Disintegration of the ecological community

In this essay, I argue that the seemingly indestructible concept of the community as a local, interacting assemblage of species has hindered progress toward understanding species richness at local to regional scales. I suggest that the distributions of species within a region reveal more about the processes that generate diversity patterns than does the co-occurrence of species at any given point. The local community is an epiphenomenon that has relatively little explanatory power in ecology and evolutionary biology. Local coexistence cannot provide insight into the ecogeographic distributions of species within a region, from which local assemblages of species derive, nor can local communities be used to test hypotheses concerning the origin, maintenance, and regulation of species richness, either locally or regionally. Ecologists are moving toward a community concept based on interactions between populations over a continuum of spatial and temporal scales within entire regions, including the population and evolutionary processes that produce new species.     

Induced defenses within food webs: The role of community trade-offs,delayed responses,and defense specificity

In nature, prey and predator species are embedded in complex networks of ecological interactions. As a consequence, organism level reactions such as predator-induced prey defenses will not only influence the dynamics of both the prey exhibiting the response and its inducer predator, but also that of a wider set of populations that interact directly or indirectly with them.In this work our aim is to determine the consequences of community-level side effects, defense specificity, and timing of inducible defenses for the stability of model ecological communities. We shall consider small webs of two and three trophic levels, containing one to three species per level. The model food webs include well-known community motifs that will be studied by means of qualitative analyses of the community matrix. Our results show that side effects that suppress non-focal interactions were able to decrease community stability, particularly when defensive responses were delayed. Conversely, side effects that increase the strength of non-focal interactions stabilized communities. This work also shows that as the defensive response became more specific, it is more likely to obtain a stable community. In general terms, our results revealed that delayed responses decrease the likelihood of system stability. Our results highlight the importance of the underlying biology of species interactions for the definition of the proper topology, and consequently dynamics, of complex ecological networks.     

The origins and detection of plant community structure: Reproductive versus vegetative processes

The exchange of ideas and information between vegetation ecology and pollination ecology is relatively restricted, yet both fields have devised methods to detect the structure of species assemblages and communities. To promote the exchange of ideas between fields I compare approaches, concepts, and problems faced by researchers working in each area. Both vegetative and reproductive interactions may generate assemblage structure through ecological sorting or through character displacement. Vegetative interactions may lead to assemblage organization more often by ecological sorting and reproductive interactions more often by character displacement. Vegetative interactions generally operate over shorter temporal and smaller spatial scales than reproductive interactions and may be affected more strongly by temporal and spatial heterogeneity in abiotic and biotic environments. These differences affect how the concept of ecological niche should be applied to plants. The Hutchinsonian concept of niche needs to be significantly modified before it can be usefully applied to plants. Null models are a valuable tool for investigating both vegetative and reproductive structuring of plant assemblages; however, the procedures followed in the application of null models need further refinement. The appropriate formulation of the null model may require information that is unavailable, hence multiple models may have to be employed to “bracket” conclusions. The literature on pollination community ecology demonstrates that difficult decisions must be made about the likely processes that have generated the structure being tested, the relevant definition of sympatry, how guid membership should be defined and employed, and what constraints should be incorporated into the null model to impose realism. Differences in these decisions will affect the outcome of the analysis. While top-down studies of pattern have numerous advantages, they usually cannot identify the process(es) that have generated the patterns. Bottom-up, experimental studies can be useful for identifying the processes, but they can rarely be used to assess the structure of an entire natural assemblage. The optimal approach to studying assemblage structure is to detect patterns with top-down analysis and use experiments to identify the processes that generate and maintain the patterns.     

