Beyond the continuum: a multi-dimensional phase space for neutral–niche community assembly

Neutral and niche processes are generally considered to interact in natural communities along a continuum, exhibiting community patterns bounded by pure neutral and pure niche processes. The continuum concept uses niche separation, an attribute of the community, to test the hypothesis that communities are bounded by pure niche or pure neutral conditions. It does not accommodate interactions via feedback between processes and the environment. By contrast, we introduce the Community Assembly Phase Space (CAPS), a multi-dimensional space that uses community processes (such as dispersal and niche selection) to define the limiting neutral and niche conditions and to test the continuum hypothesis. We compare the outputs of modelled communities in a heterogeneous landscape, assembled by pure neutral, pure niche and composite processes. Differences in patterns under different combinations of processes in CAPS reveal hidden complexity in neutral–niche community dynamics. The neutral–niche continuum only holds for strong dispersal limitation and niche separation. For weaker dispersal limitation and niche separation, neutral and niche processes amplify each other via feedback with the environment. This generates patterns that lie well beyond those predicted by a continuum. Inferences drawn from patterns about community assembly processes can therefore be misguided when based on the continuum perspective. CAPS also demonstrates the complementary information value of different patterns for inferring community processes and captures the complexity of community assembly. It provides a general tool for studying the processes structuring communities and can be applied to address a range of questions in community and metacommunity ecology.     

Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale

Extreme arid regions in the worlds'' major deserts are typified by quartz pavement terrain. Cryptic hypolithic communities colonize the ventral surface of quartz rocks and this habitat is characterized by a relative lack of environmental and trophic complexity. Combined with readily identifiable major environmental stressors this provides a tractable model system for determining the relative role of stochastic and deterministic drivers in community assembly. Through analyzing an original, worldwide data set of 16S rRNA-gene defined bacterial communities from the most extreme deserts on the Earth, we show that functional assemblages within the communities were subject to different assembly influences. Null models applied to the photosynthetic assemblage revealed that stochastic processes exerted most effect on the assemblage, although the level of community dissimilarity varied between continents in a manner not always consistent with neutral models. The heterotrophic assemblages displayed signatures of niche processes across four continents, whereas in other cases they conformed to neutral predictions. Importantly, for continents where neutrality was either rejected or accepted, assembly drivers differed between the two functional groups. This study demonstrates that multi-trophic microbial systems may not be fully described by a single set of niche or neutral assembly rules and that stochasticity is likely a major determinant of such systems, with significant variation in the influence of these determinants on a global scale.     

Compositional divergence and convergence in local communities and spatially structured landscapes

Community structure depends on both deterministic and stochastic processes. However, patterns of community dissimilarity (e.g. difference in species composition) are difficult to interpret in terms of the relative roles of these processes. Local communities can be more dissimilar (divergence) than, less dissimilar (convergence) than, or as dissimilar as a hypothetical control based on either null or neutral models. However, several mechanisms may result in the same pattern, or act concurrently to generate a pattern, and much research has recently been focusing on unravelling these mechanisms and their relative contributions. Using a simulation approach, we addressed the effect of a complex but realistic spatial structure in the distribution of the niche axis and we analysed patterns of species co-occurrence and beta diversity as measured by dissimilarity indices (e.g. Jaccard index) using either expectations under a null model or neutral dynamics (i.e., based on switching off the niche effect). The strength of niche processes, dispersal, and environmental noise strongly interacted so that niche-driven dynamics may result in local communities that either diverge or converge depending on the combination of these factors. Thus, a fundamental result is that, in real systems, interacting processes of community assembly can be disentangled only by measuring traits such as niche breadth and dispersal. The ability to detect the signal of the niche was also dependent on the spatial resolution of the sampling strategy, which must account for the multiple scale spatial patterns in the niche axis. Notably, some of the patterns we observed correspond to patterns of community dissimilarities previously observed in the field and suggest mechanistic explanations for them or the data required to solve them. Our framework offers a synthesis of the patterns of community dissimilarity produced by the interaction of deterministic and stochastic determinants of community assembly in a spatially explicit and complex context.     

