MPowering ecologists: community assembly tools for community assembly rules

Null model tests of presence–absence data (‘NMTPAs’) provide important tools for inferring effects of competition, facilitation, habitat filtering, and other ecological processes from observational data. Many NMTPAs have been developed, but they often yield conflicting conclusions when applied to the same data. Type I and II error rates, size, power, robustness and bias provide important criteria for assessing which tests are valid, but these criteria need to be evaluated contingent on the sample size, null hypothesis of interest, and assumptions that are appropriate for the data set that is being analyzed. In this paper, we confirm that this is the case using the software MPower, evaluating the validity of NMTPAs contingent on the null hypothesis being tested, assumptions that can be made, and sample size. Evaluating the validity of NMTPAs contingent on these factors is important towards ensuring that reliable inferences are drawn from observational data about the processes controlling community assembly.     

Avian community assembly rules: The foliage-gleaning guild

Summary The theory of animal community organization has been dominated by general models based on the Lotka-Volterra equations. The predictions of these models are difficult to test in particular situations. Moreover, a great deal of ecological information is incommensurate with the data requirements of these models. A different approach to community organization addresses the ecosystem assembly problem. This problem is defined to be that of constructing an algorithm which assembles a subset of a species pool in a specified environment.A model of ecosystem assembly, based on generative grammars as used in theoretical linguistics, is described. It was constructed from and validated with data collected by D.H. Morse on a guild of foliage-gleaning birds inhabiting spruce forests on islands off the coast of Maine. The data were divided into two groups. One group, from the years 1967–1970, was used for model construction; the second group, from 1971–1975, was used to validate the model.The model has two major components. One component inserts species onto islands according to the microhabitat used by each species and the resources available on each island. A second component deletes those inserted species from islands on which they were not observed to occur during 1967–1970. This component is composed of deletion rules that remove species depending on (a) their sizes and resource requirements, (b) the sizes and resource requirements of other species present in the ecosystem, and (c) the structure of the vegetation on the islands. Model validation was performed by comparing the predicted distributions of species against observed distributions not used in model construction. Model accuracy for the later data (1971–1975) was slightly higher than for the earlier data (1967–1970), approximately 88% and 84%, respectively.The behavior of the model was investigated with several simulations. These included the effects of the removal of certain deletion rules and the effects of the application of the rules without regard to their order. Other simulations demonstrated the application of the model to the prediction of the effects of habitat manipulation and the removal of particular species from the species pool.     

Genetic assembly rules and community phenotypes

We present a conceptual construct for a genetic based community assembly rule where the genetic composition of a host plant, or resource, affects the structure of the dependent community. This is related to a genetic similarity rule that states that host plants with similar genetic compositions are hosts to similar arthropod communities. We present preliminary data from the Populus system to support this concept. We review the recent literature to evaluate the current state of the assembly rule concept and interpret a set of previous studies in the context of a genetic assembly rule. We suggest that by incorporating this concept into community ecology we can begin to bring an evolutionary perspective to this discipline.     

A niche-based modeling approach to phytoplankton community assembly rules

Six niche-based models proposed by Tokeshi, based on different assumptions of resource allocation by species, were fitted on phytoplankton relative abundance distributions, and potential environmental and biotic factors supporting the applicability of the fitted models were discussed. Overall 16 assemblages corresponding to different sampling times, various environmental conditions, and resource regimes within a year were fitted to the models. Phytoplankton biovolume was used as a measure of abundance, and a randomization test was applied to compare the model fit to the field data. The majority of the phytoplankton assemblages (11 of 16) were successfully described by the Random Fraction model, which is based on the theoretical assumption that resource is apportioned by the species in a random way. Only a few assemblages (three of 16), characterized by extremes in resource availability or disturbance, were not fitted by any of the models. The Random Fraction model in particular was rejected due to a steep slope during the first ranks, while the rest of the distribution remained relatively even, providing further evidence of resilience in phytoplankton communities. Although larger cells seem to have the potential to develop higher biomass, it seems that other factors, including the surface-to-volume ratio, counterbalance this advantage, resulting in a random-like behaviour in resource acquisition by phytoplankton, irrespective of cell size or species identity.     