Ecosystem engineering moving away from just-so stories

The concept of ecosystem engineering has been proposed recently to account for key processes between organisms and their environment which are not directly trophic or competitive, and which result in the modification, maintenance and/or creation of habitats. Since the initial reporting of the idea, little work has been undertaken to apply the proposed concept to potential ecosystem engineers in the marine environment. Biological and ecological data for the burrowing ghost shrimp Callianassa filholi (Decapoda: Thalassinidea) allowed for a formal assessment of this species as an ecosystem engineer, in direct accordance with published criteria. Despite a low population density and the short durability of its burrow structures, Callianassa filholi affected a number of resource flows by its large lifetime per capita activity. Ecosystem effects were evident in significant changes in macrofauna community composition over small spatial and temporal scales. Seasonal variation in the effects of ghost shrimp activity were associated with changes in seagrass (Zostera novazelandica) biomass, which revealed the probability of interactions between antagonistic ecosystem engineers. The formal assessment of Callianassa filholi provides the opportunity to aid discussion pertaining to the development of the ecosystem engineering concept.     

Phylogenetic analysis of community assembly and structure over space and time

Evolutionary ecologists are increasingly combining phylogenetic data with distributional and ecological data to assess how and why communities of species differ from random expectations for evolutionary and ecological relatedness. Of particular interest have been the roles of environmental filtering and competitive interactions, or alternatively neutral effects, in dictating community composition. Our goal is to place current research within a dynamic framework, specifically using recent phylogenetic studies from insular environments to provide an explicit spatial and temporal context. We compare communities over a range of evolutionary, ecological and geographic scales that differ in the extent to which speciation and adaptation contribute to community assembly and structure. This perspective allows insights into the processes that can generate community structure, as well as the evolutionary dynamics of community assembly.     

Ocean acidification affects competition for space: projections of community structure using cellular automata

Historical ecological datasets from a coastal marine community of crustose coralline algae (CCA) enabled the documentation of ecological changes in this community over 30 years in the Northeast Pacific. Data on competitive interactions obtained from field surveys showed concordance between the 1980s and 2013, yet also revealed a reduction in how strongly species interact. Here, we extend these empirical findings with a cellular automaton model to forecast ecological dynamics. Our model suggests the emergence of a new dominant competitor in a global change scenario, with a reduced role of herbivory pressure, or trophic control, in regulating competition among CCA. Ocean acidification, due to its energetic demands, may now instead play this role in mediating competitive interactions and thereby promote species diversity within this guild.     

Linking community assembly and structure across scales in a wild mouse parasite community

Understanding what processes drive community structure is fundamental to ecology. Many wild animals are simultaneously infected by multiple parasite species, so host–parasite communities can be valuable tools for investigating connections between community structures at multiple scales, as each host can be considered a replicate parasite community. Like free‐living communities, within‐host–parasite communities are hierarchical; ecological interactions between hosts and parasites can occur at multiple scales (e.g., host community, host population, parasite community within the host), therefore, both extrinsic and intrinsic processes can determine parasite community structure. We combine analyses of community structure and assembly at both the host population and individual scales using extensive datasets on wild wood mice (Apodemus sylvaticus) and their parasite community. An analysis of parasite community nestedness at the host population scale provided predictions about the order of infection at the individual scale, which were then tested using parasite community assembly data from individual hosts from the same populations. Nestedness analyses revealed parasite communities were significantly more structured than random. However, observed nestedness did not differ from null models in which parasite species abundance was kept constant. We did not find consistency between observed community structure at the host population scale and within‐host order of infection. Multi‐state Markov models of parasite community assembly showed that a host's likelihood of infection with one parasite did not consistently follow previous infection by a different parasite species, suggesting there is not a deterministic order of infection among the species we investigated in wild wood mice. Our results demonstrate that patterns at one scale (i.e., host population) do not reliably predict processes at another scale (i.e., individual host), and that neutral or stochastic processes may be driving the patterns of nestedness observed in these communities. We suggest that experimental approaches that manipulate parasite communities are needed to better link processes at multiple ecological scales.     

A process‐based metacommunity framework linking local and regional scale community ecology

The metacommunity concept has the potential to integrate local and regional dynamics within a general community ecology framework. To this end, the concept must move beyond the discrete archetypes that have largely defined it (e.g. neutral vs. species sorting) and better incorporate local scale species interactions and coexistence mechanisms. Here, we present a fundamental reconception of the framework that explicitly links local coexistence theory to the spatial processes inherent to metacommunity theory, allowing for a continuous range of competitive community dynamics. These dynamics emerge from the three underlying processes that shape ecological communities: (1) density‐independent responses to abiotic conditions, (2) density‐dependent biotic interactions and (3) dispersal. Stochasticity is incorporated in the demographic realisation of each of these processes. We formalise this framework using a simulation model that explores a wide range of competitive metacommunity dynamics by varying the strength of the underlying processes. Using this model and framework, we show how existing theories, including the traditional metacommunity archetypes, are linked by this common set of processes. We then use the model to generate new hypotheses about how the three processes combine to interactively shape diversity, functioning and stability within metacommunities.     