Distinct successional patterns and processes of free-living and particle-attached bacterial communities throughout a phytoplankton bloom

1. Understanding the successional patterns of microbial communities during a phytoplankton bloom is crucial for predicting the compositional and functional stability of lake ecosystems in response to the disturbance of a bloom. Previous studies on bacterial communities associated with blooms have rarely studied the dynamics of these communities. The successional patterns of bacterial communities within different micro-habitats (i.e. water column versus particles) and mechanisms that shape these communities that differ in composition and structure remain unclear.
2. We selected a eutrophic urban lake to investigate the succession of bacterial communities during a bloom. We divided the bacterial communities into free-living (FL) and particle-attached (PA) groups based on their different lifestyles. The amplicon-based 16S rRNA gene high-throughput sequencing technology was used to obtain bacterial community composition and phylogenetic structure.
3. Our study showed distinct successional patterns between FL and PA bacterial communities, and the two bacterial lifestyles showed different responses and resilience to the bloom, in terms of diversity and relative abundance of bacterial taxa. Alpha-diversity of the PA bacterial community decreased during the bloom, whereas that of the FL bacterial community increased. More taxa in the FL bacterial community showed resilience after the disturbance than in the PA bacterial community.
4. The influence of phytoplankton blooms on the assembly of the bacterial community can be viewed as niche selection that led to the decrease in the relative importance of stochastic processes in shaping both FL and PA bacterial communities. This study shows the ecological significance of the bacterial community response to bloom events in lakes. It also shows that assembly processes differ for bacterial communities that have different lifestyles in lake ecosystems disturbed by phytoplankton blooms.

     

Dispersal and neutral sampling mediate contingent effects of disturbance on plant beta‐diversity: a meta‐analysis

A major challenge in ecology, conservation and global‐change biology is to understand why biodiversity responds differently to similar environmental changes. Contingent biodiversity responses may depend on how disturbance and dispersal interact to alter variation in community composition (β‐diversity) and assembly mechanisms. However, quantitative syntheses of these patterns and processes across studies are lacking. Using null‐models and meta‐analyses of 22 factorial experiments in herbaceous plant communities across Europe and North America, we show that disturbance diversifies communities when dispersal is limited, but homogenises communities when combined with increased immigration from the species pool. In contrast to the hypothesis that disturbance and dispersal mediate the strength of niche assembly, both processes altered β‐diversity through neutral‐sampling effects on numbers of individuals and species in communities. Our synthesis suggests that stochastic effects of disturbance and dispersal on community assembly play an important, but underappreciated, role in mediating biotic homogenisation and biodiversity responses to environmental change.     

Butterfly,seedling, sapling and tree diversity and composition in a fire‐affected Bornean rainforest

Abstract: Fire‐affected forests are becoming an increasingly important component of tropical landscapes. The impact of wildfires on rainforest communities is, however, poorly understood. In this study the density, species richness and community composition of seedlings, saplings, trees and butterflies were assessed in unburned and burned forest following the 1997/98 El Niño Southern Oscillation burn event in East Kalimantan, Indonesia. More than half a year after the fires, sapling and tree densities in the burned forest were only 2.5% and 38.8%, respectively, of those in adjacent unburned forest. Rarefied species richness and Shannon's H’ were higher in unburned forest than burned forest for all groups but only significantly so for seedlings. There were no significant differences in evenness between unburned and burned forest. Matrix regression and Akaike's information criterion (AIC) revealed that the best explanatory models of similarity included both burning and the distance between sample plots indicating that both deterministic processes (related to burning) and dispersal driven stochastic processes structure post‐disturbance rainforest assemblages. Burning though explained substantially more variation in seedling assemblage structure whereas distance was a more important explanatory variable for trees and butterflies. The results indicate that butterfly assemblages in burned forest were primarily derived from adjacent unburned rainforest, exceptions being species of grass‐feeders such as Orsotriaena medus that are normally found in open, disturbed areas, whereas burned forest seedling assemblages were dominated by typical pioneer genera, such as various Macaranga species that were absent or rare in unburned forest. Tree assemblages in the burned forest were represented by a subset of fire‐resistant species, such as Eusideroxylon zwageri and remnant dominant species from the unburned forest.     