土壤动物群落空间格局和构建机制研究进展

群落空间格局和构建机制一直是生态学研究的核心内容。在生物多样性严重丧失的背景下, 揭示群落空间格局及其构建机制, 有助于深刻理解生物多样性丧失的原因, 更有助于应对生物多样性保护等重大生态环境问题。然而, 陆地生态系统的研究多集中于地上生物群落, 对地下生态系统, 尤其是土壤动物空间格局和构建机制的研究尚不充分。事实上, 土壤动物多样性是全球生物多样性的关键组成之一, 是地下生态系统结构和功能维持的重要部分。对土壤动物空间格局和构建机制的研究, 能明确不同空间尺度条件下土壤动物多样性的维持机制。土壤动物群落常在多种空间尺度形成复杂的空间分布格局, 因此, 本文首先介绍了不同空间尺度主要土壤动物群落的空间自相关性特征, 阐述了土壤动物群落斑块和孔隙镶嵌分布的复杂空间格局。继而阐明这种空间格局主要受生物间作用、环境过滤和随机扩散的调控, 并说明这三个过程对土壤动物群落的调控能力和作用方式。作者提出, 这三个过程仍是今后土壤动物群落空间格局和构建机制研究的重点内容, 需要进一步加强以土壤动物为研究对象的群落构建理论的验证和发展。我国土壤动物群落空间格局和构建机制起步较晚, 希望本文能够促进我国土壤动物生态学相关领域的研究。     

From simple rules to cycling in community assembly

Simulation studies of community assembly have frequently observed two related phenomena: (1) the humpty dumpty effect in which communities can not be reconstructed by "sequential" invasions (i.e. single species invasions separated by long intervals of time) and (2) cycling between sub-communities. To better understand the mechanisms underlying these phenomena, we analyze a system consisting of two predators and two prey competing for a shared resource. We show how simple dominance rules (i.e. R^* and P^* rules) lead to cycling between sub-communities consisting of predator–prey pairs; predator and prey invasions alternatively lead to prey displacement via apparent competition and predator displacement via exploitative competition. We also show that these cycles are often dynamically unstable in the population phase space. More specifically, while for too slow invasion rates (i.e. "sequential" invasions) the system cycles indefinitely, faster invasion rates lead to coexistence of all species. In the later case, the assembly dynamics exhibit transient cycling between predator-prey subcommunities and the length of these transients decreases with the invasion rate and increases with habitat productivity.     

Ecological assembly rules on arthropod community inhabiting mistletoes

1. The colonisation of a new habitat by a community is led by deterministic and stochastic processes at different spatio-temporal scales. Parasitic plants, such as mistletoe, represent a new habitat within forest canopy that is free to be colonised by many organisms. 2. This study investigates how ecological factors operating at forest and plant scales drive changes in both specialist (mistletoe-dwelling) and tourist (transient visitors) arthropod communities inhabiting European mistletoe, Viscum album subsp. austriacum, in a Mediterranean pine forest. The influence of elevation along a broad elevational gradient was tested by sampling arthropod communities dwelling in mistletoe plants and host pine branches and the effects of mistletoe plant size, distances to other mistletoes, and temporal variation in arthropod assemblages inhabiting mistletoes. 3. The diversity of the specialist community remained constant along the elevational gradient and over the summer period, while the tourist and pine-dwelling arthropod communities showed species turnover. Larger mistletoes were occupied by more species and individuals, whereas more isolated mistletoes presented the same equilibrium point as the more aggregated ones. Thus, mistletoe size is key to the composition of the arthropod community. 4. In conclusion, this study's findings indicate contrasting assembly rules for specialised and tourist arthropod communities associated with mistletoe. The specialist community was highly stable and followed a deterministic trophic sequence of colonisation as the assemblage rule: first, colonisation by the main specialist herbivore, Cacopsylla visci, and, second, by its predator Anthocoris visci. Meanwhile, the tourist community, being a subset of the arthropod assemblage of the pine, acts independent of mistletoe presence.     

