The coherence problem with the Unified Neutral Theory of Biodiversity

Invertebrate diversity in groundwater-filled lava caves is influenced by both neutral- and niche-based processes

Understanding which factors shape and maintain biodiversity is essential to understand how ecosystems respond to crises. Biodiversity observed in ecological communities is a result of the interaction of various factors which can be classified as either neutral- or niche-based. The importance of these processes has been debated, but many scientists believe that both processes are important. Here, we use unique ecosystems in groundwater-filled lava caves near Lake Mývatn, to examine the importance of neutral- versus niche-based factors for shaping invertebrate communities. We studied diversity in benthic and epibenthic invertebrate communities and related them to ecological variables. We hypothesized that if neutral processes are the main drivers of community structure we would not see any clear relationship between the structure of community within caves and ecological factors. If niche-based processes are important we should see clear relationships between community structure and variation in ecological variables across caves. Both communities were species poor, with low densities of invertebrates, showing the resource limited and oligotrophic nature of these systems. Unusually for Icelandic freshwater ecosystems, the benthic communities were not dominated by Chironomidae (Diptera) larvae, but rather by crustaceans, mainly Cladocera. The epibenthic communities were not shaped by environmental variables, suggesting that they may have been structured primarily by neutral processes. The benthic communities were shaped by the availability of energy, and to some extent pH, suggesting that niche-based processes were important drivers of community structure, although neutral processes may still be relevant. The results suggest that both processes are important for invertebrate communities in freshwater, and research should focus on understanding both of these processes. The ponds we studied are representative of a number of freshwater ecosystems that are extremely vulnerable for human disturbance, making it even more important to understand how their biodiversity is shaped and maintained.

Environmental and topographic drivers of amphibian phylogenetic diversity and endemism in the Iberian Peninsula

Understanding the ecological and evolutionary processes driving biodiversity patterns and allowing their persistence is of utmost importance. Many hypotheses have been proposed to explain spatial diversity patterns, including water-energy availability, habitat heterogeneity, and historical climatic refugia. The main goal of this study is to identify if general spatial drivers of species diversity patterns of phylogenetic diversity (PD) and phylogenetic endemism (PE) at the global scale are also predictive of PD and PE at regional scales, using Iberian amphibians as a case study. Our main hypothesis assumes that topography along with contemporary and historical climate are drivers of phylogenetic diversity and endemism, but that the strength of these predictors may be weaker at the regional scale than it tends to be at the global scale. We mapped spatial patterns of Iberian amphibians' phylogenetic diversity and endemism, using previously published phylogenetic and distribution data. Furthermore, we compiled spatial data on topographic and climatic variables related to the water-energy availability, topography, and historical climatic instability hypotheses. To test our hypotheses, we used Spatial Autoregressive Models and selected the best model to explain diversity patterns based on Akaike Information Criterion. Our results show that, out of the variables tested in our study, water-energy availability and historical climate instability are the most important drivers of amphibian diversity in Iberia. However, as predicted, the strength of these predictors in our case study is weaker than it tends to be at global scales. Thus, additional drivers should also be investigated and we suggest caution when interpreting these predictors as surrogates for different components of diversity.

Niche partitioning among dead wood-dependent beetles

Niche partitioning among species with virtually the same requirements is a fundamental concept in ecology. Nevertheless, some authors suggest that niches have little involvement in structuring communities. This study was done in the Pardubice Region (Czech Republic) on saproxylic beetles with morphologically similar larvae and very specific requirements, which are related to their obligatory dependence on dead wood material: Cucujus cinnaberinus, Pyrochroa coccinea, and Schizotus pectinicornis. This work was performed on 232 dead wood pieces at the landscape scale over six years. Based on the factors studied, the relationships among these species indicated that their co-occurrence based on species presence and absence was low, which indicated niche partitioning. However, based on analyses of habitat requirements and species composition using observed species abundances, there was no strong evidence for niche partitioning at either studied habitat levels, the tree and the microhabitat. The most likely reasons for the lack of strong niche partitioning were that dead wood is a rich resource and co-occurrence of saproxylic community was not driven by resource competition. This might be consistent with the theory that biodiversity could be controlled by the neutral drift of species abundance. Nevertheless, niche partitioning could be ongoing, meaning that the expanding C. cinnaberinus may have an advantage over the pyrochroids and could dominate in the long term.

