Species abundance distributions as a proxy for the niche-neutrality continuum

Aims Species abundance distributions (SADs) are often used to verify mechanistic theories underlying community assembly. However, it is now accepted that SADs alone are not sufficient to reveal biological mechanisms. Recent attention focuses on the relative importance of stochastic dispersal processes versus deterministic processes such as interspecific competition and environmental filtering. Here, we combine a study of the commonness and rarity of species (i.e. the SAD) with mechanistic processes underlying community composition. By comparing the occurrence frequencies of each and every species with its abundance, we quantify the relative contributions of common and rare species to the maintenance of community structure. Essentially, we relate the continuum between commonness and rarity with that of niches and neutrality.Methods An individual-based, spatially explicit model was used to simulate local communities in niche spaces with the same parameters. We generated sets of assemblages from which species were eliminated in opposing sequences: from common to rare and from rare to common, and investigated the relationship between the abundance and frequency of species. We tested the predictions of our model with empirical data from a field experiment in the environmentally homogeneous alpine meadows of the Qinghai–Tibetan plateau.Important findings Our simulations support the widespread notion that common species maintain community structure, while rare species maintain species diversity, in both local and regional communities. Our results, both from theoretical simulations and from empirical observations, revealed positive correlations between the abundance of a particular species and its occurrence frequency. SAD curves describe a continuum between commonness and rarity. Removing species from the 'rare' end of this continuum has little effect on the similarity of communities, but removing species from the 'common' end of the continuum causes significant increases in beta diversity, or species turnover, between communities. In local communities distributed in a homogenous habitat, species located at the 'common' end of the continuum should be selected by environmental filtering, with niche space partitioning governed by interspecific competition. Conversely, species located at the 'rare' end of the continuum are most likely subject to stochastic dispersal processes. Species situated at intermediate locations on this continuum are therefore determined by niche and neutral processes acting together. Our results suggest that, in homogeneous habitats, SAD curves describing the common-rare continuum may also be used to describe the continuum between niches and neutrality.     

The contribution of common and rare species to species abundance patterns in alpine meadows: The effect of elevation gradients

Ecological niche modeling uses environmental variables associated with species distribution points to simulate species distribution and its importance in biodiversity conservation. This study aimed to quantify plant community composition and species abundance distribution (SAD) in alpine meadows at different elevations and to assess the contribution of rare and common species to SAD. We established a permanent study plot of 210 hm² in Gannan Tibetan Autonomous Prefecture, China, surveyed 315 sample squares (0.5 m × 0.5 m), and calculated the Hill numbers. The results showed that (1) a total of 72 species were surveyed at different altitudes, with Kobresia humilis and Kobresia macrantha as the main dominant species; (2) the SADs of overall and common species fit the ecological niche model (GSM (Geometric Sequence Model)), indicating that ecological niche differentiation is the main factor influencing SAD. The fitted model for rare species SAD varied with elevation, suggesting that various ecological processes influence rare species SAD. (3) Hill numbers showed a “single peak” pattern with increasing elevation. The number of rare species was higher than that of common species. Still, the distribution frequency of common species was significantly higher than rare species. The correlation between common-rare species sequences and cumulative species distribution was high. This indicates that common species dominate the species diversity pattern of the community, are the main contributors to the SAD pattern, and should be protected first. Rare species are also important carriers of community function and include much spatial information. Rare and common species work together in different ways to influence and maintain the species diversity patterns of alpine meadow plant communities.     

Are there differences in structure between marine and terrestrial assemblages?