利用数值模拟重构物种多样性格局的形成过程

生命形成的过程极其漫长, 经历了地球系统复杂的沧海桑田变化。当前人类所观察到的物种分布格局的形成除了由物种本身特征决定外, 还受到环境变化、人类活动以及各种随机事件的影响。受限于实验条件、时间、经费、人力等诸多因素, 我们尚无法完整地观察并记录到物种多样性形成的全过程, 只能通过片段化数据来推测该过程。信息科学中包括数值模拟在内的仿真技术以其高效、可控及全过程记录等优势, 能从某种程度上解决物种多样性格局形成过程中的部分数据黑箱问题。本文介绍了数值模拟的概念和工作原理及在物种多样性研究中应用的特点, 列举了物种生态位、扩散模式、种间互作及物种分布应对气候变化等方面的数值模拟研究, 基于已有研究系统地介绍了如何综合上述数值模拟研究构建虚拟物种、气候和场景来解释物种多样性的形成与维持机制, 并阐述了数值模拟在物种多样性研究中的优缺点及应用前景。     

华北地区胡桃楸林分布规律及群落构建机制分析

探究植物分布规律和群落构建机制是揭示植物群落空间分布、群落物种多样性的形成、发展及其影响因素的重要途径。该文以华北地区胡桃楸(Juglans mandshurica)林为研究对象, 基于野外84个样方的调查数据, 通过径级分析、典范对应分析等方法研究了胡桃楸林的空间分布规律, 并通过亲缘关系指数计算、植物功能性状等方法研究了胡桃楸林的物种共存机制。结果表明, 华北地区胡桃楸的胸径相对较小(平均5.36 cm), 种群年龄较低; 海拔、坡度、坡位和人为干扰程度是影响华北地区胡桃楸分布的主要因子。研究区域内的胡桃楸大部分生长于山体中下部海拔较低的缓坡, 且人为干扰相对较少的区域, 各分布区域中胡桃楸林的分布规律各异。胡桃楸林物种的构建由生态位机制主导, 其中河北、陕西、天津的胡桃楸林物种共存过程主要受负密度制约的影响, 北京、山西的胡桃楸林的物种共存过程主要受环境选择驱动。     

Evidence for community assembly constraints during succession in dune slack plant communities

Community assembly during succession can be constrained by both local and regional factors. Despite an increasing regional species pool size during succession, we found a limit on the number of species in 1 × 1 m plots in dune slacks. Three alternative hypotheses (habitat heterogeneity, dispersal limitation and niche limitation) explaining this community saturation were tested. A null model analysis showed that species richness in the plots had an unusually low variance suggesting that beta habitat diversity was not likely to explain the limitation on species richness. Because we did not find a correlation between the distribution of species over the slack and their dispersal capacity, we also excluded the dispersal limitation hypothesis. Finally, a guild proportionality analysis revealed that the abundances of forb, graminoid and ruderal species showed low an unusually low variance over all age classes involved. This provides evidence for nonrandom community assembly during succession, likely to be determined by competitive exclusion among species of the same guild.     

甲虫群落构建研究进展

甲虫作为节肢动物中一个庞大的类群,具有繁简各异的生活习性,在生态系统中发挥极为重要的作用.甲虫群落构建是群落生态研究的重要内容之一,可揭示不同生态环境下生物多样性的形成与维持机制.现阶段对甲虫群落构建的研究主要通过物种的功能性状,或将系统发育结构与物种功能性状相结合的方法,对群落构建过程进行解析,用以判断主要的驱动因素...     

Predictability of flood pulse driven assembly rules for restoration of a floodplain plant community