Some species flourish when many do not: a pattern in data on ecological communities

Patterns in species × sample tables of communities depend above all on the organisms of the data sets and the conditions involved. Patterns that surpass individual sets are of special interest. Our question, looking for a shared pattern in 12 sets, is if relative abundances among species are independent of the sample, or formulated alternatively, if species have abundances that are correlated with total abundances over samples. For exploration we study the overdispersion/aggregation of the data. A relatively high variation in the total abundances of samples is noticed, indicating an effect of environmental variation. Overdispersion imposes constraints on the accommodation of relatively high abundance values to samples with a relatively low total abundance. The null hypothesis of ‘no association’ is modelled by permutation/resampling of the data at the level of the individual. A correlation study of actual and permuted sets is performed. All actual sets contain a significant number of species that defy our question. These species flourish when many do not. The relation of our question with issues in theoretical ecology, such as the assumption of a neutral effect of environmental conditions and/or of neutral characteristics of species, is discussed.

Mechanistic reconciliation of community and invasion ecology

Community and invasion ecology have mostly grown independently. There is substantial overlap in the processes captured by different models in the two fields, and various frameworks have been developed to reduce this redundancy and synthesize information content. Despite broad recognition that community and invasion ecology are interconnected, a process-based framework synthesizing models across these two fields is lacking. Here we review 65 representative community and invasion models and propose a common framework articulated around six processes (dispersal, drift, abiotic interactions, within-guild interactions, cross-guild interactions, and genetic changes). The framework is designed to synthesize the content of the two fields, provide a general perspective on their development, and enable their comparison. The application of this framework and of a novel method based on network theory reveals some lack of coherence between the two fields, despite some historical similarities. Community ecology models are characterized by combinations of multiple processes, likely reflecting the search for an overarching theory to explain community assembly and structure, drawing predominantly on interaction processes, but also accounting largely for the other processes. In contrast, most models in invasion ecology invoke fewer processes and focus more on interactions between introduced species and their novel biotic and abiotic environment. The historical dominance of interaction processes and their independent developments in the two fields is also reflected in the lower level of coherence for models involving interactions, compared to models involving dispersal, drift, and genetic changes. It appears that community ecology, with a longer history than invasion ecology, has transitioned from the search for single explanations for patterns observed in nature to investigate how processes may interact mechanistically, thereby generating and testing hypotheses. Our framework paves the way for a similar transition in invasion ecology, to better capture the dynamics of multiple alien species introduced in complex communities. Reciprocally, applying insights from invasion to community ecology will help us understand and predict the future of ecological communities in the Anthropocene, in which human activities are weakening species' natural boundaries. Ultimately, the successful integration of the two fields could advance a predictive ecology that is urgently required in a rapidly changing world.

Emergent neutrality in consumer-resource dynamics

Neutral theory assumes all species and individuals in a community are ecologically equivalent. This controversial hypothesis has been tested across many taxonomic groups and environmental contexts, and successfully predicts species abundance distributions across multiple high-diversity communities. However, it has been critiqued for its failure to predict a broader range of community properties, particularly regarding community dynamics from generational to geological timescales. Moreover, it is unclear whether neutrality can ever be a true description of a community given the ubiquity of interspecific differences, which presumably lead to ecological inequivalences. Here we derive analytical predictions for when and why non-neutral communities of consumers and resources may present neutral-like outcomes, which we verify using numerical simulations. Our results, which span both static and dynamical community properties, demonstrate the limitations of summarizing distributions to detect non-neutrality, and provide a potential explanation for the successes of neutral theory as a description of macroecological pattern.

