Analyzing spatial structure of communities using the two-dimensional poisson lognormal species abundance model

The joint spatial and temporal fluctuations in the community structure of tropical butterflies are analyzed by fitting the bivariate Poisson lognormal distribution to a large number of observations in space and time. By applying multivariate dependent diffusions for describing the fluctuations in the abundances, the environmental variance is estimated to be very large and so is the strength of local density regulation. The variance in the lognormal species abundance distribution is partitioned into components expressing the heterogeneity between the species, independent noise components for the different species, a demographic stochastic component, and a component due to overdispersion in the sampling. In disagreement with the neutral theory, the estimates show that the heterogeneity component is the dominating one, representing 81% of the total variance in the lognormal model. Different spatial components of diversity, the alpha, beta, and gamma diversity, are also estimated. The spatial scale of the autocorrelation function for the community is of order 1 km, while sampling of a quadrat would need to be 10 km on a side to yield the total diversity for the community.     

A General and Dynamic Species Abundance Model, Embracing the Lognormal and the Gamma Models

One aspect of community ecology that has been given particular attention is the pattern of species abundances in a community. The species may have a wide range of abundances; some are very common and others rare. When species abundance models are fitted to observations, the lognormal model and one of the gamma models (e.g., the log-series model) are usually applied. The model that gives the best fit according to some goodness-of-fit test is then chosen. By applying a diffusion approximation for each species' dynamics with density regulation of the straight theta-logistic type, we here present a general species abundance model that embraces the two most widely applied species abundance models, the lognormal and the gamma. Our general model will, therefore, provide a better fit than the two special cases, except when it corresponds to one of them. In contrast to the classical models, ours is also dynamic, making it possible to evaluate the fluctuations in species abundance over time through both biotic and abiotic factors. The model is fitted to several species abundance data sets and our results compared to previous attempts to fit a model, usually either the lognormal or the log-series.     

Asymmetry in species regional dispersal ability and the neutral theory

The neutral assumption that individuals of either the same or different species share exactly the same birth, death, migration, and speciation probabilities is fundamental yet controversial to the neutral theory. Several theoretical studies have demonstrated that a slight difference in species per capita birth or death rates can have a profound consequence on species coexistence and community structure. Whether asymmetry in migration, a vital demographic parameter in the neutral model, plays an important role in community assembly still remains unknown. In this paper, we relaxed the ecological equivalence assumption of the neutral model by introducing differences into species regional dispersal ability. We investigated the effect of asymmetric dispersal on the neutral local community structure. We found that per capita asymmetric dispersal among species could reduce species richness of the local community and result in deviations of species abundance distributions from those predicted by the neutral model. But the effect was moderate compared with that of asymmetries in birth or death rates, unless very large asymmetries in dispersal were assumed. A large difference in species dispersal ability, if there is, can overwhelm the role of random drift and make local community dynamics deterministic. In this case, species with higher regional dispersal abilities tended to dominate in the local community. However, the species abundance distribution of the local community under asymmetric dispersal could be well fitted by the neutral model, but the neutral model generally underestimated the fundamental biodiversity number but overestimated the migration rate in such communities.     

Frequent and occasional species and the shape of relative-abundance distributions

Recently, three different models have been proposed to explain the distribution of abundances in natural communities: the self‐similarity model; the zero‐sum ecological drift model; and the occasional–frequent species model of Magurran and Henderson. Here we study patterns of relative abundance in a large community of forest Hymenoptera and show that it is indeed possible to divide the community into a group of frequent species and a group of occasional species. In accordance with the third model, frequent species followed a lognormal distribution. Relative abundances of the occasional species could be described by the self‐similarity model, but did not follow a log‐series as proposed by the occasional–frequent model. The zero‐sum ecological drift model makes no explicit predictions about frequent and occasional species but the abundance distributions of the hymenopteran species did not show the excess of rare species predicted by this model. Separate fits of this model to the frequent and to the occasional species were worse than the respective fits of the lognormal and the self‐similarity model.     