Community assembly rules were formulated to evaluate the restoration of wet prairie along the periphery of the floodplain of the Kissimmee River in central Florida. Restoration of this plant community is expected to be driven by the reestablishment of flood pulse hydrology following the ongoing dechannelization of the river. Assembly rules were assessed with plant species composition and cover data from 15 permanent plots on the restored floodplain and 6 control plots on the channelized floodplain. These sites were sampled biannually from 1998 to 2010. Mean annual hydroperiods and depths confirmed that the frequency, duration and amplitude of post-restoration flood pulses at study sites were similar to historic reference locations. Elimination of pasture grasses (primarily Paspalum notatum Flüggé) following restoration of the flood pulse validated the hypothesized deletion rule for initial transformation of the wet prairie zone. Predicted increased dominance of obligate and facultative wetland species, a “community addition rule”, also was confirmed. An index of weighted averages of wetland indicator taxa showed significant short-term responses to antecedent hydroperiods and depths, and a restoration trajectory for wetland plant species. As predicted, recruitment of wet prairie indicator species from the extant seed bank correlated with reestablishment of the flood pulse, but was greatest when inundation extended from the wet season into the dry season. Restoration of a wetland plant community did not result in the predicted increase in species richness and diversity. Colonization and expansion of the exotic grass, Hemarthria altissima (Poir.) Stapf & C.E. Hubb., disrupted community reassembly processes. By summer 2007, mean cover of this species and several other exotic grasses increased to 24%, and necessitated herbicide treatments. Assembly rules provided useful predictions for the initial restoration of wet prairie vegetation, but were eventually confounded by the spread of an exotic species that was new to the regional flora.     

放牧干扰梯度下川西亚高山植物群落的组合机理

为了阐明放牧干扰对川西亚高山区域植物群落的组合过程以及群落结构的影响, 研究了放牧干扰梯度下的功能群均匀度和群落谱系结构的变化趋势。结果显示: 在干扰较轻的阔叶林与针叶林样地, 部分样方的功能群均匀度显著高于无效模型, 随着干扰梯度的增强, 功能群均匀度呈线性下降, 样方平均值从0.930降至0.840, 其高于无效模型的次数也逐渐降低, 干扰程度较大的草甸中出现部分样方的功能群均匀度显著低于无效模型。随着干扰程度的增强, 群落的谱系结构指数也呈逐渐上升趋势, 净关联指数平均值由-0.634逐渐增加至2.360, 邻近类群指数由-0.158上升至2.179。草甸与低矮灌丛受干扰较为严重, 其大部分样方的谱系结构指数显著高于随机群落, 表明干扰群落的谱系结构呈聚集分布。功能群均匀度与谱系结构的变化趋势一致, 表明生境筛滤效应与种间竞争作用的平衡决定着群落的组合过程。干扰降低了竞争作用, 促进了少数耐干扰功能群的优势地位, 造成功能群均匀度下降, 同时通过生境筛滤作用, 使群落的谱系结构呈现出聚集分布; 而未干扰的群落中由于竞争作用的效应, 功能群均匀度较高, 谱系结构也更加分散。研究区域植物群落的功能群均匀度与物种丰富度呈负相关, 表明物种间特别是相似物种间的竞争限制了群落的物种多样性。研究结果说明, 生态位分化和物种间的相互竞争在物种共存与群落组合中具有重要作用。     

Functional traits reveal environmental constraints on amphibian community assembly in a subtropical dry forest

The relationships between functional traits and environmental gradients are useful to identify different community assembly processes. In this work, we used an approach based on functional traits to analyse if changes in hydroperiod and tree covers of ponds are relevant for local amphibian community assembly processes. Ephemeral ponds with low vegetation cover are expected to impose constraints on different species with particular trait combinations and, therefore, to exhibit communities with lower functional diversity than more stable ponds with greater tree cover. Sampling was conducted in 39 temporary ponds located along vegetation and hydroperiod gradients in the most arid portion of the Chaco ecoregion. Seven functional traits were measured in each species present in the regional pool. Associations between these traits and environmental gradients were detected using multivariate ordination techniques and permutation test (RLQ and fourth‐corner analyses respectively). Functional diversity indices were then calculated and related to variations in the environmental gradients. The results obtained allowed us to identify different sets of traits associated with hydroperiod and tree cover, suggesting that these environmental variables are relevant for structuring amphibian communities according to interspecific variations in functional traits from both, larval and adult stages. Contrary to our expectations, communities associated with more stable ponds and with greater tree cover exhibited lower functional diversity than expected by chance (and were the ponds with highest species richness). This result indicates that the reduction in relative importance of environmental restrictions imposed by a very short hydroperiod and the lack of tree cover, favours different species of the regional pool that are similar in several functional traits. Accordingly, communities associated with stable ponds with high tree cover exhibited high functional redundancy.     