The neutral theory of biodiversity assumes that species are ecologically equivalent. Given the natural history observation of ubiquitous phenotypic differences between species, it is surprising that neutral theory has successfully predicted a broad range of biodiversity patterns, and simultaneously unsurprising that these results have not convinced ecologists that the natural world is neutral. However, we have lacked a description of how neutrality can emerge in a natural way from ecological mechanisms and species differences. Our study sheds light on this question, providing a theoretical backdrop for the success of neutral theory as a description of macroecological pattern. We derive a prediction for the degree to which consumers must differ in preferences for different resources before the resulting biodiversity patterns become distinguishable from neutrality. These predictions, which we confirm using simulations, show that neutral-like outcomes are possible even when resource requirements across consumers are very far from neutral. Our results can be tested in experimental microbial communities, where, equipped with an inferred consumption network, our analysis can yield predictions for biodiversity patterns and community turnover at different taxonomic levels.

Coexistence of plant species under harsh environmental conditions: an evaluation of niche differentiation and stochasticity along salt marsh creeks

Background

Ecologists have achieved much progress in the study of mechanisms that maintain species coexistence and diversity. In this paper, we reviewed a wide range of past research related to these topics, focusing on five theoretical bodies: (1) coexistence by niche differentiation, (2) coexistence without niche differentiation, (3) coexistence along environmental stress gradients, (4) coexistence under non-equilibrium versus equilibrium conditions, and (5) modern perspectives.

Results

From the review, we identified that there are few models that can be generally and confidently applicable to different ecological systems. This problem arises mainly because most theories have not been substantiated by enough empirical research based on field data to test various coexistence hypotheses at different spatial scales. We also found that little is still known about the mechanisms of species coexistence under harsh environmental conditions. This is because most previous models treat disturbance as a key factor shaping community structure, but they do not explicitly deal with stressful systems with non-lethal conditions. We evaluated the mainstream ideas of niche differentiation and stochasticity for the coexistence of plant species across salt marsh creeks in southwestern Denmark. The results showed that diversity indices, such as Shannon–Wiener diversity, richness, and evenness, decreased with increasing surface elevation and increased with increasing niche overlap and niche breadth. The two niche parameters linearly decreased with increasing elevation. These findings imply a substantial influence of an equalizing mechanism that reduces differences in relative fitness among species in the highly stressful environments of the marsh. We propose that species evenness increases under very harsh conditions if the associated stress is not lethal. Finally, we present a conceptual model of patterns related to the level of environmental stress and niche characteristics along a microhabitat gradient (i.e., surface elevation).

Conclusions

The ecology of stressful systems with non-lethal conditions will be increasingly important as ongoing global-scale climate change extends the period of chronic stresses that are not necessarily fatal to inhabiting plants. We recommend that more ecologists continue this line of research.

Neutral syndrome

Neutral models of evolution assume the absence of natural selection. Formerly confined to ecology and evolutionary biology, neutral models are spreading. In recent years they've been applied to explaining the diversity of baby names, scientific citations, cryptocurrencies, pot decorations, literary lexica, tumour variants and much more besides. Here, we survey important neutral models and highlight their similarities. We investigate the most widely used tests of neutrality, show that they are weak and suggest more powerful methods. We conclude by discussing the role of neutral models in the explanation of diversity. We suggest that the ability of neutral models to fit low-information distributions should not be taken as evidence for the absence of selection. Nevertheless, many studies, in increasingly diverse fields, make just such claims. We call this tendency 'neutral syndrome'.

Towards an integrative understanding of soil biodiversity

Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species-energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale-dependent nature of soil biodiversity.