Recently, interest in species abundance (SAD) distributions has been revived by introduction of a new model, the zero-sum multinomial (ZSM). Yet detailed statistical analyses show that the model does not differ from the lognormal distribution proposed in the 1940s. These analyses were based on data from tropical trees where all individuals in a defined area were identified to species. For many ecological data sets it is not possible to identify and count all individuals in a given area. Here we compare data on marine benthos and fish assemblages with data on terrestrial microfauna and ants. We show that these assemblages show similar SAD patterns and that the SADs are best described by a two-group lognormal model. Whereas the 2-group model fitted all data sets the single group model fitted all except the tropical rainforest ants. However, tests comparing the fits to the 2-group versus the single lognormal model showed that the 2-group model was a significantly better fit to the fish and insect data. The two groups are of rare and common species and the rare group dominates in all four data sets. We suggest that the reason for this is that rare species are continuously immigrating from outside the sampled area. Data on tropical tree assemblages where complete accounts were made do not show such high dominance of rare species where the sampled area is large. We conclude that SAD patterns are similar in marine and terrestrial systems that are open to immigration and that the lognormal distribution is still a valid model for SADs.     

Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework

Species abundance distributions (SADs) follow one of ecology's oldest and most universal laws – every community shows a hollow curve or hyperbolic shape on a histogram with many rare species and just a few common species. Here, we review theoretical, empirical and statistical developments in the study of SADs. Several key points emerge. (i) Literally dozens of models have been proposed to explain the hollow curve. Unfortunately, very few models are ever rejected, primarily because few theories make any predictions beyond the hollow-curve SAD itself. (ii) Interesting work has been performed both empirically and theoretically, which goes beyond the hollow-curve prediction to provide a rich variety of information about how SADs behave. These include the study of SADs along environmental gradients and theories that integrate SADs with other biodiversity patterns. Central to this body of work is an effort to move beyond treating the SAD in isolation and to integrate the SAD into its ecological context to enable making many predictions. (iii) Moving forward will entail understanding how sampling and scale affect SADs and developing statistical tools for describing and comparing SADs. We are optimistic that SADs can provide significant insights into basic and applied ecological science.     

How species richness and total abundance constrain the distribution of abundance

The species abundance distribution (SAD) is one of the most intensively studied distributions in ecology and its hollow‐curve shape is one of ecology's most general patterns. We examine the SAD in the context of all possible forms having the same richness (S) and total abundance (N), i.e. the feasible set. We find that feasible sets are dominated by similarly shaped hollow curves, most of which are highly correlated with empirical SADs (most R² values > 75%), revealing a strong influence of N and S on the form of the SAD and an a priori explanation for the ubiquitous hollow curve. Empirical SADs are often more hollow and less variable than the majority of the feasible set, revealing exceptional unevenness and relatively low natural variability among ecological communities. We discuss the importance of the feasible set in understanding how general constraints determine observable variation and influence the forms of predicted and empirical patterns.     

A meta‐analysis of species–abundance distributions

The species–abundance distribution (SAD) describes the abundances of all species within a community. Many different models have been proposed to describe observed SADs. Best known are the logseries, the lognormal, and a variety of niche division models. They are most often visualized using either species richness – log abundance class (Preston) plots or abundance – species rank order (Whittaker) plots. Because many of the models predict very similar shapes, model distinction and testing become problematic. However, the variety of models can be classified into three basic types: one that predicts a double S‐shape in Whittaker plots and a unimodal distribution in Preston plots (the lognormal type), a second that lacks the mode in Preston plots (the logseries type), and a third that predicts power functions in both plotting types (the power law type). Despite the interest of ecologists in SADs no formal meta‐analysis of models and plotting types has been undertaken so far. Here we use a compilation of 558 species–abundance distributions from 306 published papers to infer the frequency of the three SAD shapes in dependence of environmental variables and type of plotting. Our results highlight the importance of distinguishing between fully censused and incompletely sampled communities in the study of SADs. We show that completely censused terrestrial or freshwater animal communities tend to follow lognormal type SADs more often than logseries or power law types irrespective of species richness, spatial scale, and geographic position. However, marine communities tend to follow the logseries type, while plant communities tend to follow the power law. In incomplete sets the power law fitted best in Whittaker plots, and the logseries in Preston plots. Finally our study favors the use of Whittaker over Preston plots.     