Relative contribution of neutral and deterministic processes in shaping fruit‐feeding butterfly assemblages in Afrotropical forests

The unified neutral theory of biodiversity and biogeography has gained the status of a quantitative null model for explaining patterns in ecological (meta)communities. The theory assumes that individuals of trophically similar species are functionally equivalent. We empirically evaluate the relative contribution of neutral and deterministic processes in shaping fruit‐feeding butterfly assemblages in three tropical forests in Africa, using both direct (confronting the neutral model with species abundance data) and indirect approaches (testing the predictions of neutral theory using data other than species abundance distributions). Abundance data were obtained by sampling butterflies using banana baited traps set at the forest canopy and understorey strata. Our results indicate a clear consistency in the kind of species or species groups observed at either the canopy or understorey in the three studied communities. Furthermore, we found significant correlation between some flight‐related morphological traits and species abundance at the forest canopy, but not at the understorey. Neutral theory's contribution to explaining our data lies largely in identifying dispersal limitation as a key process regulating fruit‐feeding butterfly community structure. Our study illustrates that using species abundance data alone in evaluating neutral theory can be informative, but is insufficient. Species‐level information such as habitat preference, host plants, geographical distribution, and phylogeny is essential in elucidating the processes that regulate biodiversity community structures and patterns.     

Biodiversity and species interactions: extending Lotka–Volterra community theory

A new analysis of the nearly century‐old Lotka–Volterra theory allows us to link species interactions to biodiversity patterns, including: species abundance distributions, estimates of total community size, patterns of community invasibility, and predicted responses to disturbance. Based on a few restrictive assumptions about species interactions, our calculations require only that the community is sufficiently large to allow a mean‐field approximation. We develop this analysis to show how an initial assemblage of species with varying interaction strengths is predicted to sort out into the final community based on the species’ predicted target densities. The sorting process yields predictions of covarying patterns of species abundance, community size, and species interaction strengths. These predictions can be tested using enrichment experiments, examination of latitudinal and productivity gradients, and features of community assembly.     

Non‐neutrality in forest communities: evolutionary and ecological determinants of tree species abundance distributions

The unified neutral theory of biodiversity and biogeography provides a promising framework that can be used to integrate stochastic and ecological processes operating in ecological communities. Based on a mechanistic non‐neutral model that incorporates density‐dependent mortality, we evaluated the deviation from a neutral pattern in tree species abundance distributions and explored the signatures of historical and ecological processes that have shaped forest biomes. We compiled a dataset documenting species abundance distributions in 1168 plots encompassing 16 973 tree species across tropical, temperate, and boreal forests. We tested whether deviations from neutrality of species abundance distributions vary with climatic and historical conditions, and whether these patterns differ among regions. Non‐neutrality in species abundance distributions was ubiquitous in tropical, temperate, and boreal forests, and regional differences in patterns of non‐neutrality were significant between biomes. Species abundance evenness/unevenness caused by negative density‐dependent or abiotic filtering effects had no clear macro‐scale climatic drivers, although temperature was non‐linearly correlated with species abundance unevenness on a global scale. These findings were not significantly biased by heterogeneity of plot data (the differences of plot area, measurement size, species richness, and the number of individuals sampled). Therefore, our results suggest that environmental filtering is not universally increasing from warm tropical to cold boreal forests, but might affect differently tree species assembly between and within biomes. Ecological processes generating particularly dominant species in local communities might be idiosyncratic or region‐specific and may be associated with geography and climate. Our study illustrates that stochastic dynamical models enable the analysis of the interplay of historical and ecological processes that influence community assemblies and the dynamics of biodiversity.     