Partitioning beta diversity in a tropical karst seasonal rainforest in Southern China

Both deterministic and stochastic processes have been linked to forest community assembly; however, their contribution to beta diversity has not been properly explored, and no studies to date have investigated their impacts on sparse depleted soils in forests that contain widespread exposed limestone karst. We found that the pairwise differences in species composition between quadrates was determined by a balanced variation in abundance, whereby the individuals of some species at one site were substituted by an equivalent number of individuals of different species at another site. Both the total beta diversity and its balanced variation in abundance declined with increasing sampling grain size. Our research indicated that environmental differences exert a strong influence on beta diversity, particularly total beta diversity and its balanced abundance variation in larger grain sizes. It was evident that deterministic and stochastic processes worked together, and that deterministic processes were more important than stochastic processes in the regulation of beta diversity in this heterogeneous tropical karst seasonal rainforest of Southern China. However, in future research a functional trait based approach will be required to tease out the relative degree of deterministic and stochastic processes toward an assessment of the temporal changes in species composition.

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research.

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research.

Drivers of metacommunity structure diverge for common and rare Amazonian tree species

We analysed the flora of 46 forest inventory plots (25 m x 100 m) in old growth forests from the Amazonian region to identify the role of environmental (topographic) and spatial variables (obtained using PCNM, Principal Coordinates of Neighbourhood Matrix analysis) for common and rare species. For the analyses, we used multiple partial regression to partition the specific effects of the topographic and spatial variables on the univariate data (standardised richness, total abundance and total biomass) and partial RDA (Redundancy Analysis) to partition these effects on composition (multivariate data) based on incidence, abundance and biomass. The different attributes (richness, abundance, biomass and composition based on incidence, abundance and biomass) used to study this metacommunity responded differently to environmental and spatial processes. Considering standardised richness, total abundance (univariate) and composition based on biomass, the results for common species differed from those obtained for all species. On the other hand, for total biomass (univariate) and for compositions based on incidence and abundance, there was a correspondence between the data obtained for the total community and for common species. Our data also show that in general, environmental and/or spatial components are important to explain the variability in tree communities for total and common species. However, with the exception of the total abundance, the environmental and spatial variables measured were insufficient to explain the attributes of the communities of rare species. These results indicate that predicting the attributes of rare tree species communities based on environmental and spatial variables is a substantial challenge. As the spatial component was relevant for several community attributes, our results demonstrate the importance of using a metacommunities approach when attempting to understand the main ecological processes underlying the diversity of tropical forest communities.

Multiple phase transitions in an agent-based evolutionary model with neutral fitness

Null models are crucial for understanding evolutionary processes such as speciation and adaptive radiation. We analyse an agent-based null model, considering a case without selection-neutral evolution-in which organisms are defined only by phenotype. Universal dynamics has previously been demonstrated in a related model on a neutral fitness landscape, showing that this system belongs to the directed percolation (DP) universality class. The traditional null condition of neutral fitness (where fitness is defined as the number of offspring each organism produces) is extended here to include equal probability of death among organisms. We identify two types of phase transition: (i) a non-equilibrium DP transition through generational time (i.e. survival), and (ii) an equilibrium ordinary percolation transition through the phenotype space (based on links between mating organisms). Owing to the dynamical rules of the DP reaction-diffusion process, organisms can only sparsely fill the phenotype space, resulting in significant phenotypic diversity within a cluster of mating organisms. This highlights the necessity of understanding hierarchical evolutionary relationships, rather than merely developing taxonomies based on phenotypic similarity, in order to develop models that can explain phylogenetic patterns found in the fossil record or to make hypotheses for the incomplete fossil record of deep time.

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.