Balance of Neutral and Deterministic Components in the Dynamics of Activated Sludge Floc Assembly

Understanding the processes that generate patterns of community structure is a central focus of ecological research. With that aim, we manipulated the structure of bacterial activated sludge to test the influence of the species richness and composition of bacterial communities on the dynamics of activated sludge floc assembly in lab-scale bioreactors. Bacterial community structure was analyzed using denaturing gradient gel electrophoresis of RT-PCR amplified 16S rRNA. Fingerprinting of four parallel reactors, started with the same source communities added in different proportions, converged to patterns that were more similar than expected by chance, suggesting a deterministic selection in floc development. Evidence for neutral dynamics was suggested by the dependence of the rate of replacement of species (bacterial taxa–time relationships) on the number of available species in the source community. Further indication of stochastic dynamics was obtained by the application of the Sloan neutral model for prokaryotes. The fitting of the observed data to the model predictions revealed that the importance of the stochastic component increased with the size of the reservoir of species richness from which the community is drawn. Taken together, the results illustrate how both neutral and deterministic dynamics operate simultaneously in the assembly of the bacterial floc and show that the balance of the two depends on the richness of the source community.     

Community assembly in Lake Tanganyika cichlid fish: quantifying the contributions of both niche‐based and neutral processes

The cichlid family features some of the most spectacular examples of adaptive radiation. Evolutionary studies have highlighted the importance of both trophic adaptation and sexual selection in cichlid speciation. However, it is poorly understood what processes drive the composition and diversity of local cichlid species assemblages on relatively short, ecological timescales. Here, we investigate the relative importance of niche‐based and neutral processes in determining the composition and diversity of cichlid communities inhabiting various environmental conditions in the littoral zone of Lake Tanganyika, Zambia. We collected data on cichlid abundance, morphometrics, and local environments. We analyzed relationships between mean trait values, community composition, and environmental variation, and used a recently developed modeling technique (STEPCAM) to estimate the contributions of niche‐based and neutral processes to community assembly. Contrary to our expectations, our results show that stochastic processes, and not niche‐based processes, were responsible for the majority of cichlid community assembly. We also found that the relative importance of niche‐based and neutral processes was constant across environments. However, we found significant relationships between environmental variation, community trait means, and community composition. These relationships were caused by niche‐based processes, as they disappeared in simulated, purely neutrally assembled communities. Importantly, these results can potentially reconcile seemingly contrasting findings in the literature about the importance of either niche‐based or neutral‐based processes in community assembly, as we show that significant trait relationships can already be found in nearly (but not completely) neutrally assembled communities; that is, even a small deviation from neutrality can have major effects on community patterns.     

Advances, challenges and a developing synthesis of ecological community assembly theory

Ecological approaches to community assembly have emphasized the interplay between neutral processes, niche-based environmental filtering and niche-based species sorting in an interactive milieu. Recently, progress has been made in terms of aligning our vocabulary with conceptual advances, assessing how trait-based community functional parameters differ from neutral expectation and assessing how traits vary along environmental gradients. Experiments have confirmed the influence of these processes on assembly and have addressed the role of dispersal in shaping local assemblages. Community phylogenetics has forged common ground between ecologists and biogeographers, but it is not a proxy for trait-based approaches. Community assembly theory is in need of a comparative synthesis that addresses how the relative importance of niche and neutral processes varies among taxa, along environmental gradients, and across scales. Towards that goal, we suggest a set of traits that probably confer increasing community neutrality and regionality and review the influences of stress, disturbance and scale on the importance of niche assembly. We advocate increasing the complexity of experiments in order to assess the relative importance of multiple processes. As an example, we provide evidence that dispersal, niche processes and trait interdependencies have about equal influence on trait-based assembly in an experimental grassland.     