Dispersal, edaphic fidelity and speciation in species-rich Western Australian shrublands: evaluating a neutral model of biodiversity

Over evolutionary time, the number of species in a community reflects the balance between the rate of speciation and the rate of extinction. Over shorter time‐scales local species richness is also affected by how often species move into and out of the local community. These processes are at the heart of Hubbell's ‘unified neutral theory of biodiversity’ ( Hubbell 2001 ). Hubbell's spatially implicit, dispersal‐limited neutral model is the most widely used of the many implementations of neutral theory and it provides an estimate of the rate of speciation in a metacommunity (if metacommunity size is known) and the rate at which species migrate into the local community from the wider metacommunity. Recently, this neutral model has been used to compare rates of speciation and migration in the species‐rich fynbos of South Africa and in neotropical forests. Here we use new analytical methods for estimating the neutral model's parameters to infer speciation and dispersal rates for three sites in species‐rich sclerophyll shrublands (equivalent to fynbos) in Western Australia (WA). Our estimates suggest that WA shrublands are intermediate between fynbos and tropical rainforest in terms of speciation and dispersal. Although a weak test, the model predicts species abundance distributions and species accumulation curves similar to those observed at the three sites. The neutral model's predictions also remain plausible when confronted with independent data describing: (1) known edaphic relationships between sites, (2) estimates of metacommunity species richness and (3) rates of speciation among resprouters and nonsprouters. Two of the site pairs, however, show species turnovers significantly different from those predicted by the spatially implicit form of the neutral model that we use. This suggests that non‐neutral processes, in this case probably edaphic specialisation, are important in the WA shrubland metacommunity. The neutral model predicts similar rates of speciation in resprouter and sprouter taxa, a finding supported by recent molecular phylogenies. Finally, when converted into temporally scaled speciation rates and species longevities, the estimates produced by the neutral model seem implausible. The apparent departure from neutrality in the turnover of species between some sites and the implausible temporal dynamics may be due to the particular model chosen and does not reduce the significance of our other results, which confirm that local dispersal limitation, coupled with broader scale edaphic fidelity, combine to structure this biodiverse metacommunity.     

Sampling Hubbell's neutral theory of biodiversity

In the context of neutral theories of community ecology, a novel genealogy‐based framework has recently furnished an analytic extension of Ewens’ sampling multivariate abundance distribution, which also applies to a random sample from a local community. Here, instead of taking a multivariate approach, we further develop the sampling theory of Hubbell's neutral spatially implicit theory and derive simple abundance distributions for a random sample both from a local community and a metacommunity. Our result is given in terms of the average number of species with a given abundance in any randomly extracted sample. Contrary to what has been widely assumed, a random sample from a metacommunity is not fully described by the Fisher log‐series, but by a new distribution. This new sample distribution matches the log‐series expectation at high biodiversity values (θ > 1) but clearly departs from it for species‐poor metacommunities (θ < 1). Our theoretical framework should be helpful in the better assessment of diversity and testing of the neutral theory by using abundance data.     

Species diversity in local neutral communities

We extend the neutral theory of macroecology by deriving biodiversity models (relative species abundance and species-area relationships) in a local community-metacommunity system in which the local community is embedded within the metacommunity. We first demonstrate that the local species diversity patterns converge to that of the metacommunity as the size (scale) of the embedded local community increases. This result shows that in continuous landscapes no sharp boundaries dividing the communities at the two scales exist; they are an artificial distinction made by the current spatially implicit neutral theory. Second, we remove the artificial restriction that speciation cannot occur in a local community, even if the effects of local speciation are small. Third, we introduce stochasticity into the immigration rate, previously treated as constant, and demonstrate that local species diversity is a function not only of the mean but also of the variance in immigration rate. High variance in immigration rates reduces species diversity in local communities. Finally, we show that a simple relationship exists between the fundamental diversity parameter of neutral theory and Simpson's index for local communities. Derivation of this relationship extends recent work on diversity indices and provides a means of evaluating the effect of immigration on estimates of the fundamental diversity parameter derived from relative species abundance data on local communities.     