Understanding how biodiversity unfolds through time under neutral theory

Theoretical predictions for biodiversity patterns are typically derived under the assumption that ecological systems have reached a dynamic equilibrium. Yet, there is increasing evidence that various aspects of ecological systems, including (but not limited to) species richness, are not at equilibrium. Here, we use simulations to analyse how biodiversity patterns unfold through time. In particular, we focus on the relative time required for various biodiversity patterns (macroecological or phylogenetic) to reach equilibrium. We simulate spatially explicit metacommunities according to the Neutral Theory of Biodiversity (NTB) under three modes of speciation, which differ in how evenly a parent species is split between its two daughter species. We find that species richness stabilizes first, followed by species area relationships (SAR) and finally species abundance distributions (SAD). The difference in timing of equilibrium between these different macroecological patterns is the largest when the split of individuals between sibling species at speciation is the most uneven. Phylogenetic patterns of biodiversity take even longer to stabilize (tens to hundreds of times longer than species richness) so that equilibrium predictions from neutral theory for these patterns are unlikely to be relevant. Our results suggest that it may be unwise to assume that biodiversity patterns are at equilibrium and provide a first step in studying how these patterns unfold through time.

Adding energy gradients and long-distance dispersal to a neutral model improves predictions of Madagascan bird diversity

Macroecological patterns are likely the result of both stochastically neutral mechanisms and deterministic differences between species. In Madagascar, the simplest stochastically neutral hypothesis - the mid-domain effects (MDE) hypothesis - has already been rejected. However, rejecting the MDE hypothesis does not necessarily refute the existence of all other neutral mechanisms. Here, we test whether adding complexity to a basic neutral model improves predictions of biodiversity patterns. The simplest MDE model assumes that: (1) species' ranges are continuous and unfragmented, (2) are randomly located throughout the landscape, and (3) can be stacked independently and indefinitely. We designed a simulation based on neutral theory that allowed us to weaken each of these assumptions incrementally by adjusting the habitat capacity as well as the likelihood of short- and long-distance dispersal. Simulated outputs were compared to four empirical patterns of bird diversity: the frequency distributions of species richness and range size, the within-island latitudinal diversity gradient, and the distance-decay of species compositional similarity. Neutral models emulated empirical diversity patterns for Madagascan birds accurately. The frequency distribution of range size, latitudinal diversity gradient, and the distance-decay of species compositional similarity could be attributed to stochastic long-distance migration events and zero-sum population dynamics. However, heterogenous environmental gradients improved predictions of the frequency distribution of species richness. Patterns of bird diversity in Madagascar can broadly be attributed to stochastic long-distance migration events and zero-sum population dynamics. This implies that rejecting simple hypotheses, such as MDE, does not serve as evidence against stochastic processes in general. However, environmental gradients were necessary to explain patterns of species richness and deterministic differences between species are probably important for explaining the distributions of narrow-range and endemic species.

Dynamics of extinction debt across five taxonomic groups

Species extinction following habitat loss is well documented. However, these extinctions do not happen immediately. The biodiversity surplus (extinction debt) declines with some delay through the process of relaxation. Estimating the time constants of relaxation, mainly the expected time to first extinction and the commonly used time for half the extinction debt to be paid off (half-life), is crucial for conservation purposes. Currently, there is no agreement on the rate of relaxation and the factors that it depends on. Here we find that half-life increases with area for all groups examined in a large meta-analysis of extinction data. A common pattern emerges if we use average number of individuals per species before habitat loss as an area index: for mammals, birds, reptiles and plants, the relationship has an exponent close to a half. We also find that the time to first determined extinction is short and increases slowly with area.

Historical and contemporary factors generate unique butterfly communities on islands

The mechanisms shaping island biotas are not yet well understood mostly because of a lack of studies comparing eco-evolutionary fingerprints over entire taxonomic groups. Here, we linked community structure (richness, frequency and nestedness) and genetic differentiation (based on mitochondrial DNA) in order to compare insular butterfly communities occurring over a key intercontinental area in the Mediterranean (Italy-Sicily-Maghreb). We found that community characteristics and genetic structure were influenced by a combination of contemporary and historical factors, and among the latter, connection during the Pleistocene had an important impact. We showed that species can be divided into two groups with radically different properties: widespread taxa had high dispersal capacity, a nested pattern of occurrence, and displayed little genetic structure, while rare species were mainly characterized by low dispersal, high turnover and genetically differentiated populations. These results offer an unprecedented view of the distinctive butterfly communities and of the main processes determining them on each studied island and highlight the importance of assessing the phylogeographic value of populations for conservation.