Community assembly and diversification in Indo-Pacific coral reef fishes

Theories of species coexistence have played a central role in ecology and evolutionary studies of the origin and maintenance of biodiversity in highly diverse communities. The concept of niche and associated theories predict that competition for available ecological space leads to a ceiling in species richness that influences further diversification patterns. By contrast, the neutral theory supports that speciation is stochastic and diversity independent. We examined the phylogenetic community structure and diversification rates in three families and 14 sites within coral reef fish communities from the Indian and Pacific oceans. Using the phylogenetic relationships among 157 species estimated with 2300 bp of mitochondrial DNA, we tested predictions in terms of species coexistence from the neutral and niche theories. At the regional scale, our findings suggest that phylogenetic community structure shifts during community assembly to a pattern of dispersion as a consequence of allopatric speciation in recent times but overall, variations in diversification rates did not relate with sea level changes. At the local scale, the phylogenetic community structure is consistent with a neutral model of community assembly since no departure from a random sorting of species was observed. The present results support a neutral model of community assembly as a consequence of the stochastic and unpredictable nature of coral reefs favoring generalist and sedentary species competing for living space rather than trophic resources. As a consequence, the observed decrease in diversification rates may be seen as the result of a limited supply of living space as expected in a finite island model.     

Biogeographic responses and niche occupancy of microbial communities following long-term land-use change

Understanding the effects of forest-to-agriculture conversion on microbial diversity has been a major goal in soil ecological studies. However, linking community assembly to the ruling ecological processes at local and regional scales remains challenging. Here, we evaluated bacterial community assembly patterns and the ecological processes governing niche specialization in a gradient of geography, seasonality, and land-use change, totaling 324 soil samples, 43 habitat characteristics (abiotic factors), and 16 metabolic and co-occurrence patterns (biotic factors), in the Brazilian Atlantic Rainforest, a subtropical biome recognized as one the world’s largest and most threatened hotspots of biodiversity. Pairwise beta diversities were lower in pastures than in forest and no-till soils. Pasture communities showed a predominantly neutral model, regarding stochastic processes, with moderate dispersion, leading to biotic homogenization. Most no-till and forest microbial communities followed a niche-based model, with low rates of dispersal and weak homogenizing selection, indicating niche specialization or variable selection. Historical and evolutionary contingencies, as represented by soil type, season, and dispersal limitation were the main drivers of microbial assembly and processes at the local scale, markedly correlated with the occurrence of endemic microbes. Our results indicate that the patterns of assembly and their governing processes are dependent on the niche occupancy of the taxa evaluated (generalists or specialists). They are also more correlated with historical and evolutionary contingencies and the interactions among taxa (i.e., co-occurrence patterns) than the land-use change itself.

     

Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities

Environmental degradation may have strong effects on community assembly processes. We examined the assembly of bacterial and fungal communities in anthropogenically altered and near‐pristine streams. Using pyrosequencing of bacterial and fungal DNA from decomposed alder Alnus incana leaves, we specifically examined if environmental degradation deterministically decreases or increases the compositional turnover of bacterial and fungal communities. Our results showed that near‐pristine streams and anthropogenically altered streams supported distinct fungal and bacterial communities. The mechanisms assembling these communities were different in near‐pristine and altered environments. Environmental disturbance homogenized bacterial communities, whereas fungal communities were more dissimilar in disturbed sites than in near‐pristine sites. Compositional variation of both bacteria and fungi was related to water chemistry variables in disturbed sites, further implying the influence of environmental degradation on community assembly. Bacterial and fungal communities in near‐pristine streams were weakly controlled by environmental factors, suggesting that the relative importance of niche‐based versus neutral processes in assembling microbial communities may strongly depend on the spatial scale and local environmental context. Our results thus suggest that environmental degradation may strongly affect the composition and β‐diversity of stream microbial communities colonizing leaf litter, and that the direction of the change can be different between bacteria and fungi. A better understanding of the environmental tolerances of microbes and the mechanisms assembling microbial communities in natural environmental settings is needed to predict how environmental alteration is likely to affect microbial communities.     

