Predicting the species abundance distribution using a model food web

A large number of models of the species abundance distribution (SAD) have been proposed, many of which are generically similar to the log-normal distribution, from which they are often indistinguishable when describing a given data set. Ecological data sets are necessarily incomplete samples of an ecosystem, subject to statistical noise, and cannot readily be combined to yield a closer approximation to the underlying distribution. In this paper, we adopt the Webworld ecosystem model to study the predicted SAD in detail. The Webworld model is complex, and does not allow analytic examination of such features; rather, we use simulation data and an approach similar to that of ecologists analysing empirical data. By examining large sets of fully described data we are able to resolve features which can distinguish between models but which have not been investigated in detail in field data. We find that the power-law normal distribution is superior to both the log-normal and logit-normal distributions, and that the data can improve on even this at the high-population cut-off.     

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.     

Assessing habitat suitability for the translocation of Ochrosia tahitensis (Apocynaceae), a critically endangered endemic plant from the island of Tahiti (South Pacific)

Reintroduction or translocation of threatened plant species, as part of in situ conservation efforts, often failed because of the lack or the poor quality of remaining natural habitats due to human disturbances and invasion by alien species, especially in island ecosystems. We conducted a study on Ochrosia tahitensis (Apocynaceae), a critically endangered endemic small tree in the tropical high volcanic island of Tahiti (French Polynesia, South Pacific) to find the most suitable sites for future translocation. Distribution models were produced based on climate, topography, and plant community inventories (i.e. species composition and abundance, canopy height and openness, basal area of woody species) of the few remnant populations. Results show that this species, comprising 32 reproductive trees within 16 populations known in the wild, remains restricted to a few ecological refuges representing a very small part of its potential ecological range located on the northwest side of the island, and shares its current habitats with a set of more common native woody species found in mesic-wet forests. The use of native plant communities as a proxy for habitat suitability along with species distribution modelling can enhance translocation success in island ecosystems, but only if the major threats causing population decrease, mainly forest destruction and fragmentation and invasive alien species, are effectively managed.     

A mathematical synthesis of niche and neutral theories in community ecology

The debate between niche-based and neutral community theories centers around the question of which forces shape predominantly ecological communities. Niche theory attributes a central role to niche differences between species, which generate a difference between the strength of intra- and interspecific interactions. Neutral theory attributes a central role to migration processes and demographic stochasticity. One possibility to bridge these two theories is to combine them in a common mathematical framework. Here we propose a mathematical model that integrates the two perspectives. From a niche-based perspective, our model can be interpreted as a Lotka-Volterra model with symmetric interactions in which we introduce immigration and demographic stochasticity. From a neutral perspective, it can be interpreted as Hubbell's local community model in which we introduce a difference between intra- and interspecific interactions. We investigate the stationary species abundance distribution and other community properties as functions of the interaction coefficient, the immigration rate and the strength of demographic stochasticity.     

大明山云贵山茉莉群落物种多度分布的Weibull模型

物种多度分布的分析对于了解群落物种多样性具有重要意义。Weibull模型是拟合物种多度分布的重要模型之一。在采用倍程对物种多度分组的基础上,用Weibull模型分别拟合广西大明山保护区云贵山茉莉群落乔木层、灌木层以及乔木+灌木物种的多度分布,结果三者均符合Weibull分布。由此表明所提出的方法应用于物种多度分布研究是理想的,从而完善了Weibull模型在物种多度分布上的应用。     

How to make more out of community data? A conceptual framework and its implementation as models and software

Community ecology aims to understand what factors determine the assembly and dynamics of species assemblages at different spatiotemporal scales. To facilitate the integration between conceptual and statistical approaches in community ecology, we propose Hierarchical Modelling of Species Communities (HMSC) as a general, flexible framework for modern analysis of community data. While non‐manipulative data allow for only correlative and not causal inference, this framework facilitates the formulation of data‐driven hypotheses regarding the processes that structure communities. We model environmental filtering by variation and covariation in the responses of individual species to the characteristics of their environment, with potential contingencies on species traits and phylogenetic relationships. We capture biotic assembly rules by species‐to‐species association matrices, which may be estimated at multiple spatial or temporal scales. We operationalise the HMSC framework as a hierarchical Bayesian joint species distribution model, and implement it as R‐ and Matlab‐packages which enable computationally efficient analyses of large data sets. Armed with this tool, community ecologists can make sense of many types of data, including spatially explicit data and time‐series data. We illustrate the use of this framework through a series of diverse ecological examples.     