Species associations structured by environment and land-use history promote beta-diversity in a temperate forest

Patterns of diversity and community composition in forests are controlled by a combination of environmental factors, historical events, and stochastic or neutral mechanisms. Each of these processes has been linked to forest community assembly, but their combined contributions to alpha and beta-diversity in forests has not been well explored. Here we use variance partitioning to analyze approximately 40,000 individual trees of 49 species, collected within 137 ha of sampling area spread across a 900-ha temperate deciduous forest reserve in Pennsylvania to ask (1) To what extent is site-to-site variation in species richness and community composition of a temperate forest explained by measured environmental gradients and by spatial descriptors (used here to estimate dispersal-assembly or unmeasured, spatially structured processes)? (2) How does the incorporation of land-use history information increase the importance attributed to deterministic community assembly? and (3) How do the distributions and abundances of individual species within the community correlate with these factors? Environmental variables (i.e., topography, soils, and distance to stream), spatial descriptors (i.e., spatial eigenvectors derived from Cartesian coordinates), and land-use history variables (i.e., land-use type and intensity, forest age, and distance to road), explained about half of the variation in both species richness and community composition. Spatial descriptors explained the most variation, followed by measured environmental variables and then by land- use history. Individual species revealed variable responses to each of these sets of predictor variables. Several species were associated with stream habitats, and others were strictly delimited across opposing north- and south-facing slopes. Several species were also associated with areas that experienced recent (i.e., <100 years) human land-use impacts. These results indicate that deterministic factors, including environmental and land-use history variables, are important drivers of community response. The large amount of "unexplained" variation seen here (about 50%) is commonly observed in other such studies attempting to explain distribution and abundance patterns of plant communities. Determining whether such large fractions of unaccounted for variation are caused by a lack of sufficient data, or are an indication of stochastic features of forest communities globally, will remain an important challenge for ecologists in the future.

When can species abundance data reveal non-neutrality?

Species abundance distributions (SAD) are probably ecology's most well-known empirical pattern, and over the last decades many models have been proposed to explain their shape. There is no consensus over which model is correct, because the degree to which different processes can be discerned from SAD patterns has not yet been rigorously quantified. We present a power calculation to quantify our ability to detect deviations from neutrality using species abundance data. We study non-neutral stochastic community models, and show that the presence of non-neutral processes is detectable if sample size is large enough and/or the amplitude of the effect is strong enough. Our framework can be used for any candidate community model that can be simulated on a computer, and determines both the sampling effort required to distinguish between alternative processes, and a range for the strength of non-neutral processes in communities whose patterns are statistically consistent with neutral theory. We find that even data sets of the scale of the 50 Ha forest plot on Barro Colorado Island, Panama, are unlikely to be large enough to detect deviations from neutrality caused by competitive interactions alone, though the presence of multiple non-neutral processes with contrasting effects on abundance distributions may be detectable.

Small-scale spatial variability in phylogenetic community structure during early plant succession depends on soil properties

During early plant succession, the phylogenetic structure of a community changes in response to important environmental filters and emerging species interactions. We traced the development of temperate-zone plant communities during the first 7 years of primary succession on catchment soils to explore patterns of initial species assembly. We found pronounced small-scale differences in the phylogenetic composition of neighbouring plant assemblages and a large-scale trend towards phylogenetic evenness. This small-scale variability appears to be mediated by soil properties, particularly carbonate content. Therefore, abiotic environmental conditions might counteract or even supersede the effects of interspecific competition among closely related species, which are usually predicted to exhibit patterns of phylogenetic evenness. We conclude that theories on phylogenetic community composition need to incorporate effects of small-scale variability of environmental factors.

