains the patterns of functional traits and phylogenetic structures. Across an 8-km long transect in the arid northwest of China, we assessed the role of environmental filtering in shaping community assemblages by testing the hypotheses that aridity and salinity stresses, interspecific competition and phylogenetic structures constrained functional diversity in the local dryland vegetation. Our results showed that aridity significantly increased convergence of the maximum plant height, specific leaf area, leaf area and leaf nitrogen concentration. However, salinity significantly promoted the convergence of only leaf area and leaf nitrogen concentration. In addition, interspecific competition increased the convergence of the maximum plant height and leaf area. Leaf area converged significantly due to phylogenetic history. Aridity filtering, but not salinity filtering, obviously increased the clustering of phylogenetic structure. Interspecific competition and phylogenetic structure had weak effects on functional diversity in local dryland vegetation. In conclusion, compared with salinity filtering, aridity filtering was more important in reducing phylogenetic diversity in dryland vegetation.