Multi-scale regulated plant community dynamics: mechanisms and implications

Plant competition is not a direct interaction, but operates via environmental feedback loops, which interconnect population densities and environmental regulating variables. It is suggested that due to scale dependent elements of these feedback loops, competition may occur eventually on very different scales, necessitating a cross-scale extension of plant competition theory. After introducing the concept of cross-scale competition, we incorporate its elements into a metacommunity model and study its implications on community organization. It is found that both the equilibrium community composition, regarding coexisting functional types, and its stability depend on scale dependent attributes of environmental feedback loops and disturbance regimes. We argue that plant communities are likely to exhibit properties, which are in line with the hierarchical ecosystem concept. Environmental feedback loops on different scales act as distinct organizational levels, what can be affected by disturbances of corresponding spatial extent.     

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。     

Redefining community: towards an ecological republicanism

This paper makes some suggestions for a concept of community which arguably satisfies the most important criteria for both human communities, as defined in the social sciences and humanities, and natural communities, as defined in ecology and biology. Beginning with the former, I arrive at two such criteria: (1) a material and social connection among members, and (2) some kind and degree of awareness of other members. These are then supplemented with a third drawn from civic republicanism, with its focus on citizenship and the common good: communities (3) enable and require certain practices for their maintainence. Turning to ecological definitions of community, I find the dominant (reductionist) one seriously deficient as compared with a more holist and ecosystemic approach. However, I invoke a nonreductive holism to defend the idea of community, and go on to argue that each of the three above-mentioned criteria can be fruitfully extended to include both social and ecological communities in a nonreductionist way – that is, in a way that neither reduces ecosystemic properties to individual organisms nor the reverse. This culminates in a discussion of what I call ecological republicanism, which I suggest could have powerfully positive effects on the contemporary crisis of undue human impact on the natural world.     

Rethinking plant community theory

Plant communities have traditionally been viewed as either a random collection of individuals or as organismal entities. For most ecologists however, neither perspective provides a modern comprehensive view of plant communities, but we have yet to formalize the view that we currently hold. Here, we assert that an explicit re-consideration of formal community theory must incorporate interactions that have recently been prominent in plant ecology, namely facilitation and indirect effects among competitors. These interactions do not suppport the traditional individualistic perspective. We believe that rejecting strict individualistic theory will allow ecologists to better explain variation occurring at different spatial scales, synthesize more general predictive theories of community dynamics, and develop models for community-level responses to global change. Here, we introduce the concept of the integrated community (IC) which proposes that natural plant communities range from highly individualistic to highly interdependent depending on synergism among: (i) stochastic processes, (ii) the abiotic tolerances of species, (iii) positive and negative interactions among plants, and (iv) indirect interactions within and between trophic levels. All of these processes are well accepted by plant ecologists, but no single theory has sought to integrate these different processes into our concept of communities.     

植物群落构建的生态过滤机制研究进展

生物多样性的形成和维持机制,即群落构建机制,一直以来都是群落生态学研究的核心问题。植物群落构建的确定性过程主要是生态过滤机制(包括环境过滤和生物过滤,其中生物过滤包括种间竞争和种内功能性状变异)作用的结果。学者们构建了大量的理论、方法、模型来解释和验证生态过滤机制对群落构建的影响,并取得了显著的成果。然而,关于生态过滤机制在不同尺度的作用、生态过滤机制的各要素分解和量化等方面的研究仍有诸多疑问。重点综述了环境过滤、种间竞争和种内功能性状变异的最新研究进展,并指出了现有研究的不足之处。在未来的研究中,应注重生态过滤机制的各要素分解和量化,加强研究手段的综合运用,关注时空动态变化对植物群落构建的影响,重视对不同植物群落构建机制的共性和个性特征的认识,同时强调与其他生态过程、群落构建机制的整合。通过这些尝试,有助于人们更好的理解植物群落构建过程中的生态过滤机制的作用。     