Phylogenetic community structure: temporal variation in fish assemblage

Hypotheses about phylogenetic relationships among species allow inferences about the mechanisms that affect species coexistence. Nevertheless, most studies assume that phylogenetic patterns identified are stable over time. We used data on monthly samples of fish from a single lake over 10 years to show that the structure in phylogenetic assemblages varies over time and conclusions depend heavily on the time scale investigated. The data set was organized in guild structures and temporal scales (grouped at three temporal scales). Phylogenetic distance was measured as the mean pairwise distances (MPD) and as mean nearest-neighbor distance (MNTD). Both distances were based on counts of nodes. We compared the observed values of MPD and MNTD with values that were generated randomly using null model independent swap. A serial runs test was used to assess the temporal independence of indices over time. The phylogenetic pattern in the whole assemblage and the functional groups varied widely over time. Conclusions about phylogenetic clustering or dispersion depended on the temporal scales. Conclusions about the frequency with which biotic processes and environmental filters affect the local assembly do not depend only on taxonomic grouping and spatial scales. While these analyzes allow the assertion that all proposed patterns apply to the fish assemblages in the floodplain, the assessment of the relative importance of these processes, and how they vary depending on the temporal scale and functional group studied, cannot be determined with the effort commonly used. It appears that, at least in the system that we studied, the assemblages are forming and breaking continuously, resulting in various phylogeny-related structures that makes summarizing difficult.

Neutral theory and the species abundance distribution: recent developments and prospects for unifying niche and neutral perspectives

Published in 2001, The Unified Neutral Theory of Biodiversity and Biogeography (UNTB) emphasizes the importance of stochastic processes in ecological community structure, and has challenged the traditional niche-based view of ecology. While neutral models have since been applied to a broad range of ecological and macroecological phenomena, the majority of research relating to neutral theory has focused exclusively on the species abundance distribution (SAD). Here, we synthesize the large body of work on neutral theory in the context of the species abundance distribution, with a particular focus on integrating ideas from neutral theory with traditional niche theory. First, we summarize the basic tenets of neutral theory; both in general and in the context of SADs. Second, we explore the issues associated with neutral theory and the SAD, such as complications with fitting and model comparison, the underlying assumptions of neutral models, and the difficultly of linking pattern to process. Third, we highlight the advances in understanding of SADs that have resulted from neutral theory and models. Finally, we focus consideration on recent developments aimed at unifying neutral- and niche-based approaches to ecology, with a particular emphasis on what this means for SAD theory, embracing, for instance, ideas of emergent neutrality and stochastic niche theory. We put forward the argument that the prospect of the unification of niche and neutral perspectives represents one of the most promising future avenues of neutral theory research.

Facilitation as a ubiquitous driver of biodiversity

Models describing the biotic drivers that create and maintain biological diversity within trophic levels have focused primarily on negative interactions (i.e. competition), leaving marginal room for positive interactions (i.e. facilitation). We show facilitation to be a ubiquitous driver of biodiversity by first noting that all species use resources and thus change the local biotic or abiotic conditions, altering the available multidimensional niches. This can cause a shift in local species composition, which can cause an increase in beta, and sometimes alpha, diversity. We show that these increases are ubiquitous across ecosystems. These positive effects on diversity occur via a broad host of disparate direct and indirect mechanisms. We identify and unify several of these facilitative mechanisms and discuss why it has been easy to underappreciate the importance of facilitation. We show that net positive effects have a long history of being considered ecologically or evolutionarily unstable, and we present recent evidence of its potential stability. Facilitation goes well beyond the common case of stress amelioration and it probably gains importance as community complexity increases. While biodiversity is, in part, created by species exploiting many niches, many niches are available to exploit only because species create them.