Self-organizing map and species abundance distribution of stream benthic macroinvertebrates in revealing community patterns in different seasons

Benthic macroinvertebrates are considered to be one of the most representative taxa in assessing the ecological integrity of aquatic ecosystems. Data for benthic macroinvertebrates collected using the Surber sampler were used for analysis at different sampling sites across different levels of pollution. Species Abundance Distribution (SAD) and Self-Organizing Map (SOM) were utilized in combination to reveal both consistency and variability in community compositions under natural and anthropogenic conditions. According to the SOM benthic macroinvertebrates were clustered in different season groups (e.g., “summer”, “autumn–winter”) at the less polluted site. SADs of the sampled communities, however, were overall stable across different seasons except the period from late spring to summer (i.e., low level of abundance for the mid-ranked species in SADs) due to heavy rainfall in the Monsoon climate. Along with increase in degree of pollution, seasonality deceased for both SOMs and SADs. In all seasons, the SAD curves were fitted to a lognormal distribution for the less polluted site while the polluted site was in accordance with a geometric series. The parameters in the SAD models were not significantly different across different seasons. Species in the highest ranks in the SADs were persistently dominant regardless of seasons, while densities of the mid-ranked species were variable in different seasons at the less and intermediately polluted sites. At the severely polluted site a few selected tolerant species showed high densities persistently and variability of densities in different seasons was minimized. Species groups clustered using the SOM also presented stronger persistence in SADs, and were feasible in addressing diverse patterns of species composition and in outlining species associations presented in different sampling sites through ordination and clustering. The combined use of SOM and SAD is highly be suitable in presenting community properties and ecological integrity in stream ecosystems in response to natural variability and anthropogenic disturbances.     

Taking species abundance distributions beyond individuals

The species abundance distribution (SAD) is one of the few universal patterns in ecology. Research on this fundamental distribution has primarily focused on the study of numerical counts, irrespective of the traits of individuals. Here we show that considering a set of Generalized Species Abundance Distributions (GSADs) encompassing several abundance measures, such as numerical abundance, biomass and resource use, can provide novel insights into the structure of ecological communities and the forces that organize them. We use a taxonomically diverse combination of macroecological data sets to investigate the similarities and differences between GSADs. We then use probability theory to explore, under parsimonious assumptions, theoretical linkages among them. Our study suggests that examining different GSADs simultaneously in natural systems may help with assessing determinants of community structure. Broadening SADs to encompass multiple abundance measures opens novel perspectives in biodiversity research and warrants future empirical and theoretical developments.     

Ecological response hides behind the species abundance distribution: Community response to low‐intensity disturbance in managed grasslands

Land‐use and management are disturbance factors that have diverse effects on community composition and structure. In traditional rural grasslands, such as meadows and pastures, low‐intensity management is maintained to enhance biodiversity. Maintenance of road verges, in turn, creates habitat, which may complement traditional rural grasslands. To evaluate the effect of low‐intensity disturbance on insect communities, we characterized species abundance distributions (SAD) for Carabidae, Formicidae, and Heteroptera in three grassland types, which differed in management: meadows, pastures, and road verges. The shape of SAD was estimated with three parameters: abundance decay rate, dominance, and rarity. We compared the SAD shape among the grassland types and tested the effect of environmental heterogeneity (plant species richness) and disturbance intensity (trampling in pastures) on SADs. The shape of SADs did not differ among the grassland types but among the taxonomic groups instead. Abundance decay rate and dominance were larger for Formicidae, and rarity smaller, than for Carabidae and Heteroptera. For Carabidae and window‐trapped Heteroptera, rarity increased with increasing plant species richness. For Formicidae, dominance increased with trampling intensity in pastures. Although the SAD shape remained largely unchanged, the identity of the dominant species tended to vary within and among grassland types. Our study shows that for a given taxonomic group, the SAD shape is similar across habitat types with low‐intensity disturbances resulting from different management. This suggests that SADs respond primarily to the intensity of disturbance and thus could be best used in monitoring communities across strong disturbance and environmental gradients. Because taxonomic groups can inherently have different SADs, taxon‐specific SADs for undisturbed communities must be empirically documented before the SAD shape can be used as an indicator of environmental change. Because the identity of the dominant species changes from management type to another, the SAD shape alone is not an adequate monitoring tool.     