Deterministic control on community assembly peaks at intermediate levels of disturbance

Despite long-standing research, the processes that drive community assembly remain poorly understood. We censused macroinvertebrate communities and measured flood disturbance in 17 Scandinavian mountain streams to assess the hypothesis that communities are shaped by stochastic processes under stable conditions, and increasingly by deterministic processes as disturbance becomes more severe. Each study stream was categorized as being stable (n=5), intermediate (n=7), or disturbed (n=5) depending on the severity of scouring floods. Following spring floods, the number of potential colonisers decreased with increasing disturbance, suggesting that disturbance filtered out species unable to cope with the stress involved. Communities at stable sites had the highest beta diversity, indicating that stochastic processes of community assembly were most important under the least disturbed conditions. In partial contrast with our predictions, the lowest beta diversity occurred between intermediate (not disturbed) sites, suggesting that increasing disturbance first enhances determinism but then rekindles stochasticity at severity levels beyond intermediate. Macroinvertebrate communities were shaped by deterministic processes, which recruit potential regional colonists depending on niche differences and disturbance conditions and by stochastic processes, which distribute the selected species randomly among individual localities. Although often considered opposing, stochastic and deterministic processes interact hierarchically, with relative strength modified by disturbance.     

Community assembly of bacteria and archaea in coastal waters governed by contrasting mechanisms: A seasonal perspective

Marine planktonic bacteria and archaea commonly exhibit pronounced seasonal succession in community composition. But the existence of seasonality in their assembly processes and between‐domain differences in underlying mechanism are largely unassessed. Using a high‐coverage sampling strategy (including single sample for each station during four cruises in different seasons), 16S rRNA gene sequencing, and null models, we investigated seasonal patterns in the processes governing spatial turnover of bacteria and archaea in surface coastal waters across a sampling grid over ~300 km in the East China Sea. We found that archaea only bloomed in prokaryotic communities during autumn and winter cruises. Seasonality mostly overwhelmed spatial variability in the compositions of both domains. Bacterial and archaeal communities were dominantly governed by deterministic and stochastic assembly processes, respectively, in autumn cruise, probably due to the differences in niche breadths (bacteria < archaea) and relative abundance (bacteria > archaea). Stochasticity dominated assembly mechanisms of both domains but was driven by distinct processes in winter cruise. Determinism‐dominated assembly mechanisms of bacteria rebounded in spring and summer cruises, reflecting seasonal variability in bacterial community assembly. This could be attributed to seasonal changes in bacterial niche breadths and habitat heterogeneity across the study area. There were seasonal changes in environmental factors mediating the determinism‐stochasticity balance of bacterial community assembly, holding a probability of the existence of unmeasured mediators. Our results suggest contrasting assembly mechanisms of bacteria and archaea in terms of determinism‐vs.‐stochasticity pattern and its seasonality, highlighting the importance of seasonal perspective on microbial community assembly in marine ecosystems.     

Prescribed fire selects for a pyrophilous soil sub-community in a northern California mixed conifer forest

Prescribed fire is a critical strategy for mitigating the effects of catastrophic wildfires. While the above-ground response to fire has been well-documented, fewer studies have addressed the effect of prescribed fire on soil microorganisms. To understand how soil microbial communities respond to prescribed fire, we sampled four plots at a high temporal resolution (two burned, two controls), for 17 months, in a mixed conifer forest in northern California, USA. Using amplicon sequencing, we found that prescribed fire significantly altered both fungal and bacterial community structure. We found that most differentially abundant fungal taxa had a positive fold-change, while differentially abundant bacterial taxa generally had a negative fold-change. We tested the null hypothesis that these communities assembled due to neutral processes (i.e., drift and/or dispersal), finding that >90% of taxa fit this neutral prediction. However, a dynamic sub-community composed of burn-associated indicator taxa that were positively differentially abundant was enriched for non-neutral amplicon sequence variants, suggesting assembly via deterministic processes. In synthesizing these results, we identified 15 pyrophilous taxa with a significant and positive response to prescribed burns. Together, these results lay the foundation for building a process-driven understanding of microbial community assembly in the context of the classical disturbance regime of fire.     