The co-occurrence of species and the co-diversity of sites in neutral models of biodiversity

Patterns of co-occurrence of species are widely used to assess the fit of ecological neutral models to empirical patterns. The mathematically equivalent patterns of co-diversity of sites, in contrast, have been considered only indirectly and analyses normally are focused on the spatial distribution of species richness, rather than on the patterns of species sharing. Here we use two analytical tools (range-diversity plots and rank plots) to assess the predictions of simple neutral models in relation to patterns of co-occurrence and co-diversity. Whereas a fully stochastic null model predicts zero average among species and among sites, neutral models generate systems with low levels of covariance among species and high levels of positive covariance among sites. These patterns vary with different combinations of dispersal and speciation rates, but are always linked to the shape, symmetry, and spread of the range-size and species-richness frequency distributions. Non-homogeneous patterns of diversity and distribution arise in neutral models because of the spatial arrangement of sites and their concomitant similarity, which is reflected also in the spread of the range-size frequency distribution. The nearly null covariance among species, in contrast, implies low variance in species richness of sites and very slim frequency distributions. In real world assemblages of Mexican volant and non-volant mammals, patterns of range-size and species-richness frequency distribution are similar to those generated by neutral models. However, when the comparison includes the covariance both for species (co-occurrence) and for sites (co-diversity), empirical patterns differ significantly from the predictions of neutral models. Because of the mathematical links between the covariance in the distribution of species and the variance of species-richness values and between the covariance in species sharing among sites and the variance of range-size values, a full understanding of patterns of diversity calls for the simultaneous analysis of co-occurrence and co-diversity.

Species-specific traits plus stabilizing processes best explain coexistence in biodiverse fire-prone plant communities

Coexistence in fire-prone Mediterranean-type shrublands has been explored in the past using both neutral and niche-based models. However, distinct differences between plant functional types (PFTs), such as fire-killed vs resprouting responses to fire, and the relative similarity of species within a PFT, suggest that coexistence models might benefit from combining both neutral and niche-based (stabilizing) approaches. We developed a multispecies metacommunity model where species are grouped into two PFTs (fire-killed vs resprouting) to investigate the roles of neutral and stabilizing processes on species richness and rank-abundance distributions. Our results show that species richness can be maintained in two ways: i) strictly neutral species within each PFT, or ii) species within PFTs differing in key demographic properties, provided that additional stabilizing processes, such as negative density regulation, also operate. However, only simulations including stabilizing processes resulted in structurally realistic rank-abundance distributions over plausible time scales. This result underscores the importance of including both key species traits and stabilizing (niche) processes in explaining species coexistence and community structure.

Modelling the effects of dispersal mechanisms and hydrodynamic regimes upon the structure of microbial communities within fluvial biofilms

The spatial distribution of microbial taxa is determined primarily by physical and chemical environments and by dispersal. In a homogeneous landscape with limited dispersal, the similarity in abundance of taxa in samples declines with separation distance. We present a one-dimensional model for the spatial autocorrelation in abundances arising from immigration from some remote community and dispersal between environmentally similar landscape patches. Spatial correlation in taxa abundances were calculated from biofilms from the beds of two flumes which differed only in their bedform profiles; one flat and the other a periodic sawtooth shape. The hydraulic regime is approximately uniform over the flat bed, whereas the sawtooth induces fast flow over the peaks and recirculation in the troughs. On the flat bed, the correlation decline between samples was reproduced by a model using one biologically reasonable parameter. A decline was apparent in the other flume; however, a better fit was achieved when dispersal was not assumed constant everywhere. However, analysis of finer-resolution data for the heterogeneous flume suggested even this model did not adequately capture the community's complexity. We conclude that hydrodynamics are a strong driver of taxa-abundance patterns in stream biofilms. However, local adaptability must also be considered to build up a complete mechanistic model.