Is there an ecological basis for species abundance distributions?

Community ecologists have attempted to explain species abundance distribution (SAD) shape for more than 80 years, but usually without relating SAD shape explicitly to ecological variables. We explored whether the scale (total assemblage abundance) and shape (assemblage evenness) of avifaunal SADs were related to ecological covariates. We used data on avifaunas, in-site habitat structure and landscape context that were assembled from previous studies; this amounted to 197 transects distributed across 16,000 km² of the box-ironbark forests of southeastern Australia. We used Bayesian conditional autoregressive models to link SAD scale and shape to these ecological covariates. Variation in SAD scale was relatable to some ecological covariates, especially to landscape vegetation cover and to tree height. We could not find any relationships between SAD shape and ecological covariates. SAD shape, the core component in SAD theory, may hold little information about how assemblages are governed ecologically and may result from statistical processes, which, if general, would indicate that SAD shape is not useful for distinguishing among theories of assemblage structure.     

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.     

Universal scaling of species‐abundance distributions across multiple scales

The scale‐dependent species abundance distribution (SAD) is fundamental in ecology, but few spatially explicit models of this pattern have thus far been studied. Here we show spatially explicit neutral model predictions for SADs over a wide range of spatial scales, which appear to match empirical patterns qualitatively. We find that the assumption of a log‐series SAD in the metacommunity made by spatially implicit neutral models can be justified with a spatially explicit model in the large area limit. Furthermore, our model predicts that SADs on multiple scales are characterized by a single, compound parameter that represents the ratio of the survey area to the species’ average biogeographic range (which is in turn set by the speciation rate and the dispersal distance). This intriguing prediction is in line with recent empirical evidence for a universal scaling of the species‐area curve. Hence we hypothesize that empirical SAD patterns will show a similar universal scaling for many different taxa and across multiple spatial scales.     

Evidence from GC-TRFLP that bacterial communities in soil are lognormally distributed

The Species Abundance Distribution (SAD) is a fundamental property of ecological communities and the form and formation of SADs have been examined for a wide range of communities including those of microorganisms. Progress in understanding microbial SADs, however, has been limited by the remarkable diversity and vast size of microbial communities. As a result, few microbial systems have been sampled with sufficient depth to generate reliable estimates of the community SAD. We have used a novel approach to characterize the SAD of bacterial communities by coupling genomic DNA fractionation with analysis of terminal restriction fragment length polymorphisms (GC-TRFLP). Examination of a soil microbial community through GC-TRFLP revealed 731 bacterial operational taxonomic units (OTUs) that followed a lognormal distribution. To recover the same 731 OTUs through analysis of DNA sequence data is estimated to require analysis of 86,264 16S rRNA sequences. The approach is examined and validated through construction and analysis of simulated microbial communities in silico. Additional simulations performed to assess the potential effects of PCR bias show that biased amplification can cause a community whose distribution follows a power-law function to appear lognormally distributed. We also show that TRFLP analysis, in contrast to GC-TRFLP, is not able to effectively distinguish between competing SAD models. Our analysis supports use of the lognormal as the null distribution for studying the SAD of bacterial communities as for plant and animal communities.     

Do persistent rare species experience stronger negative frequency dependence than common species?