Species pool: the concept,its determination and significance for community restoration

Abstract. The concept of species pool is reviewed. It is suggested to maintain the terms regional pool and local pool but replace actual pool by community pool. The regional and local pool are considered as selections from the regional and local flora based on ecological similarity. It is also suggested to include in the community pool a selection of species present only as diaspores in the diaspore bank (including diaspores from the seed rain), the selection being based on the same ecological criteria. Four approaches to determine the species pool are discussed: ecological, functional and phytosociological similarity, and an experimental approach. The phytosociological approach appears to be promising. The species pool is elaborated as a fuzzy set in the sense that each species of a community or a local or regional flora is a member of any community, local or regional species pool with different degrees of membership. This membership is defined as a probability of a species to become part of the community pool of a target community which is a function of the ecological (environmen-tal/functional/phytosociological) similarity of the species with the target community; the shortness of the distance of its nearest populations, the frequency/abundance, the dispersal capacity, the actual presence of dispersal mechanisms, the germinability of newly arrived diaspores, and the longevity of seeds (viability) in the diaspore bank. The information on species pools is needed for designing experiments where the number of species in a community is to be manipulated, for instance in restoration management.     

Interactions retain the co‐phylogenetic matching that communities lost

Both species and their interactions are affected by changes that occur at evolutionary time‐scales, and these changes shape both ecological communities and their phylogenetic structure. That said, extant ecological community structure is contingent upon random chance, environmental filters and local effects. It is therefore unclear how much ecological signal local communities should retain. Here we show that, in a host–parasite system where species interactions vary substantially over a continental gradient, the ecological significance of individual interactions is maintained across different scales. Notably, this occurs despite the fact that observed community variation at the local scale frequently tends to weaken or remove community‐wide phylogenetic signal. When considered in terms of the interplay between community ecology and coevolutionary theory, our results demonstrate that individual interactions are capable and indeed likely to show a consistent signature of past evolutionary history even when woven into communities that do not.     

Combining mechanism and drift in community ecology: a novel statistical mechanics approach

A key challenge for models of community ecology is to combine deterministic mechanism and stochastic drift in a systematic, transparent and tractable manner. Another challenge is to explain and unify different ecological patterns, hitherto modelled in isolation, within a single modelling framework. Here, we show that statistical mechanics provides an effective way to meet both challenges. We apply the statistical principle of maximum entropy (MaxEnt) to a simple resource-based, non-neutral model of a plant community. In contrast to previous ecological applications of MaxEnt, our use of MaxEnt emphasises its theoretical basis in the combinatorics of sampling frequencies, an approach that clarifies its ecological interpretation. In this approach, mechanism and drift are identified, respectively, with ecological resource constraints and entropy maximization. We obtain realistic predictions for species abundance distributions as well as contrasting stability-diversity relationships at community and population levels. The model also predicts critical behaviour that may provide a basis for understanding desertification and other ecological tipping points. Our results complement and extend previous ecological applications of MaxEnt to new areas of community ecology, and further illustrate MaxEnt as a powerful yet simple modelling tool for combining mechanism and drift in a way that unifies disparate ecological patterns.     

Understanding and predicting effects of modified interactions through a qualitative analysis of community structure

Models of ecological communities are traditionally based on relationships between pairs of species, where the strengths of per capita interactions are fixed and independent of population abundance. A growing body of literature, however; describes interactions whose strength is modified by the density of either a third species or by one of the species involved in a pairwise interaction. These modified interactions have been treated as indirect effects, and the terminology addressing them is diverse and overlapping. In this paper we develop a general analytical framework based on a qualitative analysis of community structure to account for the consequence of modified interactions in complex ecological communities. Modified interactions are found to create both direct and indirect effects between species. The sign of a direct effect can change in some instances depending on the magnitude of a key variable or parameter, which leads to a threshold change in system structure and dynamics. By considering alternative structures of a community, we extend our ability to model perturbations that move the system far from a previous equilibrium. Using specific examples, we reinterpret existing results, develop hypotheses to guide experiments or management interventions, and explore the role of modified interactions and positive feedback in creating and maintaining alternative stable states. Through a qualitative analysis of community structure, system feedback is demonstrated as being key in understanding and predicting the dynamics of complex ecological communities.     