A neutral model of edge effects

In this paper a spatially implicit neutral model for explaining the edge effects between habitats is proposed. To analyze this model we use two different approaches: a discrete approach that is based on the Master equation for a one step jump process and a continuous approach based on the approximation of the discrete jump process with the Kolmogorov-Fokker-Planck forward and backward equations. The discrete and continuous approaches are applied to analyze the species abundance distributions and the time to species extinction. Moreover, with the aid of the continuous approach a realistic classification of the behavior of species in local communities is developed. The species abundance dynamics at the edge between two distinct habitats is compared with those located in the homogeneous interior habitats using species abundance distributions and the first time to species extinction. We show that the structure of the links between local community and the metacommunity plays an important role on species persistence. Specifically, species at the edge between two distinct metacommunities have higher extinction rate than those in the interior habitats connected only to one metacommunity. Moreover, the same species might be persistent in the homogeneous interior habitat, but its probability of extinction from the edge local community could be very high.     

Responses of species abundance distribution patterns to spatial scaling in subtropical secondary forests

To quantify and assess the processes underlying community assembly and driving tree species abundance distributions(SADs) with spatial scale variation in two typical subtropical secondary forests in Dashanchong state‐owned forest farm, two 1‐ha permanent study plots (100‐m × 100‐m) were established. We selected four diversity indices including species richness, Shannon–Wiener, Simpson and Pielou, and relative importance values to quantify community assembly and biodiversity. Empirical cumulative distribution and species accumulation curves were utilized to describe the SADs of two forests communities trees. Three types of models, including statistic model (lognormal and logseries model), niche model (broken‐stick, niche preemption, and Zipf‐Mandelbrodt model), and neutral theory model, were estimated by the fitted SADs. Simulation effects were tested by Akaike's information criterion (AIC) and Kolmogorov–Smirnov test. Results found that the Fagaceae and Anacardiaceae families were their respective dominance family in the evergreen broad‐leaved and deciduous mixed communities. According to original data and random sampling predictions, the SADs were hump‐shaped for intermediate abundance classes, peaking between 8 and 32 in the evergreen broad‐leaved community, but this maximum increased with size of total sampled area size in the deciduous mixed community. All niche models could only explain SADs patterns at smaller spatial scales. However, both the neutral theory and purely statistical models were suitable for explaining the SADs for secondary forest communities when the sampling plot exceeded 40 m. The results showed the SADs indicated a clear directional trend toward convergence and similar predominating ecological processes in two typical subtropical secondary forests. The neutral process gradually replaced the niche process in importance and become the main mechanism for determining SADs of forest trees as the sampling scale expanded. Thus, we can preliminarily conclude that neutral processes had a major effect on biodiversity patterns in these two subtropical secondary forests but exclude possible contributions of other processes.     

亚高寒草甸植物群落的中性理论验证

 该文以物种组成较为复杂的青藏高原东部亚高寒草甸为背景,结合最新的群落中性理论,以解释亚高寒草甸草本植物群落的物种分布格局和生物多样性的维持机制。通过对阴坡、阳坡和滩地3个生境进行随机取样调查,用中性模型对所得多样性数据进行拟合,并分别应用置信区间检验、拟合优度检验和多样性指数检验3种方法对拟合效果进行检验。研究结果表明,在拟合优度检验中,3个生境中中性理论预测和实际物种多度分布之间没有显著差异(p>0.05);实际观测值基本全部落入模型预测分布的95%的置信区间之内（仅滩地草本植物群落的63个物种中的1个以及阴坡草本植物群落75个物种中的2个偏离95%的置信区间）;对群落多样性的预测也和实际观测没有显著差异,其中丰富度预测拟合得最好(0.49相似文献   