The reliability of a composite biodiversity indicator in predicting bird species richness at different spatial scales

Several biodiversity features can be linked to landscape heterogeneity, that, in turn, can be informative for management and conservation purposes. Usually, the more the landscape is complex the more the biodiversity increases. Biodiversity indicators can be a useful tool to assess biodiversity status, in function of landscape heterogeneity. In this study, we developed a biodiversity indicator, based on Shannon diversity index and built from distribution maps of protected species. With such an approach, we seek to evaluate the feasibility of using a combination of target species as a surrogate for assessing the status of the whole bird community. Our approach was spread over multiple spatial scales, to determine which was the most informative. We selected four species protected by European regulation and generated a presence-absence map from species distribution modelling. We, therefore, used the FRAGSTATS biodiversity metric to calculate Shannon index for the overlapped presence-absence maps, at two spatial scales (500 m and 1000 m). Then, the relationships with the whole community was assessed through generalised least square models, at the spatial scale of 4 ha, 9 ha and 25 ha. Results showed that the higher rate of variability of community was explained by the biodiversity indicator at 1000 m scale. Indeed, the more informative spatial scale for the whole bird community was 9 ha. In addition, a pattern emerged about the relationships between biodiversity indicator and community richness, that is worth of further research. Our study demonstrates that the usefulness of surrogate species for biodiversity and community assessment can become clear only at a certain spatial scales. Indeed, they can be highly predictive of the whole community, and highly informative for conservation planning. Moreover, their use can optimize biodiversity monitoring and conservation, focusing on a small number of noteworthy species.     

Tree shape, forest structure and diversity of drosophilid community: Comparison between boreal and temperate birch forests

Some models, based on the latitudinal variation in sun angle distribution, predict that trees at high latitudes have narrowly conical crowns and constitute simple-layered forests, whereas trees at low latitudes have shallowly dome-shaped and form more structurally complex multilayered forests. There is a hypothesis that structurally complex habitats can harbor potentially more species than simple ones. In this study, we examined latitudinal correlations between tree shape, forest structure and diversity in drosophilid communities, comparing boreal and cool-temperate forests. We selected secondary birch forests with a common canopy tree species, white birch (Betula platyphylla Sukatchev), as study sites. The crown shape of white birch tended to be spherical in the cool-temperate forest, but narrowly conical in the boreal forest. The foliage structure differed between the two forests. The cool-temperate forest was characterized by a clearly two-layered structure, whereas foliage in the boreal forest was less clearly stratified, being distributed somewhat continuously from the ground to the canopy at lower densities. The structural complexity expressed by foliage height diversity was greater in the cool-temperate forest than in the boreal forest. Various measures of drosophilid diversity were higher in the cool-temperate forest than in the boreal forest, probably resulting from the impoverishment of the canopy subcommunity in the boreal forest. Thus, a physical environmental factor (i.e. the angle of solar inclination) could be a potentially important factor in structuring latitudinal patterns of sylvan animal communities through changes in plant structure at the individual and community levels.     

中国刺栲林的分类与分布初探

介绍了中国刺栲林的群落生态学特性及其分布特征等,根据刺栲在群落中的地位(优势种、共建种、伴生种或偶见种),将刺栲林分为三种主要的群落类型,每一大类中,又依据分布地的环境状况等,各分为几种不同的亚型。值得注意的是,在以刺栲为优势种的群落类型中,随着海拔的升高,其共建种表现出独特的替代规律。同时,进一步探讨了刺栲群落形成与维持机制,认为在刺栲自身生物学和生态学特性的基础上,生境异质性和环境及人为干扰导致刺栲形成了不同群落类型,但其内在机制的揭示还需进行深入的研究。最后,对其速生丰产林和混交林营造提出了一些建议。     

钉螺在枫杨防护林和芦林分布密度的比较研究

通过对长江外滩枫杨防护林和芦林钉螺分布密度的调查比较,结果表明：枫杨林钉螺分布密度明显低于芦林;两种群落钉螺分布密度不同程度受长江洪泛的影响;两种群落中４种抑制钉螺的植物对钉螺分布密度的影响相似。     

Species co‐occurrence patterns and dietary resource competition in primates

Diamond (Assembly of species communities. In: Cody ML, Diamond JM, editors. Ecology and evolution of communities. Cambridge: Belknap. p 342–444 ( 1975 )) argued that interspecific competition between species occupying similar niches results in a nonrandom pattern of species distributions. In particular, some species pairs may never be found in the same community due to competitive exclusion. Rigorous analytical methods have been developed to investigate the possible role that interspecific competition has on the evolution of communities. Many studies that have implemented these methods have shown support for Diamond's assembly rules, yet there are numerous exceptions. We build on this previous research by examining the co‐occurrence patterns of primate species in 109 communities from across the world. We used EcoSim to calculate a checkerboard (C) score for each region. The C score provides a measure of the proportion of species pairs that do not co‐occur in a set of communities. High C scores indicate that species are nonrandomly distributed throughout a region, and interspecific competition may be driving patterns of competitive exclusion. We conducted two sets of analyses. One included all primate species per region, and the second analysis assigned each species to one of four dietary guilds: frugivores, folivores, insectivores, and frugivore‐insectivores. Using all species per region, we found significantly high C scores in 9 of 10 regions examined. For frugivores, we found significantly high‐C scores in more than 50% of regions. In contrast, only 23% of regions exhibited significantly high‐C scores for folivores. Our results suggest that communities are nonrandomly structured and may be the result of greater levels of interspecific competition between frugivores compared to folivores. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