Ontogenetic trait variation and metacommunity effects influence species relative abundances during tree community assembly

Predicting species abundance is one of the most fundamental pursuits of ecology. Combining the information encoded in functional traits and metacommunities provides a new perspective to predict the abundance of species in communities. We applied a community assembly via trait selection model to predict quadrat-scale species abundances using functional trait variation on ontogenetic stages and metacommunity information for over 490 plant species in a subtropical forest and a lowland tropical forest in Yunnan, China. The relative importance of trait-based selection, mass effects, and stochasticity in shaping local species abundances is evaluated using different null models. We found both mass effects and trait selection contribute to local abundance patterns. Trait selection was detectable at all studied spatial scales (0.04–1 ha), with its strength stronger at larger scales and in the subtropical forest. In contrast, the importance of stochasticity decreased with spatial scale. A significant mass effect of the metacommunity was observed at small spatial scales. Our results indicate that tree community assembly is primarily driven by ontogenetic traits and metacommunity effects. Our findings also demonstrate that including ontogenetic trait variation into predictive frameworks allows ecologists to infer ecological mechanisms operating in community assembly at the individual level.     

高阶相互作用对宿主-寄生群落动态的影响

物种间相互作用是影响生物群落稳定性和多样性的重要因素。基于Lotka-Volterra竞争模型,通过构建多宿主种群的种内和种间高阶相互作用模型,研究宿主种群的间接竞争效应对寄生群落动态的影响机制。为有效地揭示高阶作用对种群动态的影响,通过对比宿主-寄生群落的现象模型以及机制模型,利用机制模型产生的合理数据集对现象模型中高阶项的参数进行拟合,进而探讨了高阶相互作用在群落动态中的作用。结果显示,完整的高阶相互作用模型在描述多宿主-寄生系统的群落动态中表现最优,而直接相互作用模型对群落动态的描述相对较差,即同时考虑种间和种内的高阶相互作用模型更加符合机制模型所描述的群落动态。此外,种内高阶作用和种间高阶作用产生不对称效应,宿主间的种间高阶作用对群落产生的影响较种内高阶作用更为显著。该研究结果在一定意义上丰富了宿主-寄生生物群落的稳定性研究,为理解物种间相互作用的多样性研究提供了依据。     

Nested species interactions promote feasibility over stability during the assembly of a pollinator community

The foundational concepts behind the persistence of ecological communities have been based on two ecological properties: dynamical stability and feasibility. The former is typically regarded as the capacity of a community to return to an original equilibrium state after a perturbation in species abundances and is usually linked to the strength of interspecific interactions. The latter is the capacity to sustain positive abundances on all its constituent species and is linked to both interspecific interactions and species demographic characteristics. Over the last 40 years, theoretical research in ecology has emphasized the search for conditions leading to the dynamical stability of ecological communities, while the conditions leading to feasibility have been overlooked. However, thus far, we have no evidence of whether species interactions are more conditioned by the community''s need to be stable or feasible. Here, we introduce novel quantitative methods and use empirical data to investigate the consequences of species interactions on the dynamical stability and feasibility of mutualistic communities. First, we demonstrate that the more nested the species interactions in a community are, the lower the mutualistic strength that the community can tolerate without losing dynamical stability. Second, we show that high feasibility in a community can be reached either with high mutualistic strength or with highly nested species interactions. Third, we find that during the assembly process of a seasonal pollinator community located at The Zackenberg Research Station (northeastern Greenland), a high feasibility is reached through the nested species interactions established between newcomer and resident species. Our findings imply that nested mutualistic communities promote feasibility over stability, which may suggest that the former can be key for community persistence.