Understanding why so many species are rare yet persistent remains a significant challenge for both theoretical and empirical ecologists. Yenni et al. (2012, Ecology, 93, 456–461) proposed that strong negative frequency dependence causes species to be rare while simultaneously buffering them against extinction. This hypothesis predicts that, on average, rare species should experience stronger negative frequency dependence than common species. However, it is unknown if ecological communities generally show this theoretical pattern. We discuss the implications of this phenomenon for community dynamics, and develop a method to test for a non‐random relationship between negative frequency dependence and relative abundance using species abundance data from 90 communities across a broad range of environments and taxonomic groups. To account for biases introduced by measurement error, we compared the observed correlation between species relative abundance and the strength of frequency dependence against expectations from a randomization procedure. In approximately half of the analysed communities, we found increasingly strong negative frequency dependence with decreasing relative abundance: rare species experienced stronger frequency dependence than common species. The randomization test never detected stronger negative frequency dependence in more common species. Our results suggest that strong negative frequency dependence is a signature of persistent, rare species in many communities.     

The implicit assumption of symmetry and the species abundance distribution

Species abundance distributions (SADs) have played a historical role in the development of community ecology. They summarize information about the number and the relative abundance of the species encountered in a sample from a given community. For years ecologists have developed theory to characterize species abundance patterns, and the study of these patterns has received special attention in recent years. In particular, ecologists have developed statistical sampling theories to predict the SAD expected in a sample taken from a region. Here, we emphasize an important limitation of all current sampling theories: they ignore species identity. We present an alternative formulation of statistical sampling theory that incorporates species asymmetries in sampling and dynamics, and relate, in a general way, the community-level SAD to the distribution of population abundances of the species integrating the community. We illustrate the theory on a stochastic community model that can accommodate species asymmetry. Finally, we discuss the potentially important role of species asymmetries in shaping recently observed multi-humped SADs and in comparisons of the relative success of niche and neutral theories at predicting SADs.     

长白山阔叶红松林草本层物种多度分布格局及其季节动态

草本层是森林生态系统的重要组成部分, 对维持森林生物多样性具有重要意义。本文以长白山阔叶红松(Pinus koraiensis)林25 ha固定监测样地为研究平台, 运用不同的统计模型(对数正态模型和对数级数模型)及机理模型(包括生态位模型: 断棍模型和生态位优先占领模型; 中性模型: 复合群落零和多项式模型和Volkov模型), 对不同季节草本物种多度分布进行拟合。采用Kolmogorov-Smirnov和AIC检验确定最优模型, 以揭示草本层物种多度分布格局随季节的变化规律, 探讨草本层物种组成与结构背后的生态学过程。结果表明: (1)草本层物种多度分布季节差异明显。春季各多度级物种数差异不大, 夏季中间种较多, 秋季则是稀有种较多; (2)模型拟合结果显示, 不同季节草本层物种多度分布的最优拟合模型相近。统计模型中对数级数模型表现最优, 机理模型中中性模型的拟合效果优于生态位模型。复合群落零和多项式模型较好地拟合了春夏季草本物种多度分布, Volkov模型较好地拟合了秋季草本物种多度分布。综上所述, 尽管长白山阔叶红松林草本植物不同季节的物种多度分布格局不尽一致, 但其背后的构建机制相似, 中性随机过程在草本层物种多样性维持过程中显得更为重要。     

Effects of community structure on the species–area relationship in China's forests

The species–area relationship (SAR) is the oldest and most frequently documented law in ecology. In a community, the SAR is regulated by the abiotic environment and biotic interactions and depends on the individual–spatial distribution of species (ISD) and the species–abundance distribution (SAD). In this study, we explored the effects of aggregation of ISDs and unevenness of SADs on SARs in forests of China by comparing the empirical and simulated SARs of 32 nested plots distributed along an extensive latitudinal gradient. Both aggregation and unevenness affected the shape of SARs significantly: ISDs accounted for 12.6 ± 4.0% of the incremental increase in species richness with area, and SADs accounted for 18.7 ± 3.8 and 23.5 ± 3.9% under the broken‐stick model and even abundance model, respectively. Effects of both aggregation and unevenness decreased as temperature increased, suggesting that individuals of a species were spatially more aggregated than random, and the individuals among species were more discrepant from the null distribution (broken‐stick model and even abundance model in this study), in the cold than in the warm areas. Taken together, our results demonstrate that ISDs and SADs within communities can shape SARs, but these effects vary along latitudinal gradients, and are likely mediated by temperature.     