Soil Properties and Spatial Processes Influence Bacterial Metacommunities within a Grassland Restoration Experiment

Metacommunity theory proposes that a collection of local communities are linked by dispersal and the resulting compositions are a product of both niche‐based (species sorting) and spatial processes. Determining which of these factors is most important in different habitats can provide insight into the regulation of community assembly. To date, the metacommunity organization of heterotrophic soil bacteria is largely unknown. Spatial variation of soil bacterial communities could arise from (1) the resource heterogeneity produced by plant communities through root exudation and/or litter inputs; (2) the heterogeneity of soil environmental properties; and (3) pure spatial processes, including dispersal limitation and stochastic assembly. Understanding the relative importance of these factors for soil bacterial community structure and function could increase our ability to restore soil communities. We utilized an ongoing tallgrass prairie restoration experiment in northeastern Kansas to assess if restoring native plant communities produced changes in bacterial communities 6 years after restoration. We further examined the relative importance of the spatial heterogeneity of plant communities, soil properties, and pure spatial effects for bacterial community structure in the old‐field restoration site. We found that soil bacterial communities were not influenced by plant restoration, but rather, by the local heterogeneity of soil environmental properties (16.9% of bacterial community variation) and pure spatial effects (11.1%). This work also stresses the idea that restoring bacterial communities can take many years to accomplish due to the inherent changes that occur to the soil after cultivation and the time it takes for the re‐establishment of soil quality.     

Phylogenetic distance–decay patterns are not explained by local community assembly processes in freshwater lake microbial communities

While water and sediment microbial communities exhibit pronounced spatio-temporal patterns in freshwater lakes, the underlying drivers are yet poorly understood. Here, we evaluated the importance of spatial and temporal variation in abiotic environmental factors for bacterial and microeukaryotic community assembly and distance–decay relationships in water and sediment niches in Hongze Lake. By sampling across the whole lake during both Autumn and Spring sampling time points, we show that only bacterial sediment communities were governed by deterministic community assembly processes due to abiotic environmental drivers. Nevertheless, consistent distance–decay relationships were found with both bacterial and microeukaryotic communities, which were relatively stable with both sampling time points. Our results suggest that spatio-temporal variation in environmental factors was important in explaining mainly bacterial community assembly in the sediment, possibly due lesser disturbance. However, clear distance–decay patterns emerged also when the community assembly was stochastic. Together, these results suggest that abiotic environmental factors do not clearly drive the spatial structuring of lake microbial communities, highlighting the need to understand the role of other potential drivers, such as spatial heterogeneity and biotic species interactions.     

Neutral processes and species sorting in benthic microalgal community assembly: effects of tidal resuspension

Benthic microalgae (BMA) provide vital food resources for heterotrophs and stabilize sediments with their extracellular secretions. A central goal in ecology is to understand how processes such as species interactions and dispersal, contribute to observed patterns of species abundance and distribution. Our objectives were to assess the effects of sediment resuspension on microalgal community structure. We tested whether taxa‐abundance distributions could be predicted using neutral community models (NCMs) and also specific hypotheses about passive migration: (i) As migration decreases in sediment patches, BMA α‐diversity will decrease, and (ii) As migration decreases, BMA community dissimilarity (β‐diversity) will increase. Co‐occurrence indices (checkerboard score and variance ratio) were also computed to test for deterministic factors, such as competition and niche differentiation, in shaping communities. Two intertidal sites (mudflat and sand bar) differing in resuspension regime were sampled throughout the tidal cycle. Fluorometry and denaturing gradient gel electrophoresis were utilized to investigate diatom community structure. Observed taxa‐abundances fit those predicted from NCMs reasonably well (R² of 0.68–0.93), although comparisons of observed local communities to artificial randomly assembled communities rejected the null hypothesis that diatom communities were assembled solely by stochastic processes. No co‐occurrence tests indicated a significant role for competitive exclusion or niche partitioning in microalgal community assembly. In general, predictions about relationships between migration and species diversity were supported for local community dynamics. BMA at low tide (lowest migration) exhibited reduced α‐diversity as compared to periods of immersion at both mudflat and sand bar sites. β‐diversity was higher during low tide emersion on the mudflat, but did not differ temporally at the sand bar site. In between‐site metacommunity comparisons, low‐ and high‐resuspension sites exhibited distinct community compositions while the low‐energy mudflats contained higher microalgal biomass and greater α‐diversity. To our knowledge this is the first study to test the relevance of neutral processes in structuring marine microalgal communities. Our results demonstrate a prominent role for stochastic factors in structuring local BMA community assembly, although unidentified nonrandom processes also appear to play some role. High passive migration, in particular, appears to help maintain species diversity and structure communities in both sand and muddy habitats.     