荒漠灌丛土壤动物分布及其生态功能

在干旱、半干旱荒漠生态系统中,灌丛作为一种重要的植被类型,其独特的形态和生理适应特性能够有效促进退化生态系统结构与功能的恢复。土壤动物是荒漠生态系统中不可或缺的重要组成部分,对促进灌丛"肥岛"演变具有重要的生态作用,有利于灌丛生态功能的发挥及退化生态系统的恢复。近年来,国内外学者对荒漠灌丛微生境土壤动物的研究逐步深入,取得大量的研究成果。在此基础上,首先综述荒漠灌丛微生境土壤动物群落分布和生态功能,总结灌丛与土壤动物分布间作用关系的数学模型,针对荒漠灌丛土壤动物研究中存在的问题提出了未来可能的研究方向和建议。     

白音华矿区草地群落主要物种组成及空间分布

以内蒙古白音华矿区周边草地为对象,研究了矿区草地植物群落的主要物种组成及其空间分布特征。结果表明: 草地群落共出现55种植物,优势种为大针茅、黄囊苔草和糙隐子草,常见种有羊草、冰草和知母等,该6个物种的累计相对重要值为79.6%,其密度分别为 26.6、204.7、105.4、107.1、68.2和55.1株·m^-2。对6个主要物种的种群密度通过半方差函数进行模型拟合, 其种群分布分别符合指数模型、指数模型、指数模型、球状模型、线性模型和高斯模型;对其空间分布格局进行分析,各种群的结构比分别为59.2%、97.2%、89.1%、94.5%、62.6%和72.1%,表明黄囊苔草、糙隐子草和羊草种群的空间自相关性程度均较高, 主要受结构性因素影响, 而大针茅、冰草和知母种群主要受随机性因素影响。对分形维数进行分析发现, 大针茅、黄囊苔草、糙隐子草和冰草种群分布格局较简单,空间依赖性较强,而羊草和知母种群分布格局较复杂,空间依赖性较弱,结合2D及3D图看, 大针茅和知母呈现出梯度扩散,而黄囊苔草、糙隐子草、羊草和冰草则主要呈现斑块化分布,表明矿区草地群落主要物种的空间分布与开矿无显著关联性。     

Analytical theory of species abundance distributions of a random community model

We review the history and recent progress of the analytical theories of a random community models. In particular, we focus on a global stability analysis of replicator equations with random interactions and species abundance distributions based on statistical mechanics.     

A Short-Term Study of Vertical and Horizontal Distribution of Zooplankton During Thermal Stratification in Lake Kinneret,Israel

This study documents for the first time both vertical and horizontal distribution patterns of the zooplankton community in Lake Kinneret during the period of thermal stratification. The zooplankton distribution patterns were explored in relation to abiotic (temperature, oxygen) and biotic (picocyanobacteria, ciliates, flagellates, phytoplankton, fish) environmental gradients. Sampling was carried out on 6–7 July 1992 at five stations and six depths from nearshore to offshore. Zooplankton abundance and biomass varied from 5 to 267 ind. l^–1(mean: 95 ind. l^–1), and from 0.1 to 65 d.w. mg m^–3(mean: 24 d.w. mg m^–3). Zooplankton taxonomic groups (Rotifera, Cladocera, Cyclopoida, Calanoida) and size classes (micro-, meso- and macrozooplankton) showed peaks of maximal density and biomass in the epilimnetic and metalimnetic strata (5 and 14 m). Depth, accounting for 31–39% of total spatial variation, reflected the vertical distribution of zooplankton in relation to temperature and oxygen declines, and the higher concentration of food resources (protists and phytoplankton) in the epilimnion and metalimnion. Onshore–offshore distance, accounting for 17–22% of the total spatial variance, reflected different distribution patterns shown among zooplankton groups and size classes. The macrozooplankton (Copepoda, Cladocera) was more abundant offshore, whereas microzooplankton (Rotifera and nauplii) predominated nearshore. These horizontal distribution patterns were related to small increases in temperature and phytoplankton biomass, and higher concentrations of fish in the littoral zone. Although limited to a short temporal scale, our study indicated that zooplankton spatial distribution in Lake Kinneret during the period of thermal stratification was related to physicochemical, food and predation factors, manifested differently along the vertical and nearshore–offshore gradients.     

种间作用对物种分布模拟的影响及建模方法

物种分布模型(SDMs)通过量化物种分布和环境变量之间的关系,并将其外推到未知的景观单元,模拟、预测地理空间中生物的潜在分布,是生态学、生物地理学、保护生物学等研究领域的重要工具.然而,目前物种分布模型主要采用非生物因素作为预测变量,由于数据量化和建模表达困难,生物因素特别是种间作用在物种分布模型中常被忽略,将种间作用...