Hubbell's fundamental biodiversity parameter and the Simpson diversity index

Central to Hubbell's neutral theory of biodiversity is a universal, dimensionless fundamental biodiversity parameter that is the product of community size and speciation rate. One of the most important discoveries of Hubbell's theory is that the species‐abundance distribution and the species–area relationship of the neutral metacommunity is completely determined by this fundamental biodiversity parameter, although the diversity patterns of the local community are collectively determined by the biodiversity parameter and migration. Using the relative abundance of species and following the concept of heterozygosity of population genetics, here we developed an analytical relationship between this biodiversity parameter and the well‐known Simpson diversity index. This relationship helps bridge the evolutionary aspect of biodiversity to the ecological and statistical aspect of the diversity. The relationship between these two parameters suggests that diversity patterns of the metacommunity can also be equally described by the Simpson index. This relationship provides an alternative approach to interpret and estimate the fundamental biodiversity parameter for the metacommunity.     

Distance decay of similarity,effects of environmental noise and ecological heterogeneity among species in the spatio‐temporal dynamics of a dispersal‐limited community

The joint spatial and temporal fluctuations in community structure may be due to dispersal, variation in environmental conditions, ecological heterogeneity among species and demographic stochasticity. These factors are not mutually exclusive, and their relative contribution towards shaping species abundance distributions and in causing species fluctuations have been hard to disentangle. To better understand community dynamics when the exchange of individuals between localities is very low, we studied the dynamics of the freshwater zooplankton communities in 17 lakes located in independent catchment areas, sampled at end of summer from 2002 to 2008 in Norway. We analysed the joint spatial and temporal fluctuations in the community structure by fitting the two‐dimensional Poisson lognormal model under a two‐stage sampling scheme. We partitioned the variance of the distribution of log abundance for a random species at a random time and location into components of demographic stochasticity, ecological heterogeneity among species, and independent environmental noise components for the different species. Non‐neutral mechanisms such as ecological heterogeneity among species (20%) and spatiotemporal variation in the environment (75%) explained the majority of the variance in log abundances. Overdispersion relative to Poisson sampling and demographic stochasticity had a small contribution to the variance (5%). Among a set of environmental variables, lake acidity was the environmental variable that was most strongly related to decay of community similarity in space and time.     

塔里木荒漠河岸林不同生境群落物种多度分布格局

为解释塔里木荒漠河岸林群落构建和物种多度分布格局形成的机理, 本文以塔里木荒漠河岸林2个不同生境(沙地、河漫滩) 4 ha固定监测样地为研究对象, 基于两样地物种调查数据, 采用统计模型(对数级数模型、对数正态模型、泊松对数正态分布模型、Weibull分布模型)、生态位模型(生态位优先占领模型、断棍模型)和中性理论模型(复合群落零和多项式模型、Volkov模型)拟合荒漠河岸林群落物种多度分布, 并用K-S检验与赤池信息准则(AIC)筛选最优拟合模型。结果表明: (1)随生境恶化(土壤水分降低), 植物物种多度分布曲线变化减小, 群落物种多样性、多度和群落盖度降低, 常见种数减少。(2)选用的3类模型均可拟合荒漠河岸林不同生境群落物种多度分布格局, 统计模型和中性理论模型拟合效果均优于生态位模型。复合群落零和多项式模型对远离河岸的干旱沙地生境拟合效果最好; 对数正态模型和泊松对数正态模型对洪水漫溢的河漫滩生境拟合效果最优; 中性理论模型与统计模型无显著差异。初步推断中性过程在荒漠河岸林群落构建中发挥着主导作用, 但模型拟合结果只能作为推断群落构建过程的必要非充分条件, 不能排除生态位过程的潜在作用。     

Scaling issues of neutral theory reveal violations of ecological equivalence for dominant Amazonian tree species

Neutral models are often used as null models, testing the relative importance of niche versus neutral processes in shaping diversity. Most versions, however, focus only on regional scale predictions and neglect local level contributions. Recently, a new formulation of spatial neutral theory was published showing an incompatibility between regional and local scale fits where especially the number of rare species was dramatically under‐predicted. Using a forward in time semi‐spatially explicit neutral model and a unique large‐scale Amazonian tree inventory data set, we show that neutral theory not only underestimates the number of rare species but also fails in predicting the excessive dominance of species on both regional and local levels. We show that although there are clear relationships between species composition, spatial and environmental distances, there is also a clear differentiation between species able to attain dominance with and without restriction to specific habitats. We conclude therefore that the apparent dominance of these species is real, and that their excessive abundance can be attributed to fitness differences in different ways, a clear violation of the ecological equivalence assumption of neutral theory.     