Temporal and spatial constraints on community assembly during microbial colonization of wood in seawater

Wood falls on the ocean floor form chemosynthetic ecosystems that remain poorly studied compared with features such as hydrothermal vents or whale falls. In particular, the microbes forming the base of this unique ecosystem are not well characterized and the ecology of communities is not known. Here we use wood as a model to study microorganisms that establish and maintain a chemosynthetic ecosystem. We conducted both aquaria and in situ deep-sea experiments to test how different environmental constraints structure the assembly of bacterial, archaeal and fungal communities. We also measured changes in wood lipid concentrations and monitored sulfide production as a way to detect potential microbial activity. We show that wood falls are dynamic ecosystems with high spatial and temporal community turnover, and that the patterns of microbial colonization change depending on the scale of observation. The most illustrative example was the difference observed between pine and oak wood community dynamics. In pine, communities changed spatially, with strong differences in community composition between wood microhabitats, whereas in oak, communities changed more significantly with time of incubation. Changes in community assembly were reflected by changes in phylogenetic diversity that could be interpreted as shifts between assemblies ruled by species sorting to assemblies structured by competitive exclusion. These ecological interactions followed the dynamics of the potential microbial metabolisms accompanying wood degradation in the sea. Our work showed that wood is a good model for creating and manipulating chemosynthetic ecosystems in the laboratory, and attracting not only typical chemosynthetic microbes but also emblematic macrofaunal species.     

Spatial indicators of plant community assembly from a 453-year sand-dune chronosequence

Background : We explored evidence for spatial patterning in vegetation across a sand-dune chronosequence spanning 453 years of primary succession to test for indications of a temporal signature of niche versus neutral processes during community assembly.

Methods : The study was conducted on a series of dune-capped beach ridges located in Wilderness State Park in Emmet County of northern Lower Michigan, United States (45° 43′ N, 84° 56′ E). Nearest-neighbour survey data were subjected to species dispersion and association analyses.

Results : Both species richness and species evenness showed the classic ‘hump-shaped’ relationship across successional time, suggesting that competition is an important force in structuring this community. However, the only evidence of intra-specific aggregation occurred in the youngest dune. Older dunes displayed random spatial structure and the oldest dunes tended toward a mix of random patterns and intra-specific segregation, i.e. with nearest neighbours more likely than by chance to be inter-specific. In addition, the frequency of species having lower neighbour-species richness than expected by chance was higher in younger, not older dunes. Species with significantly low neighbour richness (based on absolute nearest neighbours) on later dunes tended to have a high proportion of nearest neighbours that were intra-specific.

Conclusions : The data provided no evidence that resident species in later succession have greater intra-specific aggregation or more niche differentiation based on horizontal niche space. The data are more consistent with theories of community assembly involving competitive equivalence and/or effects of facilitation.     

Functional traits of individual trees reveal ecological constraints on community assembly in tropical rain forests

Niche differentiation and ecological filtering are primary ecological processes that shape community assembly, but their relative importance remains poorly understood. Analyses of the distributions of functional traits can provide insight into the community structure generated by these processes. We predicted the trait distributions expected under the ecological processes of niche differentiation and environmental filtering, then tested these predictions with a dataset of 4672 trees located in nine 1‐ha plots of tropical rain forest in French Guiana. Five traits related to leaf function (foliar N concentration, chlorophyll content, toughness, tissue density and specific leaf area), and three traits related to stem function (trunk sapwood density, branch sapwood density, and trunk bark thickness), as well as laminar surface area, were measured on every individual tree. There was far more evidence for environmental filtering than for niche differentiation in these forests. Furthermore, we contrasted results from species‐mean and individual‐level trait values. Analyses that took within‐species trait variation into account were far more sensitive indicators of niche differentiation and ecological filtering. Species‐mean analyses, by contrast, may underestimate the effects of ecological processes on community assembly. Environmental filtering appeared somewhat more intense on leaf traits than on stem traits, whereas niche differentiation affected neither strongly. By accounting for within‐species trait variation, we were able to more properly consider the ecological interactions among individual trees and between individual trees and their environment. In so doing, our results suggest that the ecological processes of niche differentiation and environmental filtering may be more pervasive than previously believed.     