A neutral theory with environmental stochasticity explains static and dynamic properties of ecological communities

Understanding the forces shaping ecological communities is crucial to basic science and conservation. Neutral theory has made considerable progress in explaining static properties of communities, like species abundance distributions (SADs), with a simple and generic model, but was criticised for making unrealistic predictions of fundamental dynamic patterns and for being sensitive to interspecific differences in fitness. Here, we show that a generalised neutral theory incorporating environmental stochasticity may resolve these limitations. We apply the theory to real data (the tropical forest of Barro Colorado Island) and demonstrate that it much better explains the properties of short‐term population fluctuations and the decay of compositional similarity with time, while retaining the ability to explain SADs. Furthermore, the predictions are considerably more robust to interspecific fitness differences. Our results suggest that this integration of niches and stochasticity may serve as a minimalistic framework explaining fundamental static and dynamic characteristics of ecological communities.     

Spatial scaling and transition in pneumatophore arthropod communities

Although most ecological variables are scale-dependent, few studies cover a broad range of spatial scales. Here, we consider South African mangrove pneumatophore arthropod communities (mites, crustaceans and insects), across seven spatial scales (from 10  cm to 100  km). We plot spatial autocorrelation in individual species, evaluate if resource and habitat availability determine spatial patterning, and identify the scales of community transition. Spatial autocorrelation in most ecological variables decreased with increasing spatial scale, with notable exceptions for the larger scales. Negative abundance autocorrelation was stronger at 10  km than at 100  km for common species, while the opposite was true for rare species. Spatial autocorrelation in species richness decreased from 1  m (strong positive) to 10  km (strong negative), but was not significant at the 100  km scale. These patterns reflect the patchy distribution of pneumatophores within mangrove forests, that of the forests along the coast, and the poor dispersal abilities of most of the arthropods sampled, in a highly dynamic environment. Although resource and habitat availability exhibited a similar autocorrelation pattern to that of the community, the total mass of pneumatophores did not appear to be an important determinant of community structure. Variations in the abundance of common species, as well as the restricted distribution of rare species caused assemblage structure to change gradually with increasing distance from 10 cm to 100 km, but only marginally from 10 to 100  km. We highlight the need for cross-scale studies in bridging the gap between two key ecological concepts: potential ecological niche and realized geographic range.     

Evaluating the performance of neutrality tests of a local community using a niche‐structured simulation model

Understanding the processes that underlie species diversity and abundance in a community is a fundamental issue in community ecology. While the species abundance distributions (SADs) of various natural communities may be well explained by Hubbell's neutral model, it has been repeatedly pointed out that Hubbell's SAD‐fitting approach lacks the ability to detect the effects of non‐neutral factors such as niche differentiation; however, our understanding of its quantitative effect is limited. Herein, we conducted extensive simulations to quantitatively evaluate the performance of the SAD‐fitting method and other recently developed tests. For simulations, we developed a niche model that incorporates the random stochastic demography of individuals and the nonrandom replacements of those individuals, i.e. niche differentiation. It therefore allows us to explore situations with various degrees of niche differentiation. We found that niche differentiation has strong effects on SADs and the number of species in the community under this model. We then examined the performance of these neutrality tests, including Hubbell's SAD‐fitting method, using extensive simulations. It was demonstrated that all these tests have relatively poor performance except for the cases with very strong niche structure, which is in accordance with previous studies. This is likely because two important parameters in Hubbell's model are usually unknown and are commonly estimated from the data to be tested. To demonstrate this point, we showed that the precise estimation of the two parameters substantially improved the performance of these neutrality tests, indicating that poor performance can be owed to overfitting Hubbell's neutral model with unrealistic parameters. Our results therefore emphasize the importance of accurate parameter estimation, which should be obtained from data independent of the local community to be tested.