Estimating similarity of communities: a parametric approach to spatio‐temporal analysis of species diversity

Several stochastic models with environmental noise generate spatio‐temporal Gaussian fields of log densities for the species in a community. Combinations of such models for many species often lead to lognormal species abundance distributions. In spatio‐temporal analysis it is often realistic to assume that the same species are expected to occur at different times and/or locations because extinctions are rare events. Spatial and temporal β‐diversity can then be analyzed by studying pairs of communities at different times or locations defined by a bivariate lognormal species abundance model in which a single correlation occurs. This correlation, which is a measure of similarity between two communities, can be estimated from samples even if the sampling intensities vary and are unknown, using the bivariate Poisson lognormal distribution. The estimators are approximately unbiased, although each specific correlation may be rather uncertain when the sampling effort is low with only a small fraction of the species represented in the samples. An important characteristic of this community correlation is that it relates to the classical Jaccard‐ or the Sørensen‐indices of similarity based on the number of species present or absent in two communities. However, these indices calculated from samples of species in a community do not necessarily reflect similarity of the communities because the observed number of species depends strongly on the sampling intensities. Thus, we propose that our community correlation should be considered as an alternative to these indices when comparing similarity of communities. We illustrate the application of the correlation method by computing the similarity between temperate bird communities.     

Confronting different models of community structure to species-abundance data: a Bayesian model comparison

Species abundances are undoubtedly the most widely available macroecological data, but can we use them to distinguish among several models of community structure? Here we present a Bayesian analysis of species‐abundance data that yields a full joint probability distribution of each model's parameters plus a relatively parameter‐independent criterion, the posterior Bayes factor, to compare these models. We illustrate our approach by comparing three classical distributions: the zero‐sum multinomial (ZSM) distribution, based on Hubbell's neutral model, the multivariate Poisson lognormal distribution (MPLN), based on niche arguments, and the discrete broken stick (DBS) distribution, based on MacArthur's broken stick model. We give explicit formulas for the probability of observing a particular species‐abundance data set in each model, and argue that conditioning on both sample size and species count is needed to allow comparisons between the two distributions. We apply our approach to two neotropical communities (trees, fish). We find that DBS is largely inferior to ZSM and MPLN for both communities. The tree data do not allow discrimination between ZSM and MPLN, but for the fish data ZSM (neutral model) overwhelmingly outperforms MPLN (niche model), suggesting that dispersal plays a previously underestimated role in structuring tropical freshwater fish communities. We advocate this approach for identifying the relative importance of dispersal and niche‐partitioning in determining diversity of different ecological groups of species under different environmental conditions.     

A unified model explains commonness and rarity on coral reefs

Abundance patterns in ecological communities have important implications for biodiversity maintenance and ecosystem functioning. However, ecological theory has been largely unsuccessful at capturing multiple macroecological abundance patterns simultaneously. Here, we propose a parsimonious model that unifies widespread ecological relationships involving local aggregation, species‐abundance distributions, and species associations, and we test this model against the metacommunity structure of reef‐building corals and coral reef fishes across the western and central Pacific. For both corals and fishes, the unified model simultaneously captures extremely well local species‐abundance distributions, interspecific variation in the strength of spatial aggregation, patterns of community similarity, species accumulation, and regional species richness, performing far better than alternative models also examined here and in previous work on coral reefs. Our approach contributes to the development of synthetic theory for large‐scale patterns of community structure in nature, and to addressing ongoing challenges in biodiversity conservation at macroecological scales.