Defining marine bacterioplankton community assembly rules by contrasting the importance of environmental determinants and biotic interactions

Bacterioplankton communities govern marine productivity and biogeochemical cycling, yet drivers of bacterioplankton assembly remain unclear. Here, we contrast the relative contribution of deterministic processes (environmental factors and biotic interactions) in driving temporal dynamics of bacterioplankton diversity at three different oceanographic time series locations, spanning 15° of latitude, which are each characterized by different environmental conditions and varying degrees of seasonality. Monthly surface samples (5.5 years) were analysed using 16S rRNA amplicon sequencing. The high- and mid-latitude sites of Maria Island and Port Hacking were characterized by high and intermediate levels of environmental heterogeneity, respectively, with both alpha diversity (72%; 24% of total variation) and beta diversity (32%; 30%) patterns within bacterioplankton assemblages explained by day length, ammonium, and mixed layer depth. In contrast, North Stradbroke Island, a sub-tropical location where environmental conditions are less variable, interspecific interactions were of increased importance in structuring bacterioplankton diversity (alpha: 33%; beta: 26%) with environment only contributing 11% and 13% to predicting diversity, respectively. Our results demonstrate that bacterioplankton diversity is the result of both deterministic environmental and biotic processes and that the importance of these different deterministic processes varies, potential in response to environmental heterogeneity.     

The contribution of species–genetic diversity correlations to the understanding of community assembly rules

Community genetics aims at understanding how within‐species variation, species diversity and environmental factors interact to shape community assembly. An approach that emerged a few years ago has been to quantify the correlation between the neutral genetic diversity of a focal species and species diversity of the surrounding community (species–genetic diversity correlations, or SGDCs). We here review this approach and discuss its interpretative framework in a community ecology context. First, we show that the case for mostly positive SGDCs is probably overstated due to publication bias – only 11% are significantly positive, a fraction comparable to the significantly negative ones. This suggests that variation in area and connectivity among habitat patches, theoretically leading to positive SGDCs, is not the only factor affecting SGDCs. Second, building upon previous contributions, we propose a general framework to identify the multiple factors underpinning SGDCs, and argue that it will help deepen our understanding of community assembly, especially with regard to the ecological factors playing at metacommunity scale. Our framework distinguishes between site and community factors which can affect SGDCs either positively or negatively, depending on whether the focal species and the rest of the community are similar or dissimilar, in terms of realized niches and dispersal abilities. Empirical studies should thus go beyond simply computing SGDCs, and we provide statistical methods (e.g. structural equation modelling) to decompose SGDCs into the multiple contributions of site and community factors. As an example, we use a published dataset (freshwater snail metacommunity), and show how the role of focal population size on SGDCs had hitherto not been detected. We further discuss how considering several focal species and various delimitations of the community may help one to identify clusters of ecologically similar species. We eventually highlight the benefit that SGDC studies would get from integrating β‐diversities.     

A computer simulation study of the hierarchical assembly behaviour of triblock patchy particles

We study the hierarchical self-assembly behaviour of ACB triblock patchy particles via Brownian dynamics (BD) simulations, where the product of the first stage is set as the initial structure for the second stage. We offer a promising design rule to investigate the assembly mechanism of ACB triblock patchy particles in selective solvent conditions by two-stage optimisation. At the first stage, the attractive hydrophobic interactions only exist between patches A at low concentration in order to generate subunits. At the second stage, the attractions also exist between patches B for studying the assembly process from subunits to target structures by heating/cooling method. By regulating the interactions between patches B as well as the concentrations of patchy particles, the ordered structures that determined by various influence factors are studied. Via properly designing the assembly models and routes, we can observe the formation process of simple cubic lattice and kagome lattice structures, respectively. The results reveal that the concentration and attractive strength play the critical roles in the whole process of hierarchical self-assembly.