Patterns of phylogenetic community structure of sand dune plant communities in the Yucatan Peninsula: the role of deterministic and stochastic processes in community assembly

ABSTRACT

Background: Tropical sand dunes are ideal systems for understanding drivers of community assembly as dunes are subject to both deterministic and stochastic processes. However, studies that evaluate the factors that mediate plant community assembly in these ecosystems are few.

Aims: We evaluated phylogenetic community structure to elucidate the role of deterministic and stochastic processes in mediating the assembly of plant communities along the north of the Yucatan Peninsula, Mexico.

Methods: We used plastid genetic markers to evaluate phylogenetic relationships in 16 sand-dune communities. To evaluate the role of climate in shaping plant community structure we carried out linear regressions between climatic variables and mean phylogenetic distance. We estimated the Net Relatedness Index and Nearest Taxon Index to identify ecological processes mediating community assembly.

Results: Observed phylogenetic structure was not different from random, suggesting that stochastic processes are the major determinants of community assembly. Climate was slightly correlated with phylogenetic diversity suggesting that abiotic environment plays a minimal role in community assembly.

Conclusions: Random assembly appears to be the primary factor structuring the studied sand dune plant communities. Environmental filters may represent a secondary factor contributing to the observed phylogenetic structure. Thus, both processes may act simultaneously to mediate the assembly of sand-dune plant communities.     

Ecological filtering or random extinction? Beta‐diversity patterns and the importance of niche‐based and neutral processes following habitat loss

Although both niche‐based and neutral processes are involved in community assembly, most models on the effects of habitat loss are stochastic, assuming neutral communities mainly affected by ecological drift and random extinction. Given that habitat loss is considered the most important driver of the current biodiversity crisis, unraveling the processes underlying the effects of habitat loss is critical from both a theoretical and an applied perspective. Here we unveil the importance of niche‐based and neutral processes to species extinction and community assembly across a gradient of habitat loss, challenging the predictions of neutral models. We draw on a large dataset containing the distribution of 3653 individuals of 42 species, representing 35% of the small mammal species of the Atlantic Forest hotspot, obtained in 68 sites across three continuously‐forested landscapes and three adjacent 10 000‐ha fragmented landscapes differing in the amount of remaining forest (50%, 30% and 10%). By applying a null‐model approach, we investigated β‐diversity patterns by detecting deviations of observed community similarity from the similarity between randomly assembled communities. Species extinction following habitat loss was decidedly non‐random, in contrast to the notion that fragmented communities are mainly driven by ecological drift. Instead, habitat loss led to a strong biotic homogenization. Moreover, species composition changed abruptly at the same level of landscape‐scale habitat loss that has already been associated with a drastic decline in species richness. Habitat loss, as other anthropogenic disturbances, can thus be seen as a strong ecological filter that increases (rather than decreases) the importance of deterministic processes in community assembly. As such, critical advances for the development of conservation science lie on the incorporation of the relevant niche traits associated with extinction proneness into models of habitat loss. The results also underscore the fundamental importance of pro‐active measures to prevent human‐modified landscapes surpassing critical ecological thresholds.